@article {pmid39720616,
year = {2024},
author = {Zhang, A and Wang, Z and Sheng, H and Yang, J},
title = {Systemic Scedosporium apiospermum Infection Affecting Multiple Sites After Near-Drowning: A Case Report.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {5739-5744},
pmid = {39720616},
issn = {1178-6973},
abstract = {Scedosporium apiospermum (S. apiospermum) can cause fungal infections in near-drowning victims, and an increasing number of cases have been reported. However, cases of bone and joint infections caused by S. apiospermum are rare. In this case, a 35-year-old otherwise healthy Chinese female presented with aspiration pneumonia and knee arthritis after accidentally falling into sewage and near-drowning and underwent macrogenomic second-generation sequencing of arthrocentesis fluid, which showed S. apiospermum. However, new lesions involving the hip joint and spine continued to develop under voriconazole monotherapy. The patient was treated with voriconazole combined with amphotericin B cholesterol sulfate lipid complex for 30 consecutive days. The patient's symptoms improved significantly. This case highlights the robust invasiveness of S. apiospermum and the extensive spread of infection, underscoring the importance of prompt diagnosis and treatment. A combined therapeutic approach may offer a safe and efficacious option for managing S. apiospermum infection.},
}

@article {pmid39720533,
year = {2024},
author = {Levallois, V and Andreace, F and Le Gal, B and Dufresne, Y and Peterlongo, P},
title = {The backpack quotient filter: A dynamic and space-efficient data structure for querying k-mers with abundance.},
journal = {iScience},
volume = {27},
number = {12},
pages = {111435},
pmid = {39720533},
issn = {2589-0042},
abstract = {Genomic data sequencing is crucial for understanding biological systems. As genomic databases like the European Nucleotide Archive expand exponentially, efficient data manipulation is essential. A key challenge is querying these databases to determine the presence or absence of specific sequences and their abundance within datasets. This paper presents the Backpack Quotient Filter (BQF), a data structure for indexing k-mers (substrings of length k), which offers greater space efficiency than the Counting Quotient Filter (CQF). The BQF maintains essential features such as abundance information and dynamicity, with an extremely low false positive rate of less than 10 - 5 % . Our method redefines abundance information handling and implements an independent strategy for space efficiency. The BQF uses four times less space than the CQF on complex datasets such as sea-water metagenomics sequences. Additionally, its space efficiency improves with larger datasets, addressing the need for scalable data solutions.},
}

@article {pmid39719725,
year = {2024},
author = {Deng, K and Shen, L and Xue, Z and Li, BY and Tang, J and Zhao, H and Xu, F and Miao, Z and Cai, X and Hu, W and Fu, Y and Jiang, Z and Liang, X and Xiao, C and Shuai, M and Gou, W and Yue, L and Xie, Y and Sun, TY and Guo, T and Chen, YM and Zheng, JS},
title = {Association of the EAT-Lancet diet, serial measures of serum proteome and gut microbiome, and cardiometabolic health: a prospective study of Chinese middle-aged and elderly adults.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2024.10.011},
pmid = {39719725},
issn = {1938-3207},
abstract = {BACKGROUND: The EAT-Lancet diet was reported to be mutually beneficial for the human cardiometabolic system and planetary health. However, mechanistic evidence linking the EAT-Lancet diet and human cardiometabolic health is lacking.

OBJECTIVES: We aimed to investigate the role of blood proteins in the association between the EAT-Lancet diet and cardiometabolic health and explore the underlying gut microbiota-blood protein interplay.

METHODS: Our study was based on a prospective cohort including 3742 Chinese participants enrolled from 2008-2013 with serum proteome data repeatedly measured ≤3 times (Nproteome = 7514) and 1195 with gut metagenomic data measured ≤2 times over 9 y (Nmicrobiota = 1695). Least absolute shrinkage and selection operator and multivariable linear regression were used to explore the associations of the EAT-Lancet diet (assessed by semi-quantitative food frequency questionnaire) with serum proteins and gut microbes. Linear mixed-effect model and logistic regression were used to examine the associations of selected proteins with 11 cardiometabolic risk factors and 4 cardiometabolic diseases, respectively. Mediation analysis was used to identify potential mediation effects. Multiple comparisons were adjusted using the Benjamini-Hochberg method.

RESULTS: The mean (standard deviation) age of enrolled participants was 58.4 (6.1) y (31.6% men). The EAT-Lancet diet was prospectively associated with 4 core proteins, including α-2-macroglobulin (A2M) (pooled β: 0.12; 95% confidence interval [CI]: 0.05, 0.2), retinol-binding protein 4 (pooled β: -0.14; 95% CI: -0.24, -0.04), TBC1 domain family member 31 (pooled β: -0.11; 95% CI: -0.22, 0), and adenylate kinase 4 (pooled β: -0.19; 95% CI: -0.3, -0.08). The identified proteins were prospectively associated with cardiometabolic diseases (pooled odds ratio ranged from 0.8-1.18) and risk factors (pooled β ranged from -0.1 to 0.12), mediating the association between the EAT-Lancet diet and blood triglycerides. We then identified 5 gut microbial biomarkers of the EAT-Lancet diet, and discovered a potential gut microbiota-blood protein interplay (EAT-Lancet diet→Rothia mucilaginosa→A2M) underlying the EAT-Lancet diet-cardiometabolic health association.

CONCLUSIONS: Our study presents key molecular evidence to support the role of EAT-Lancet diet adherence in promoting cardiometabolic health.},
}

@article {pmid39719706,
year = {2024},
author = {Zhang, AN and Gaston, JM and Cárdenas, P and Zhao, S and Gu, X and Alm, EJ},
title = {CRISPR-Cas spacer acquisition is a rare event in human gut microbiome.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {100725},
doi = {10.1016/j.xgen.2024.100725},
pmid = {39719706},
issn = {2666-979X},
abstract = {Host-parasite relationships drive the evolution of both parties. In microbe-phage dynamics, CRISPR functions as an adaptive defense mechanism, updating immunity via spacer acquisition. Here, we investigated these interactions within the human gut microbiome, uncovering low frequencies of spacer acquisition at an average rate of one spacer every ∼2.9 point mutations using isolates' whole genomes and ∼2.7 years using metagenome time series. We identified a highly prevalent CRISPR array in Bifidobacterium longum spreading via horizontal gene transfer (HGT), with six spacers found in various genomic regions in 15 persons from the United States and Europe. These spacers, targeting two prominent Bifidobacterium phages, comprised 76% of spacer occurrence of all spacers targeting these phages in all B. longum populations. This result suggests that HGT of an entire CRISPR-Cas system introduced three times more spacers than local CRISPR-Cas acquisition in B. longum. Overall, our findings identified key ecological and evolutionary factors in prokaryote adaptive immunity.},
}

@article {pmid39719433,
year = {2024},
author = {Jia, M and Fan, Y and Ma, Q and Yang, D and Wang, Y and He, X and Zhao, B and Zhan, X and Qi, Z and Ren, Y and Dong, Z and Zhu, F and Wang, W and Gao, Y and Ma, X},
title = {Gut microbiota dysbiosis promotes cognitive impairment via bile acid metabolism in major depressive disorder.},
journal = {Translational psychiatry},
volume = {14},
number = {1},
pages = {503},
pmid = {39719433},
issn = {2158-3188},
support = {82230044//National Science Foundation of China | Key Programme/ ; 82171505//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Depressive Disorder, Major/metabolism/microbiology ; *Bile Acids and Salts/metabolism ; Male ; Female ; *Dysbiosis/metabolism/complications ; *Cognitive Dysfunction/metabolism/etiology/microbiology ; Adult ; Middle Aged ; Feces/microbiology ; Metabolomics ; Case-Control Studies ; Brain-Gut Axis ; },
abstract = {Evidence suggests that complex interactions among the gut microbiome, metabolic abnormalities, and brain have important etiological and therapeutic implications in major depressive disorder (MDD). However, the influence of microbiome-gut-brain cross-talk on cognitive impairment in MDD remains poorly characterized. We performed serum metabolomic profiling on 104 patients with MDD and 77 healthy controls (HCs), and also performed fecal metagenomic sequencing on a subset of these individuals, including 79 MDD patients and 60 HCs. The findings were validated in a separate cohort that included 40 patients with MDD and 40 HCs using serum-targeted metabolomics. Abnormal bile acid metabolism was observed in patients with MDD, which is related to cognitive dysfunction. The following gut microbiota corresponded to changes in bile acid metabolism and enzyme activities involved in the bile acid metabolic pathway, including Lachnospiraceae (Blautia_massiliensis, Anaerostipes_hadrus, Dorea_formicigenerans, and Fusicatenibacter_saccharivorans), Ruminococcaceae (Ruminococcus_bromii, Flavonifractor_plautii, and Ruthenibacterium_lactatiformans), and Escherichia_coli. Furthermore, a combinatorial marker classifier that robustly differentiated patients with MDD from HCs was identified. In conclusion, this study provides insights into the gut-brain interactions in the cognitive phenotype of MDD, indicating a potential therapeutic strategy for MDD-associated cognitive impairment by targeting the gut microbiota and bile acid metabolism.},
}

Humans
*Gastrointestinal Microbiome
*Depressive Disorder, Major/metabolism/microbiology
*Bile Acids and Salts/metabolism
Male
Female
*Dysbiosis/metabolism/complications
*Cognitive Dysfunction/metabolism/etiology/microbiology
Adult
Middle Aged
Feces/microbiology
Metabolomics
Case-Control Studies
Brain-Gut Axis

@article {pmid39719199,
year = {2024},
author = {Qi, Y and Fu, R and Yan, C and Liu, X and Liu, N},
title = {Enrichment of a heterotrophic nitrifying and aerobic denitrifying bacterial consortium: Microbial community succession and nitrogen removal characteristics and mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132013},
doi = {10.1016/j.biortech.2024.132013},
pmid = {39719199},
issn = {1873-2976},
abstract = {This study cultivated a bacterial consortium (S60) from landfill leachate that exhibited effective heterotrophic nitrification and aerobic denitrification (HN-AD) properties. Under aerobic conditions, the removal of NH4[+]-N reached 100 % when the S60 consortium utilised NH4[+]-N either as the sole nitrogen source or in combination with NO2[-]-N and NO3[-]-N. Optimal HN-AD performance was achieved with sodium acetate as a carbon source and a pH of 7.0-8.0, dissolved oxygen concentration of 4.0-5.0 mg/L, and a C/N ratio of 10. Furthermore, the presence of functional genes (amoA, hao, napA, nirK, nirS, nosZ), hydroxylamine oxidase, nitrate reductase, and nitrite reductase was confirmed in the S60 consortium. Drawing from these findings, two HN-AD pathways were delineated: NH4[+]-N → NH2OH → NO2[-]-N → NO3[-]-N → NO2[-]-N → NO → N2O → N2 and NH4[+]-N → NH2OH → N2O → N2. Metagenomic binning analysis of the S60 consortium uncovered complete pathways for dissimilatory nitrate reduction and denitrification within Halomonas, Zobellella, Stutzerimonas, Marinobacter, and Pannonibacter. These findings offer new insights into the application of HN-AD bacteria and their collaborative nitrogen removal in environments with varying nitrogen sources.},
}

@article {pmid39719115,
year = {2024},
author = {Slavov, SN},
title = {Routine Detection of Viruses Through Metagenomics: Where Do We Stand?.},
journal = {The American journal of tropical medicine and hygiene},
volume = {},
number = {},
pages = {},
doi = {10.4269/ajtmh.24-0652},
pmid = {39719115},
issn = {1476-1645},
}

@article {pmid39719110,
year = {2024},
author = {Koné, A and Kané, F and Neal, A and Konate, I and Coulibaly, B and Dabitao, DK and Diarra, B and Sanogo, I and Sarro, YDS and Coulibaly, TA and Diallo, D and Samake, S and Dicko, I and Diallo, M and Diarra, A and Coulibaly, MD and Keita, D and Coulibaly, N and Koloma, I and Perou, M and Diarra, HB and Cisse, BE and Togo, ACG and Coulibaly, G and Traoré, FG and Sanogo, M and Diakité, M and Aboulhab, J and Akpa, E and Fouth-Tchos, K and Shaw-Saliba, K and Collins, J and Lu, XJ and Nischay, M and Wickiser, JK and Briese, T and Lipkin, WI and Chen, RY and Doumbia, S and Dao, S},
title = {Adding Virome Capture Metagenomic Sequencing to Conventional Laboratory Testing Increases Unknown Fever Etiology Determination in Bamako, Mali.},
journal = {The American journal of tropical medicine and hygiene},
volume = {},
number = {},
pages = {},
doi = {10.4269/ajtmh.24-0449},
pmid = {39719110},
issn = {1476-1645},
abstract = {Unexplained fever poses significant diagnostic challenges in resource-limited settings like Bamako, Mali, where overlapping endemic diseases include malaria, HIV/AIDS, yellow fever, typhoid, and others. This study aimed to elucidate the infectious etiologies of acute febrile illnesses in this context. Acute febrile patients of any age were enrolled after informed consent or assent. Baseline clinical and demographic data were collected, and samples were analyzed by using rapid diagnostic tests, reverse transcriptase polymerase chain reaction, ELISA, and virus-targeted metagenomic sequencing (virome capture sequencing platform for vertebrate viruses [VirCapSeq-VERT]). Among 108 enrolled subjects, most were male (51.9%) and under 15 years old (56.5%). Measles virus was identified in 39.8% of cases, primarily among children. Other findings included Plasmodium spp. (12%), Salmonella spp. (13%), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; 8.7%). The virome capture sequencing platform for vertebrate viruses was used for 101 subjects, corroborating many routine test results and identifying additional cases of measles virus (1), SARS-CoV-2 (5), and numerous other agents. Notably, nearly all subjects showed evidence of herpesviruses (90%) and anelloviruses (98%). Hemorrhagic fever viruses were not observed. With the inclusion of VirCapSeq-VERT, identifiable pathogens were found in 79.6% of cases, leaving 20.4% without a clear etiology. The identification of more than one concurrent pathogen was common (41.5%). Integrating metagenomic sequencing with routine laboratory diagnostic testing enhances the detection of pathogens in acute febrile illnesses, highlighting its potential value in identifying infectious etiologies in resource-limited settings.},
}

@article {pmid39718972,
year = {2024},
author = {Pittaluga, AM and Miccoli, FE and Guerrero, LD and Relling, AE},
title = {Effect of multispecies fungal extract supplementation on growth performance, nutrient digestibility, ruminal fermentation, and the rumen microbiome composition of beef cattle fed forage-based diets.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skae387},
pmid = {39718972},
issn = {1525-3163},
abstract = {Our objective was to evaluate the effect of a multispecies fungal extract (MFE) on growth performance, apparent total tract digestibility (ATTD), fermentation characteristics, and rumen microbiome composition of beef cattle fed forage-based diets. For experiment 1, ruminally cannulated Angus × SimAngus cows (n = 4; body weight [BW] = 569 ± 21 kg) were used in a randomized crossover design with two 21-d study periods and a 23-d washout period to evaluate the effect of dietary inclusion of a MFE on in situ digestion, ruminal fermentation, and the composition of the rumen microbiome. Treatments consisted of a forage-based diet with or without the inclusion of a MFE. Rumen samples were collected on days 5, 10, and 20. Experiment 2 evaluated different inclusion rates of the MFE in a randomized complete block design using Angus × SimAngus-crossbred steers (n = 80; BW = 370 ± 44 kg). Steers were blocked by BW and randomly assigned to 1 of 4 treatments (2 pens/treatment): diet with no MFE, 0.02%, 0.04%, and 0.08% of the MFE (dry matter (DM) basis). Steers were fed a forage-based diet for 122 d. Subsets of 10 steers/treatment were randomly selected for the determination of ATTD on d 20, 40, and 60. All data were analyzed using the MIXED procedure of SAS. In exp 1, adding the MFE to the diet tended to increase the ruminal disappearance rate of the DM on d 10 (P = 0.06). No interactions or treatment effects were observed for the short-chain fatty acid profile of the rumen fluid (P ≥ 0.13). Metagenomic analysis of the rumen microbiome showed a MFE × d interaction for the Fibrobacter genus (P = 0.01), which on d 20 was less abundant in the rumen of cows fed the MFE. In exp 2, steers supplemented with 0.04% of MFE had a lower average daily gain and were lighter at the end of the experiment (cubic, P ≤ 0.04) compared to steers supplemented with 0.02% MFE. Steers fed the diet with 0.02% of MFE had the greatest gain to feed ratio among the MFE-supplemented groups (cubic, P < 0.01). Dietary inclusion of the MFE increased neutral detergent fiber digestibility (linear, P = 0.05). Steers supplemented with 0.04% of MFE had the greatest acid detergent fiber digestibility among treatments (quadratic, P = 0.03). Collectively, results showed that ruminal disappearance rate and digestibility of forage-based diets increased due to MFE supplementation, but did not translate into growth performance improvements or beneficially alter rumen fermentation.},
}

@article {pmid39718649,
year = {2024},
author = {Sanusi, IO and Olutona, GO and Wawata, IG and Onohuean, H and Adepoju, AA},
title = {Geospatial monitoring and human health risk assessment of pharmaceutical residues in groundwater and surface water in Kampala and Mbarara Districts, Uganda.},
journal = {Environmental geochemistry and health},
volume = {47},
number = {2},
pages = {30},
pmid = {39718649},
issn = {1573-2983},
mesh = {Uganda ; *Groundwater/chemistry ; *Water Pollutants, Chemical/analysis ; Humans ; Risk Assessment ; *Environmental Monitoring ; Pharmaceutical Preparations/analysis ; Seasons ; Geographic Information Systems ; },
abstract = {This study investigated the occurrence, concentration and human health risks of five pharmaceutical residues-metronidazole, sulfamethoxazole, ciprofloxacin, carbamazepine, and caffeine-in groundwater and surface water samples from Kampala and Mbarara districts of Uganda. The present study also employed techniques of remote sensing and geographic information system (GIS); thereby, emphasizing the importance of thematic mapping, land use classification, and spatial buffering to evaluate pharmaceutical contaminants in an environmental setting. The risk quotient (RQ) approach was also employed to assess the risk of exposure to the pharmaceutical contaminants. Caffeine was found with the highest average concentration in groundwater (53.515 µg/L), whereas carbamazepine had the highest average concentration in surface water (48.635 µg/L) during the dry season. Ciprofloxacin consistently recorded the lowest average concentrations in both groundwater and surface water across all seasons. Overall, the data revealed high concentrations of pharmaceutical residues in surface water compared to groundwater during both seasons, except for caffeine which was not detected in surface water across the seasons. Notable seasonal changes were also observed in caffeine and metronidazole concentrations, indicating the role of human activities and environmental factors in influencing contamination patterns during specific seasons. The factor analysis revealed that consumption rate of pharmaceuticals and anthropogenic activities are the main factors responsible for the contamination of groundwater and surface water. Moreover, results revealed that the risk of adverse human health effects for carbamazepine and metronidazole during both seasons were high (RQ > 1), thereby highlighting the prioritization of frequent monitoring by the environmental protection agencies. Given that the combined risk of exposure for all the pharmaceuticals exceeded one, adopting stringent pharmaceutical disposal and control measures are essential for mitigating potential human health risks associated with their exposure. Further investigation into optimal and effective pharmaceutical remediation strategies for both groundwater and surface water are highly recommended.},
}

Uganda
*Groundwater/chemistry
*Water Pollutants, Chemical/analysis
Humans
Risk Assessment
*Environmental Monitoring
Pharmaceutical Preparations/analysis
Seasons
Geographic Information Systems

@article {pmid39718602,
year = {2024},
author = {Lotankar, M and Houttu, N and Mokkala, K and Laitinen, K},
title = {Diet-Gut Microbiota Relations: Critical Appraisal of Evidence From Studies Using Metagenomics.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuae192},
pmid = {39718602},
issn = {1753-4887},
abstract = {Diet may influence the gut microbiota and subsequently affect the host's health. Recent developments in methods analyzing the composition and function of the gut microbiota allow a deeper understanding of diet-gut microbiota relationships. A state-of-the-art methodology, shotgun metagenomics sequencing, offers a higher taxonomic resolution of the gut microbiota at the bacterial species and strain levels, and more accurate information regarding the functional potential of gut microbiota. Here, the available evidence on the relationship between diet and gut microbiota was critically reviewed, focusing on results emerging from recent metagenomics sequencing studies applied in randomized controlled trials and observational studies. The PubMed and Embase databases were used to search publications between January 2011 and September 2023. Thus far, the number of studies is limited, and the study designs and methods utilized have been variable. Nevertheless, the cumulative evidence from interventions relates to dietary fiber as a modifier of bacterial species, such as Anaerostipes hadrus and Faecalibacterium prausnitzii. Furthermore, observational studies have detected associations between different dietary patterns and food groups with certain microbial species. Utilization of metagenomics sequencing is becoming more common and will undoubtedly provide further insights into diet-gut microbiota relationships at the species level as well as their functional pathways in the near future. For reproducible results and to draw reliable conclusions across various studies on diet-gut microbiota relationships, there is a need for harmonization of the study designs and standardized ways of reporting.},
}

@article {pmid39718600,
year = {2024},
author = {Koujalagi, T and Ruhal, R},
title = {Mitigating Health Risks Through Environmental Tracking of Pseudomonas aeruginosa.},
journal = {Current microbiology},
volume = {82},
number = {1},
pages = {57},
pmid = {39718600},
issn = {1432-0991},
mesh = {*Pseudomonas aeruginosa/genetics/drug effects/isolation & purification ; Humans ; *Pseudomonas Infections/microbiology/epidemiology ; Environmental Monitoring ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Environmental Microbiology ; },
abstract = {Pseudomonas aeruginosa is a prevalent nosocomial pathogen and a significant reservoir of antimicrobial resistance genes in residential and built environments. It is also widespread in various indoor and outdoor settings, including sewage, surface waters, soil, recreational waters (both treated and untreated), and industrial effluents. Surveillance efforts for P. aeruginosa are primarily focused on hospitals rather than built environments. However, evidence links multidrug-resistant P. aeruginosa of human origin with activity in built environments and hospital settings. Consequently, tracking this pathogen across all environments is crucial for understanding the mechanisms of reverse transmission from built environments to humans. This review explores public health hygiene by examining the prevalence of P. aeruginosa in various environments, its sequence types, the factors contributing to multidrug resistance, and the identification methods through global surveillance. Whole-genome sequencing with sequence typing and real-time quantitative PCR are widely used to identify and study antimicrobial-resistant strains worldwide. Additionally, advanced techniques such as functional metagenomics, next-generation sequencing, MALDI-TOF, and biosensors are being extensively employed to detect antimicrobial-resistant strains and mitigate the ongoing evolution of bacterial resistance to antibiotics. Our review strongly underscores the importance of environmental monitoring of P. aeruginosa in preventing human infections. Furthermore, strategic planning in built environments is essential for effective epidemiological surveillance of P. aeruginosa and the development of comprehensive risk assessment models.},
}

*Pseudomonas aeruginosa/genetics/drug effects/isolation & purification
Humans
*Pseudomonas Infections/microbiology/epidemiology
Environmental Monitoring
Anti-Bacterial Agents/pharmacology
Drug Resistance, Multiple, Bacterial/genetics
Environmental Microbiology

@article {pmid39717705,
year = {2024},
author = {Ben Chéhida, S and Devi Bunwaree, H and Hoareau, M and Moubset, O and Julian, C and Blondin, L and Filloux, D and Lavergne, C and Roumagnac, P and Varsani, A and Martin, DP and Lett, JM and Lefeuvre, P},
title = {Increase of niche filling with increase of host richness for plant-infecting mastreviruses.},
journal = {Virus evolution},
volume = {10},
number = {1},
pages = {veae107},
pmid = {39717705},
issn = {2057-1577},
abstract = {Now that it has been realized that viruses are ubiquitous, questions have been raised on factors influencing their diversity and distribution. For phytoviruses, understanding the interplay between plant diversity and virus species richness and prevalence remains cardinal. As both the amplification and the dilution of viral species richness due to increasing host diversity have been theorized and observed, a deeper understanding of how plants and viruses interact in natural environments is needed to explore how host availability conditions viral diversity and distributions. From a unique dataset, this study explores interactions of Mastrevirus species (family Geminiviridae) with Poales order hosts across 10 sites from three contrasting ecosystems on La Réunion. Among 273 plant pools, representing 61 Poales species, 15 Mastrevirus species were characterized from 22 hosts. The analysis revealed a strong association of mastreviruses with hosts from agroecosystems, the rare presence of viruses in coastal grasslands, and the absence of mastreviruses in subalpine areas, areas dominated by native plants. This suggests that detected mastreviruses were introduced through anthropogenic activities, emphasizing the role of humans in shaping the global pathobiome. By reconstructing the realized host-virus infection network, besides revealing a pattern of increasing viral richness with increasing host richness, we observed increasing viral niche occupancies with increasing host species richness, implying that virus realized richness at any given site is conditioned on the global capacity of the plant populations to host diverse mastreviruses. Whether this tendency is driven by synergy between viruses or by an interplay between vector population and plant richness remains to be established.},
}

@article {pmid39717545,
year = {2024},
author = {Ma, J and Jiang, Y and He, Y and Zhou, H},
title = {The value of metagenomic next-generation sequencing with blood samples for the diagnosis of disseminated tuberculosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1456119},
pmid = {39717545},
issn = {2235-2988},
mesh = {Humans ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Female ; *Metagenomics/methods ; Middle Aged ; Adult ; *Tuberculosis/diagnosis/microbiology/blood ; *HIV Infections/diagnosis/complications/blood ; *Mycobacterium tuberculosis/genetics ; *Sensitivity and Specificity ; Aged ; CD4 Lymphocyte Count ; Young Adult ; },
abstract = {OBJECTIVE: The aim of this study was to assess the clinical value of metagenomic next-generation sequencing (mNGS) of blood samples for the identification of disseminated tuberculosis (DTB).

METHODS: A total of 48 individuals suspected of DTB were enrolled. All patients underwent mNGS of peripheral blood and conventional microbiological tests. Patient characteristics were collected from their medical records.

RESULTS: A total of 28 patients were diagnosed with DTB, whereas 20 patients were confirmed as non-DTB cases. In the DTB groups, 19 (67.9%) contained TB sequences, with specific reads of TB ranging from 1 to 219. The TB sequence was more detectable by mNGS in male patients, those with elevated PCT levels, those who are HIV positive, and those with a decreased CD4 T-cell count. The HIV-positive group shows higher TB mNGS reads (p = 0.012) and TB mNGS sensitivity (p = 0.05). The sensitivity of TB mNGS in blood samples was 80% for HIV-infected patients and 44.4% for non-HIV-infected individuals (p = 0.05). The non-HIV group had a higher prevalence of miliary tuberculosis (p = 0.018), and extrapulmonary tuberculosis was more prevalent in the HIV-positive group.

CONCLUSION: Our research has shown that the mNGS of blood samples has excellent sensitivity for the diagnosis of DTB. The TB sequence was more detectable by mNGS in patients with elevated PCT levels, those who are HIV positive, and those with a decreased CD4 T-cell count.},
}

Humans
Male
*High-Throughput Nucleotide Sequencing/methods
Female
*Metagenomics/methods
Middle Aged
Adult
*Tuberculosis/diagnosis/microbiology/blood
*HIV Infections/diagnosis/complications/blood
*Mycobacterium tuberculosis/genetics
*Sensitivity and Specificity
Aged
CD4 Lymphocyte Count
Young Adult

@article {pmid39717490,
year = {2024},
author = {Shah, JR and Sohail, MR and Lasco, T and Goss, JA and Mohajer, MA and Khalil, S},
title = {Clinical utility of plasma microbial cell-free DNA sequencing in determining microbiologic etiology of infectious syndromes in solid organ transplant recipients.},
journal = {Therapeutic advances in infectious disease},
volume = {11},
number = {},
pages = {20499361241308643},
pmid = {39717490},
issn = {2049-9361},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is increasingly being used for microbial detection in various infectious syndromes. However, data regarding the use of mNGS in solid organ transplant recipients (SOTR) are lacking.

OBJECTIVES: To describe and analyze real-world clinical impact of mNGS using plasma microbial cell-free DNA (mcfDNA) in SOTR.Design: Retrospectively reviewed all adult SOTR who underwent mNGS testing using plasma mcfDNA at Baylor St Luke's Medical Center from March 2017 to February 2023.

METHODS: Clinical impact (positive, neutral, and negative) was assessed using standardized objective criteria. Three Infectious Diseases physicians independently performed clinical adjudication to determine the correlation of mcfDNA results with clinical diagnosis. A descriptive analysis of the patient and clinical characteristics was performed.

RESULTS: A total of 113 mcfDNA tests in liver (42%), kidney (35%), lung (20%) and heart (13%) transplant recipients were performed in the study period. The most common clinical syndromes were pneumonia (36%), fever of unknown origin (16%), and intra-abdominal infections (15%). Most (80, 71%) of the mcfDNA test results were positive for microorganisms. Twenty-seven (24%) cases were classified as positive clinical impact, 82 (73%) were neutral and 4 (3%) were negative, respectively.

CONCLUSION: In SOTR, mcfDNA sequencing can add a positive clinical impact in a quarter of the cases and identify microorganisms beyond conventional microbiological testing across clinical syndromes. The negative clinical impact was rare. However, larger prospective studies are needed to define the optimal timing and utilization of mcfDNA in the sequence of diagnostic evaluation for syndrome-specific workup in SOTR.

SUMMARY: Metagenomic next-generation sequencing (mNGS) is a novel diagnostic tool that can identify difficult-to-detect microorganisms in SOTR. Our study demonstrates that the mNGS test resulted in a positive clinical impact in 1 out of 4 patients.},
}

@article {pmid39717271,
year = {2024},
author = {Wang, B and Tan, S and Wu, M and Feng, Y and Yan, W and Yun, Q and Ji, X and Lin, R and Zhao, Z},
title = {Effects of two Bacillus velezensis strains isolated from different sources on the growth of Capsicum annum.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1504660},
pmid = {39717271},
issn = {1664-302X},
abstract = {Microbial inoculants offer an environmentally friendly approach to enhance plant growth and control disease. In this study, two Bacillus velezensis strains, HKSSLJEBR3 (R3) and Ya-1 were isolated from pepper plant roots and tropical rainforest soil, respectively. Both strains exhibited strong antifungal activity against Fusarium oxysporum f. sp. capsici, with inhibition rates of 48.54 ± 0.66% for R3 and 49.35 ± 1.44% for Ya-1. In greenhouse trials, R3 significantly boosted pepper growth, with a 22.12% increase in plant height, 46.44% more leaves, and 56.29% greater fresh weight. These enhancements were likely due to the strong affinity between R3 and pepper plants. Both strains also improved soil quality, with R3 increasing available potassium (AK) by 5.13% and soil organic matter (SOM) by 4.03%, while Ya-1 showed more significant increases. Metagenomic analysis revealed that both strains altered the rhizosphere microbiome, with R3 promoting Pseudomonas and suppressing Fusarium. These results suggest that the R3 strain has strong potential for enhancing pepper growth, improving soil health, and reshaping the rhizosphere microbiome.},
}

@article {pmid39717063,
year = {2024},
author = {Peng, HB and Liu, Y and Hou, F and Zhao, S and Zhang, YZ and He, ZY and Liu, JY and Xiong, HF and Sun, LY},
title = {Clinical Application of Metagenomic Next-Generation Sequencing (mNGS) in Patients with Early Pulmonary Infection After Liver Transplantation.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {5685-5698},
pmid = {39717063},
issn = {1178-6973},
abstract = {PURPOSE: To examine the clinical utility of metagenomic next-generation sequencing (mNGS) in individuals with early pulmonary infection following liver transplantation.

PATIENTS AND METHODS: mNGS and traditional detection results were retrospectively collected from 99 patients with pulmonary infection within one week following liver transplantation. These patients were admitted to the Department of Critical Liver Diseases at Beijing Friendship Hospital from February 2022 to February 2024, along with their general clinical data.

RESULTS: mNGS exhibited a significantly higher detection rate than traditional methods (92.93% vs 54.55%, P < 0.05) and was more effective in identifying mixed infections (67.68% vs 14.81%, P < 0.05). mNGS identified 303 pathogens in 92 patients, with Enterococcus faecium, Pneumocystis jirovecii, and human herpesvirus types 5 and 7 being the most prevalent bacteria, fungi, and viruses. A total of 26 positive cases were identified through traditional culture methods (sputum and bronchoalveolar lavage fluid), with 18 cases consistent with mNGS detection results, representing 69.23% consistency. Among the three drug-resistant bacteria that showed positivity in mNGS and traditional culture, the presence of drug-resistance genes-mecA in Staphylococcus aureus; KPC-2, KPC-9, KPC-18, KPC-26, OXA27, OXA423 in Klebsiella pneumoniae; and OXA488 and NDM6 in Pseudomonas aeruginosa-reliably predicted drug-resistance phenotype. The treatment regimen for 76 of the 92 patients with positive mNGS relied on these results; 74 exhibited significant symptom improvement, yielding a 97.37% recovery rate. The overall prognosis was favorable.

CONCLUSION: mNGS offers rapid detection, a high positivity rate, insensitivity to antibiotics, and a superior ability to detect mixed infections in patients with early post-transplant pulmonary infections. Additionally, mNGS shows good consistency with traditional culture and can predict drug-resistant phenotypes to guide targeted antibiotic therapy for early-stage post-transplant pulmonary infection after liver transplantation. Patients whose antibiotic therapy is based on mNGS results have experienced decreased mortality rates and overall improved prognosis.},
}

@article {pmid39716679,
year = {2024},
author = {Bai, X and Wu, J and Zhang, B and Zhao, H and Tian, F and Wang, B},
title = {Metagenomics reveals functional profiles of soil nitrogen and phosphorus cycling under different amendments in saline-alkali soil.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120686},
doi = {10.1016/j.envres.2024.120686},
pmid = {39716679},
issn = {1096-0953},
abstract = {High salinity, low fertility and poor structure in saline-alkali soils led to nutrient cycling slow and microbial activity loss. The application of amendments has proven effective in enhancing soil nutrients, which significantly affects soil nitrogen and phosphorus cycling process. However, the specific impact of different amendments on the microbial functional potential related to nutrient cycling in saline-alkali soils remains unclear. Hence, metagenomics sequencing was used to investigate soil microbial communities and nitrogen and phosphorus cycling genes in response to different amendments, and to examine the influence of soil physicochemical properties on functional genes in the Hetao irrigation district of China. The results showed that amendments application enriched the Proteobacteria abundance, while inhibiting oligotrophic groups such as Chloroflexi. Compared to the control (CK), the combined application of desulfurization gypsum and cattle manure (DC) notably increased nasA (assimilatory nitrate reduction) and nirB (dissimilatory nitrate reduction), as well as phoD and phoA genes (organic P mineralization). Furthermore, soil AK and AP were primary factors affecting microbial communities and N and P cycling genes. Overall, this study offers valuable insights into soil nitrogen and phosphorus cycling genes and their interactions in response to different amendments, where the application of amendments affects nitrogen and phosphorus cycling by altering soil nutrient availability.},
}

@article {pmid39716502,
year = {2024},
author = {Zheng, J and Li, YY and Lu, YS and Wang, D and Liu, C and Peng, HL and Shi, CH and Xie, KZ and Zhang, K and Sun, LL and Zhou, CM and Gu, WJ},
title = {Impact of different continuous fertilizations on the antibiotic resistome associated with a subtropical triple-cropping system over one decade.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125564},
doi = {10.1016/j.envpol.2024.125564},
pmid = {39716502},
issn = {1873-6424},
abstract = {The prevalence of antibiotic resistance genes (ARGs) in agricultural soils has garnered significant attention. However, the long-term impacts of various nitroge (N)-substitution fertilization regimes on the distribution of soil ARGs and their dominant drivers in a subtropical triple-cropping system remain largely unexplored. This study employed a metagenomic approach to analyze soil ARGs, microbial communities, mobile genetic elements (MGEs), and viruses from a maize-maize-cabbage rotation field experiment with five different fertilization regimes. Soil samples were collected in 2012 and 2021. A total of 615 unique ARG subtypes were identified, with multidrug, bacitracin, and rifamycin resistance genes being the most abundant. Notably, ARG types. the continuous application of fresh chicken manure (CM) over 10 years significantly increased both the count of unique ARG subtypes and the total ARG abundance compared to other fertilization regimes, such as inorganic fertilizer and composted chicken manure. Specifically, the abundance of genes associated with antibiotic target replacement (e.g., sul1 and sul2) in the CM-treated soil rose by 8.83-fold from 2021 to 2012. Our random forest analysis revealed that the abundance of three MGEs (QacEdelta, plasmids, and IstB), two viral families (Myoviridae and Podoviridae), two bacterial phyla (Chloroflexi and Planctomycetes), and two environmental factors (pH and soil organic matter (SOM)) significantly influenced the distribution of ARGs. Furthermore, variance decomposition analysis underscored the critical roles of the three MGEs and the two viral families in the dissemination of ARGs, suggesting that horizontal gene transfer (HGT) may play a key role in ARG spread. These findings enhance our understanding of how different fertilization practices influence ARG dissemination in subtropical triple-cropping agroecosystems over the long term and provide valuable insights for optimizing fertilization management strategies.},
}

@article {pmid39716130,
year = {2024},
author = {Gao, X and Chen, L and Yang, S and Zhu, C and Wang, D},
title = {Donor-derived carbapenem-resistant Klebsiella Pneumoniae infections leading to retroperitoneal abscesses in kidney transplant recipients: a report of two cases.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {1459},
pmid = {39716130},
issn = {1471-2334},
support = {LQZD-QG//Key specialty of Joint Logistic Medicine of the Joint Logistic Support Force/ ; },
mesh = {Humans ; Male ; *Kidney Transplantation/adverse effects ; Middle Aged ; *Klebsiella Infections/microbiology/drug therapy ; *Klebsiella pneumoniae/isolation & purification/genetics ; *Anti-Bacterial Agents/therapeutic use ; Carbapenems/therapeutic use/pharmacology ; Tissue Donors ; Transplant Recipients ; Retroperitoneal Space/microbiology ; Abdominal Abscess/microbiology ; Drainage ; },
abstract = {BACKGROUND: Retroperitoneal abscesses caused by donor-derived Carbapenem-Resistant Klebsiella Pneumoniae (CRKP) infections are rare and often challenging to diagnose early due to a lack of specific symptoms.

CASE PRESENTATION: In case one, a 64-year-old male presented with unexplained fever and emaciation three months after undergoing a kidney transplant for end-stage renal disease. Metagenomic Next-Generation Sequencing identified CRKP in peripheral blood samples, and CT scans confirmed a retroperitoneal abscess. Considering the infectious status of the donor and other recipients, donor-derived infection (DDI) was suspected. Surgical incision and drainage were performed along with anti-infection treatment and immunosuppressive agents were adjusted. There was no recurrence of infection after a six-month follow-up. In case two, a 45-year-old male was readmitted due to light red pus discharge from the drainage tube fistula on day 32 after undergoing a kidney transplant for end-stage renal disease. A CT scan confirmed a retroperitoneal abscess between the kidney allograft and the spinal column. Based on the culture results of the purulent sample and perfusion fluid from the donor kidney, DDI was suspected, leading to prompt surgical incision and drainage, along with anti-infection treatment. After a five-month follow-up period, no infection recurrence was observed.

CONCLUSIONS: This study reported two cases of retroperitoneal abscesses caused by DDI following kidney transplantation, highlighting the importance of considering donor-derived CRKP infections in transplant recipients presenting with unexplained symptoms. Timely interventions are crucial for effective management and prevention of recurrence.},
}

Humans
Male
*Kidney Transplantation/adverse effects
Middle Aged
*Klebsiella Infections/microbiology/drug therapy
*Klebsiella pneumoniae/isolation & purification/genetics
*Anti-Bacterial Agents/therapeutic use
Carbapenems/therapeutic use/pharmacology
Tissue Donors
Transplant Recipients
Retroperitoneal Space/microbiology
Abdominal Abscess/microbiology
Drainage

@article {pmid39716092,
year = {2024},
author = {Chapman, JA and Wroot, E and Brown, T and Beck, LC and Embleton, ND and Berrington, JE and Stewart, CJ},
title = {Characterising the metabolic functionality of the preterm neonatal gut microbiome prior to the onset of necrotising enterocolitis: a pilot study.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {533},
pmid = {39716092},
issn = {1471-2180},
mesh = {Humans ; *Enterocolitis, Necrotizing/microbiology/metabolism ; *Gastrointestinal Microbiome ; Pilot Projects ; Infant, Newborn ; *Infant, Premature ; Female ; Male ; Bacteria/classification/metabolism/isolation & purification/genetics ; Feces/microbiology ; Case-Control Studies ; Metagenome ; },
abstract = {BACKGROUND: Necrotising enterocolitis (NEC) is a devastating bowel disease that primarily occurs in infants born prematurely and is associated with abnormal gut microbiome development. While gut microbiome compositions associated with NEC have been well studied, there is a lack of experimental work investigating microbiota functions and their associations with disease onset. The aim of this pilot study was to characterise the metabolic functionality of the preterm gut microbiome prior to the onset of NEC compared with healthy controls.

RESULTS: Eight NEC infants were selected of median gestation 26.5 weeks and median day of life (DOL) of NEC onset 20, with one sample used per infant, collected within one to eight days (median four) before NEC onset. Each NEC case was matched to a control infant based on gestation and sample DOL, the main driver of microbiome composition in this population, giving a total cohort of 16 infants for this study. Dietary exposures were well matched. The microbiota of NEC and control infants showed similar wide-ranging metabolic functionalities. All 94 carbon sources were utilised to varying extents but NEC and control samples clustered separately by supervised ordination based on carbon source utilisation profiles. For a subset of eight samples (four NEC, four control) for which pre-existing metagenome data was available, microbiome composition was found to correlate significantly with metabolic activity measured on Biolog plates (p = 0.035). Comparisons across all 16 samples showed the NEC microbiota to have greater utilisation of carbon sources that are the products of proteolytic fermentation, specifically amino acids. In pairwise comparisons, L-methionine was highly utilised in NEC samples, but poorly utilised in controls (p = 0.043). Carbon sources identified as discriminatory for NEC also showed a greater enrichment for established markers of inflammatory disease, such as inflammatory bowel disease, irritable bowel syndrome and diverticular disease.

CONCLUSIONS: Before NEC onset, the preterm gut microbiota showed greater metabolic utilisation of amino acids, potentially indicating a shift from predominantly saccharolytic to proteolytic fermentation. Products of amino acid breakdown could therefore act as biomarkers for NEC development. A larger study is warranted, ideally with infants from multiple sites.},
}

Humans
*Enterocolitis, Necrotizing/microbiology/metabolism
*Gastrointestinal Microbiome
Pilot Projects
Infant, Newborn
*Infant, Premature
Female
Male
Bacteria/classification/metabolism/isolation & purification/genetics
Feces/microbiology
Case-Control Studies
Metagenome

@article {pmid39716085,
year = {2024},
author = {Meyer-Rust, KA and Strickland, A and Lee, BY and Sevigny, JL and Bradt, G and Brown, BL},
title = {Diet of the blue crab (Callinectes sapidus) during range expansion in Great Bay Estuary, New Hampshire.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1238},
pmid = {39716085},
issn = {1471-2164},
support = {TBD//New Hampshire Sea Grant, University of New Hampshire/ ; TBD//New Hampshire Sea Grant, University of New Hampshire/ ; TBD//School of Marine Science and Ocean Engineering, University of New Hampshire/ ; TBD//College of Life Sciences and Agriculture, University of New Hampshire/ ; TBD//New Hampshire Agricultural Experiment Station/ ; TBD//New Hampshire Agricultural Experiment Station/ ; },
mesh = {Animals ; *Brachyura/genetics ; *Estuaries ; *Diet ; New Hampshire ; Bays ; Metagenomics/methods ; Ecosystem ; },
abstract = {Great Bay Estuary (GBE), within the rapidly warming Gulf of Maine, has experienced significant ecological shifts this century due to naturalization of invasive species. The range expansion of the American blue crab (Callinectes sapidus) currently underway from the mid-Atlantic northward brings the possibility of similar ecological shifts. This study accounts recent trapping and diet analysis of C. sapidus in GBE. Diet is an important component of understanding how the blue crab range expansion may affect GBE ecosystem functions. Across all sites and trap types, 27 blue crabs were captured. Metagenomic analysis of shotgun sequencing techniques were used on the gut contents of blue crabs captured. Most specimens had > 50% Eukaryote sequences. Overall results of this gut content study confirm a mixed diet indicative of an opportunistic feeder. Using metagenomics to analyze the diet of blue crabs as they establish viable populations in GBE will be a useful tool for predicting how these range expanding organisms are interacting within this important estuarine ecosystem, which will promote sustainable development by informing end users who may be affected by these crabs to help them meet their needs in the present and future. This project falls within Global Goal SDG14: Life Below Water.},
}

Animals
*Brachyura/genetics
*Estuaries
*Diet
New Hampshire
Bays
Metagenomics/methods
Ecosystem

@article {pmid39716039,
year = {2025},
author = {Du, Q and Liu, X and Zhang, R and Hu, G and Liu, Q and Wang, R and Ma, W and Hu, Y and Fan, Z and Li, J},
title = {Placental and Fetal Microbiota in Rhesus Macaque: A Case Study Using Metagenomic Sequencing.},
journal = {American journal of primatology},
volume = {87},
number = {1},
pages = {e23718},
doi = {10.1002/ajp.23718},
pmid = {39716039},
issn = {1098-2345},
support = {//This work was supported by the National Natural Science Foundation of China (32171607)/ ; },
mesh = {Animals ; *Macaca mulatta/microbiology ; Female ; Pregnancy ; *Fetus/microbiology ; *Placenta/microbiology ; *Microbiota ; *Metagenomics ; Umbilical Cord/microbiology ; Gastrointestinal Microbiome ; },
abstract = {Recent evidence challenging the notion of a sterile intrauterine environment has sparked research into the origins and effects of fetal microbiota on immunity development during gestation. Rhesus macaques (RMs) serve as valuable nonhuman primate models due to their similarities to humans in development, placental structure, and immune response. In this study, metagenomic analysis was applied to the placenta, umbilical cord, spleen, gastrointestinal tissues of an unborn RM fetus, and the maternal intestine, revealing the diversity and functionality of microbes in these tissues. Additionally, gut metagenomic data of adult Rhesus macaques from our previous study, along with data from a human fetus obtained from public databases, were included for comparison. We observed substantial microbial sharing between the mother and fetus, with the microbial composition of the placenta and umbilical cord more closely resembling that of the fetal organs than the maternal intestine. Notably, compared with other adult RMs, there was a clear convergence between maternal and fetal microbiota, alongside distinct differences between the microbiota of adults and the fetus, which underscores the unique microbial profiles in fetal environments. Furthermore, the fetal microbiota displayed a less developed carbohydrate metabolism capacity than adult RMs. It also shared antibiotic resistance genes with both maternal and adult RM microbiomes, indicating potential vertical transmission. Comparative analysis of the metagenomes between the RM fetus and a human fetus revealed significant differences in microbial composition and genes, yet also showed similarities in certain abundant microbiota. Collectively, our results contribute to a more comprehensive understanding of the intrauterine microbial environment in macaques.},
}

Animals
*Macaca mulatta/microbiology
Female
Pregnancy
*Fetus/microbiology
*Placenta/microbiology
*Microbiota
*Metagenomics
Umbilical Cord/microbiology
Gastrointestinal Microbiome

@article {pmid39715919,
year = {2024},
author = {Jiang, ZB and Zhang, H and Tian, JJ and Guo, HH and Zhou, LR and Ma, XL},
title = {The Microbial Diversity of Biological Moss Crust: Application in Saline-Alkali Soil Management.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {162},
pmid = {39715919},
issn = {1432-184X},
support = {82160672//the National Natural Science Foundation of China/ ; 2022AAC05041 and 2023AAC05048//Outstanding Youth Program of Ningxia Natural Science Foundation/ ; 2021BEB04019//the Key R&D Projects in Ningxia/ ; 2021AAC03210 and 2019AAC03113//the Ningxia Natural Science Foundation/ ; },
mesh = {*Soil/chemistry ; *Soil Microbiology ; *Bryophyta/microbiology ; China ; Biodiversity ; Alkalies/analysis ; Salinity ; Bacteria/classification/genetics/isolation & purification/metabolism ; Chlorophyll/analysis ; },
abstract = {Soil salinization poses a substantial threat to global food security, particularly under the influence of climate change, and is recognized as one of the most urgent challenges in land degradation. This study aims to elucidate the challenges associated with managing arid and semi-arid saline-alkali lands in China's Ningxia province and propose feasible solutions. To assess moss crust colonization, we measured changes in organic matter and chlorophyll levels. Additionally, we investigated the impact of an interlayer composed of Goji berry root bark using liquid chromatography-mass spectrometry analysis, biological enzyme activity analysis, and metagenomic sequencing. A total of 45 endophytes were isolated from the moss crust. The most significant colonization of moss crusts was observed when the Goji berry root bark was used as the interlayer, resulting in a significant increase in chlorophyll content. Several responses were identified as pivotal factors facilitating moss crust growth when the Goji berry root bark was used as the interlayer. In saline-alkali soil, the Goji berry root bark interlayer increased the activities of sucrase, urease, and alkaline phosphatase. Metagenomic data analysis revealed variations in the relative abundance of microorganisms at the phylum level, although these differences were not statistically significant. Evaluation of the impact of physical isolation and moss crust transplantation on the ecological restoration of saline-alkali soil using liquid chromatography-tandem mass spectrometry and metagenomic sequencing indicated that the Goji berry root bark as a physical isolation method promotes moss crust colonization in saline-alkali soil and increases soil organic matter and nutrient elements, offering valuable insights for the ecological management of saline-alkali land and serving as a reference for future research in this field.},
}

*Soil/chemistry
*Soil Microbiology
*Bryophyta/microbiology
China
Biodiversity
Alkalies/analysis
Salinity
Bacteria/classification/genetics/isolation & purification/metabolism
Chlorophyll/analysis

@article {pmid39605597,
year = {2024},
author = {Popowitch, EB and Tran, TH and Escapa, IF and Bhatt, E and Sozat, AK and Ahmed, N and Deming, C and Roberts, AQ and , and Segre, JA and Kong, HH and Conlan, S and Lemon, KP and Kelly, MS},
title = {Description of two novel Corynebacterium species isolated from human nasal passages and skin.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39605597},
issn = {2692-8205},
abstract = {Strains of two novel Corynebacterium species were cultured from samples of human nostrils and skin collected in the United States and Botswana. These strains demonstrated growth on Columbia Colistin-Nalidixic Acid agar with 5% sheep blood and in liquid media (brain heart infusion and tryptic soy broth) supplemented with Tween 80, a source of the fatty acid oleic acid. Cells were Gram-positive, non-spore-forming, non-motile bacilli that showed catalase but not oxidase activity. Major fatty acids in both of these species were 18:1 ω9c (oleic acid), 16:0 (palmitic acid), and 18:0 (stearic acid). Analysis of the 16S ribosomal RNA gene sequences identified these strains as belonging to the genus Corynebacterium (family Corynebacteriaceae). Whole-genome sequencing revealed that these strains formed distinct branches on a phylogenomic tree, with C. tuberculostearicum being the closest relative but with average nucleotide identities of < 95% relative to all previously described species. These results indicate that these strains represent novel species of Corynebacterium, for which we propose the names Corynebacterium hallux sp. nov., with the type strain CTNIH22[T] (=ATCC TSD-435[T]=DSM 117774[T]), and Corynebacterium nasorum sp. nov., with the type strain KPL3804[T] (=ATCC TSD-439[T]=DSM 117767[T]). We also describe the characteristics of two strains isolated from human nasal passages that are members of the recently named species Corynebacterium yonathiae.},
}

@article {pmid39714548,
year = {2024},
author = {Wang, W and Zhang, Z and Sun, M and Li, C and Yan, M and Wang, C},
title = {Mechanism of decolorization and degradation of direct brown D3G by a halo-thermophilic consortium.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {1},
pages = {11},
pmid = {39714548},
issn = {1433-4909},
support = {22B610001//the Key Scientific Research Project in Colleges and Universities of Henan Province of China/ ; HDXJJG2023-058//the teaching reform project of Henan University/ ; },
mesh = {*Azo Compounds/metabolism/chemistry ; Microbial Consortia ; Biodegradation, Environmental ; Halomonas/metabolism ; Coloring Agents/metabolism/chemistry ; Laccase/metabolism ; Bacillus/metabolism ; },
abstract = {Azo dye wastewater has garnered significant attention from researchers because of its association with high-temperature, high-salt, and high-alkali conditions. In this study, consortium ZZ efficiently decolorized brown D3G under halophilic and thermophilic conditions. he results indicated that consortium ZZ, which was mainly dominated by Marinobacter, Bacillus, and Halomonas, was achieved decolorization rates ranging from 1 to 10% at temperatures between 40 °C and 50 °C, while maintaining a pH range of 7 to 10 for direct brown D3G degradation. Through the comprehensive utilization of UV-vis spectral analysis, Fourier transform infrared (FTIR), gas chromatography mass spectrometric (GC-MS) techniques, as well as metagenomic analysis, the decolorization and degradation pathway of direct brown by consortium ZZ was proposed. The azo dye reductase, lignin peroxidase, and laccase were also highly expressed in the decolorization process. Additionally, phytotoxicity tests using seeds of Cucumis sativus and Oryza sativa revealed that the intermediates generated showed no significant toxicity compared with distilled water. This investigation elucidated the pivotal contribution of consortium ZZ to azo dye degradation and provided novel theoretical insights along with practical guidance for azo dye treatment at halo-thermophilic conditions.},
}

*Azo Compounds/metabolism/chemistry
Microbial Consortia
Biodegradation, Environmental
Halomonas/metabolism
Coloring Agents/metabolism/chemistry
Laccase/metabolism
Bacillus/metabolism

@article {pmid39714212,
year = {2024},
author = {Fang, Y and Meng, L and Xia, J and Gotoh, Y and Hayashi, T and Nagasaki, K and Endo, H and Okazaki, Y and Ogata, H},
title = {Genome-resolved year-round dynamics reveal a broad range of giant virus microdiversity.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0116824},
doi = {10.1128/msystems.01168-24},
pmid = {39714212},
issn = {2379-5077},
abstract = {Giant viruses are crucial for marine ecosystem dynamics because they regulate microeukaryotic community structure, accelerate carbon and nutrient cycles, and drive the evolution of their hosts through co-evolutionary processes. Previously reported long-term observations revealed that these viruses display seasonal fluctuations in abundance. However, the underlying genetic mechanisms driving such dynamics of these viruses remain largely unknown. In this study, we investigated the dynamics of giant viruses using time-series metagenomes from eutrophic coastal seawater samples collected over 20 months. A newly developed computational pipeline generated 1,065 high-quality genomes covering six major giant virus lineages. These genomic data revealed year-round recovery of the viral community structure at the study site and distinct dynamics of viral populations that were classified as persistent (n = 9), seasonal (n = 389), sporadic (n = 318), or others. By profiling the intra-species nucleotide-resolved microdiversity through read mapping, we also identified year-round recovery dynamics at subpopulation level for viruses classified as persistent or seasonal. Our results further indicated that giant viruses with broader niche breadth tended to exhibit higher levels of microdiversity. We argue that greater microdiversity of viruses likely enhances adaptability and thus survival under the virus-host arms race during prolonged interactions with their hosts.IMPORTANCERecent genome-resolved metagenomic surveys have uncovered the vast genomic diversity of giant viruses, which play significant roles in aquatic ecosystems by acting as bloom terminators and influencing biogeochemical cycles. However, the relationship between the ecological dynamics of giant viruses and underlying genetic structures of viral populations remains unresolved. In this study, we performed deep metagenomic sequencing of seawater samples collected across a time-series from a coastal area in Japan. The results revealed a significant positive correlation between microdiversity and temporal persistence of giant virus populations, suggesting that population structure is a crucial factor for adaptation and survival in the interactions with their hosts.},
}

@article {pmid39714211,
year = {2024},
author = {Facimoto, CT and Clements, KD and White, WL and Handley, KM},
title = {Hindguts of Kyphosus sydneyanus harbor phylogenetically and genomically distinct Alistipes capable of degrading algal polysaccharides and diazotrophy.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0100724},
doi = {10.1128/msystems.01007-24},
pmid = {39714211},
issn = {2379-5077},
abstract = {The genus Alistipes (Bacteroidota) is most often associated with human clinical samples and livestock. However, Alistipes are also prevalent in the hindgut of the marine herbivorous fish Kyphosus sydneyanus (Silver Drummer), and analysis of their carbohydrate-active enzyme (CAZyme) encoding gene repertoires suggests Alistipes degrade macroalgal biomass to support fish nutrition. To further explore host-associated traits unique to K. sydneyanus-derived Alistipes, we compared 445 high-quality genomes of Alistipes available in public databases (e.g., human and ruminant associated) with 99 metagenome-assembled genomes (MAGs) from the K. sydneyanus gut. Analyses showed that Alistipes from K. sydneyanus are phylogenetically distinct from other hosts and comprise 26 species based on genomic average nucleotide identity (ANI) analyses. Ruminant- and fish-derived Alistipes had significantly smaller genomes than human-derived strains, and lower GC contents, possibly reflecting a symbiotic relationship with their hosts. The fish-derived Alistipes were further delineated by their genetic capacity to fix nitrogen, biosynthesize cobalamin (vitamin B12), and utilize marine polysaccharides (e.g., alginate and carrageenan). The distribution of CAZymes encoded by Alistipes from K. sydneyanus was not phylogenetically conserved. Distinct CAZyme gene compositions were observed between closely related species. Conversely, CAZyme gene clusters (operons) targeting the same substrates were found across diverse species. Nonetheless, transcriptional data suggest that closely related Alistipes target specific groups of substrates within the fish hindgut. Results highlight host-specific adaptations among Alistipes in the fish hindgut that likely contribute to K. sydneyanus digesting their seaweed diet, and diverse and redundant carbohydrate-degrading capabilities across these Alistipes species.IMPORTANCEDespite numerous reports of the Alistipes genus in humans and ruminants, its diversity and function remain understudied, and there is no clear consensus on whether it positively or negatively impacts host health. Given the symbiotic role of gut communities in the Kyphosus sydneyanus hindgut, where Alistipes are prevalent, and the diversity of carbohydrate-active enzymes (CAZymes) encoded that likely contribute to the breakdown of important substrates in the host diet, it is likely that this genus provides essential services to the fish host. Therefore, considering its metabolism in various contexts and hosts is crucial for understanding the ecology of the genus. Our study highlights the distinct genetic traits of Alistipes based on host association, and the potential of fish-associated Alistipes to transform macroalgae biomass into nutraceuticals (alginate oligosaccharides, β-glucans, sulfated galactans, and sulfated fucans).},
}

@article {pmid39714209,
year = {2024},
author = {Payne, PE and Knobbe, LN and Chanton, P and Zaugg, J and Mortazavi, B and Mason, OU},
title = {Uncovering novel functions of the enigmatic, abundant, and active Anaerolineae in a salt marsh ecosystem.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0116224},
doi = {10.1128/msystems.01162-24},
pmid = {39714209},
issn = {2379-5077},
abstract = {Anaerolineae, particularly uncultured representatives, are one of the most abundant microbial groups in coastal salt marshes, dominating the belowground rhizosphere, where over half of plant biomass production occurs. However, this class generally remains poorly understood, particularly in a salt marsh context. Here, novel Anaerolineae metagenome-assembled genomes (MAGs) were generated from the salt marsh rhizosphere representing Anaerolineales, Promineifilales, JAAYZQ01, B4-G1, JAFGEY01, UCB3, and Caldilineales orders. Metagenome and metatranscriptome reads were mapped to annotated MAGs, revealing nearly all Anaerolineae encoded and transcribed genes required for oxidation of carbon compounds ranging from simple sugars to complex polysaccharides, fermentation, and carbon fixation. Furthermore, the majority of Anaerolineae expressed genes involved in anaerobic and aerobic respiration and secondary metabolite production. The data revealed that the belowground salt marsh Anaerolineae in the rhizosphere are important players in carbon cycling, including degradation of simple carbon compounds and more recalcitrant plant material, such as cellulose, using a diversity of electron acceptors and represent an unexplored reservoir of novel secondary metabolites.IMPORTANCEGiven that coastal salt marshes are recognized as biogeochemical hotspots, it is fundamentally important to understand the functional role of the microbiome in this ecosystem. In particular, Anaerolineae are abundant members of the salt marsh rhizosphere and have been identified as core microbes, suggesting they play an important functional role. Yet, little is known about the metabolic pathways encoded and expressed in this abundant salt marsh clade. Using an 'omics-based approach, we determined that Anaerolineae are capable of oxidizing a range of carbon compounds, including simple sugars to complex carbon compounds, while also encoding fermentation and carbon fixation. Surprisingly, Anaerolineae encoded and transcribed genes involved in aerobic respiration, which was unexpected given the reduced nature of the salt marsh rhizosphere. Finally, the majority of Anaerolineae appear to be involved in secondary metabolite production, suggesting that this group represents an unexplored reservoir of novel and important secondary metabolites.},
}

@article {pmid39714193,
year = {2024},
author = {Midot, F and Goh, KM and Liew, KJ and Lau, SYL and Espenberg, M and Mander, Ü and Melling, L},
title = {Temporal dynamics of soil microbial C and N cycles with GHG fluxes in the transition from tropical peatland forest to oil palm plantation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0198624},
doi = {10.1128/aem.01986-24},
pmid = {39714193},
issn = {1098-5336},
abstract = {Tropical peatlands significantly influence local and global carbon and nitrogen cycles, yet they face growing pressure from anthropogenic activities. Land use changes, such as peatland forests conversion to oil palm plantations, affect the soil microbiome and greenhouse gas (GHG) emissions. However, the temporal dynamics of microbial community changes and their role as GHG indicators are not well understood. This study examines the dynamics of peat chemistry, soil microbial communities, and GHG emissions from 2016 to 2020 in a logged-over secondary peat swamp forest in Sarawak, Malaysia, which transitioned to an oil palm plantation. This study focuses on changes in genetic composition governing plant litter degradation, methane (CH4), and nitrous oxide (N2O) fluxes. Soil CO2 emission increased (doubling from approximately 200 mg C m[-2] h[-1]), while CH4 emissions decreased (from 200 µg C m[-2] h[-1] to slightly negative) following land use changes. The N2O emissions in the oil palm plantation reached approximately 1,510 µg N m[-2] h[-1], significantly higher than previous land uses. The CH4 fluxes were driven by groundwater table, humification levels, and C:N ratio, with Methanomicrobia populations dominating methanogenesis and Methylocystis as the main CH4 oxidizer. The N2O fluxes correlated with groundwater table, total nitrogen, and C:N ratio with dominant nirK-type denitrifiers (13-fold nir to nosZ) and a minor role by nitrification (a threefold increase in amoA) in the plantation. Proteobacteria and Acidobacteria encoding incomplete denitrification genes potentially impact N2O emissions. These findings highlighted complex interactions between microbial communities and environmental factors influencing GHG fluxes in altered tropical peatland ecosystems.IMPORTANCETropical peatlands are carbon-rich environments that release significant amounts of greenhouse gases when drained or disturbed. This study assesses the impact of land use change on a secondary tropical peat swamp forest site converted into an oil palm plantation. The transformation lowered groundwater levels and changed soil properties. Consequently, the oil palm plantation site released higher carbon dioxide and nitrous oxide compared to previous land uses. As microbial communities play crucial roles in carbon and nitrogen cycles, this study identified environmental factors associated with microbial diversity, including genes and specific microbial groups related to nitrous oxide and methane emissions. Understanding the factors driving microbial composition shifts and greenhouse gas emissions in tropical peatlands provides baseline information to potentially mitigate environmental consequences of land use change, leading to a broader impact on climate change mitigation efforts and proper land management practices.},
}

@article {pmid39714168,
year = {2024},
author = {Bhosle, A and Jackson, MI and Walsh, AM and Franzosa, EA and Badri, DV and Huttenhower, C},
title = {Response of the gut microbiome and metabolome to dietary fiber in healthy dogs.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0045224},
doi = {10.1128/msystems.00452-24},
pmid = {39714168},
issn = {2379-5077},
abstract = {UNLABELLED: Dietary fiber confers multiple health benefits originating from the expansion of beneficial gut microbial activity. However, very few studies have established the metabolic consequences of interactions among specific fibers, microbiome composition, and function in either human or representative animal models. In a study design reflective of realistic population dietary variation, fecal metagenomic and metabolomic profiles were analyzed from healthy dogs fed 12 test foods containing different fiber sources and quantities (5-13% as-fed basis). Taxa and functions were identified whose abundances were associated either with overall fiber intake or with specific fiber compositions. Fourteen microbial species were significantly enriched in response to ≥1 specific fiber source; enrichment of fiber-derived metabolites was more pronounced in response to these fiber sources. Positively associated fecal metabolites, including short-chain fatty acids, acylglycerols, fiber bound sugars, and polyphenols, co-occurred with microbes enriched in specific food groups. Critically, the specific metabolite pools responsive to differential fiber intake were dependent on differences both in individual microbial community membership and in overall ecological configuration. This helps to explain, for the first time, differences in microbiome-diet associations observed in companion animal epidemiology. Thus, our study corroborates findings in human cohorts and reinforces the role of personalized microbiomes even in seemingly phenotypically homogeneous subjects.

IMPORTANCE: Consumption of dietary fiber changes the composition of the gut microbiome and, to a larger extent, the associated metabolites. Production of health-relevant metabolites such as short-chain fatty acids from fiber depends both on the consumption of a specific fiber and on the enrichment of beneficial metabolite-producing species in response to it. Even in a seemingly homogeneous population, the benefit received from fiber consumption is personalized and emphasizes specific fiber-microbe-host interactions. These observations are relevant for both population-wide and personalized nutrition applications.},
}

@article {pmid39714161,
year = {2024},
author = {Neumann, CJ and Mohammadzadeh, R and Woh, PY and Kobal, T and Pausan, M-R and Shinde, T and Haid, V and Mertelj, P and Weiss, E-C and Kolovetsiou-Kreiner, V and Mahnert, A and Kumpitsch, C and Jantscher-Krenn, E and Moissl-Eichinger, C},
title = {First-year dynamics of the anaerobic microbiome and archaeome in infants' oral and gastrointestinal systems.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0107124},
doi = {10.1128/msystems.01071-24},
pmid = {39714161},
issn = {2379-5077},
abstract = {UNLABELLED: Recent research provides new insights into the early establishment of the infant gut microbiome, emphasizing the influence of breastfeeding on the development of gastrointestinal microbiomes. In our study, we longitudinally examined the taxonomic and functional dynamics of the oral and gastrointestinal tract (GIT) microbiomes of healthy infants (n = 30) in their first year, focusing on the often-over-looked aspects, the development of archaeal and anaerobic microbiomes. Breastfed (BF) infants exhibit a more defined transitional phase in their oral microbiome compared to non-breastfed (NBF) infants, marked by a decrease in Streptococcus and the emergence of anaerobic genera such as Granulicatella. This phase, characterized by increased alpha-diversity and significant changes in beta-diversity, occurs earlier in NBF infants (months 1-3) than in BF infants (months 4-6), suggesting that breastfeeding supports later, more defined microbiome maturation. We demonstrated the presence of archaea in the infant oral cavity and GIT microbiome from early infancy, with Methanobrevibacter being the predominant genus. Still, transient patterns show that no stable archaeome is formed. The GIT microbiome exhibited gradual development, with BF infants showing increased diversity and complexity between the third and eighth months, marked by anaerobic microbial networks. NBF infants showed complex microbial co-occurrence patterns from the start. These strong differences between BF and NBF infants' GIT microbiomes are less pronounced on functional levels than on taxonomic levels. Overall, the infant microbiome differentiates and stabilizes over the first year, with breastfeeding playing a crucial role in shaping anaerobic microbial networks and overall microbiome maturation.

IMPORTANCE: The first year of life is a crucial period for establishing a healthy human microbiome. Our study analyses the role of archaea and obligate anaerobes in the development of the human oral and gut microbiome, with a specific focus on the impact of breastfeeding in this process. Our findings demonstrated that the oral and gut microbiomes of breastfed infants undergo distinct phases of increased dynamics within the first year of life. In contrast, the microbiomes of non-breastfed infants are more mature from the first month, leading to a steadier development without distinct transitional phases in the first year. Additionally, we found that archaeal signatures are present in infants under 1 year of age, but they do not form a stable archaeome. In contrast to this, we could track specific bacterial strains transitioning from oral to gut or persisting in the gut over time.},
}

@article {pmid39714117,
year = {2024},
author = {Caille, C and Duhamel, S and Latifi, A and Rabouille, S},
title = {Adaptive Responses of Cyanobacteria to Phosphate Limitation: A Focus on Marine Diazotrophs.},
journal = {Environmental microbiology},
volume = {26},
number = {12},
pages = {e70023},
doi = {10.1111/1462-2920.70023},
pmid = {39714117},
issn = {1462-2920},
support = {//LEFE-CYBER/ ; },
mesh = {*Cyanobacteria/metabolism/genetics ; *Phosphates/metabolism ; *Nitrogen Fixation ; *Adaptation, Physiological ; *Seawater/microbiology ; Phosphorus/metabolism ; },
abstract = {Phosphorus is an essential component of numerous macromolecules and is vital for life. Its availability significantly influences primary production, particularly in oligotrophic environments. Marine diazotrophic cyanobacteria, which play key roles in biogeochemical cycles through nitrogen fixation (N2 fixation), have adapted to thrive in phosphate (Pi)-poor areas. However, the molecular mechanisms that facilitate their adaptation to such conditions remain incompletely understood. Bacteria have evolved various strategies to cope with Pi limitation, including detecting Pi availability, utilising high-affinity Pi transporters, and hydrolyzing dissolved organic phosphorus (DOP) with various enzymes. This review synthesises current knowledge regarding how cyanobacteria adapt to Pi scarcity, with particular emphasis on subtropical marine free-living diazotrophs and their ability to utilise diverse DOP molecules. Omics approaches, such as (meta)genomics and (meta)transcriptomics, reveal the resilience of marine diazotrophs in the face of Pi scarcity and highlight the need for further research into their molecular adaptive strategies. Adaptation to Pi limitation is often intertwined with the broader response of cyanobacteria to multiple limitations and stresses. This underscores the importance of understanding Pi adaptation to assess the ecological resilience of these crucial microorganisms in dynamic environments, particularly in the context of global climate change.},
}

*Cyanobacteria/metabolism/genetics
*Phosphates/metabolism
*Nitrogen Fixation
*Adaptation, Physiological
*Seawater/microbiology
Phosphorus/metabolism

@article {pmid39714075,
year = {2025},
author = {Minty, M and Germain, A and Sun, J and Kaglan, G and Servant, F and Lelouvier, B and Misselis, E and Neagoe, RM and Rossella, M and Cardellini, M and Burcelin, R and Federici, M and Fernandez-Real, JM and Blasco-Baque, V},
title = {Identifying the location-dependent adipose tissue bacterial DNA signatures in obese patients that predict body weight loss.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2439105},
doi = {10.1080/19490976.2024.2439105},
pmid = {39714075},
issn = {1949-0984},
mesh = {Humans ; *Weight Loss ; *Obesity/microbiology/genetics/metabolism ; *DNA, Bacterial/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Female ; Male ; *Bariatric Surgery ; Adult ; Adipose Tissue/metabolism/microbiology ; Middle Aged ; Longitudinal Studies ; },
abstract = {Recent sets of evidence have described profiles of 16S rDNA sequences in host tissues, notably in fat pads that are significantly overrepresented and can serve as signatures of metabolic disease. However, these recent and original observations need to be further detailed and functionally defined. Here, using state-of-the-art targeted DNA sequencing and discriminant predictive approaches, we describe, from the longitudinal FLORINASH cohort of patients who underwent bariatric surgery, visceral, and subcutaneous fat pad-specific bacterial 16SrRNA signatures. The corresponding Porphyromonadaceae, Campylobacteraceae, Prevotellaceae, Actimomycetaceae, Veillonellaceae, Anaerivoracaceae, Fusobacteriaceae, and the Clostridium family XI 16SrRNA DNA segment profiles are signatures of the subcutaneous adipose depot while Pseudomonadaceae and Micrococcacecae, 16SrRNA DNA sequence profiles characterize the visceral adipose depot. In addition, we have further identified that a specific pre-bariatric surgery adipose tissue bacterial DNA signature predicts the efficacy of body weight loss in obese patients 5-10 years after the surgery. 16SrRNA signatures discriminate (ROC ~ 1) the patients who did not maintain bodyweight loss and those who did. Second, from the 16SrRNA sequences we infer potential pathways suggestive of catabolic biochemical activities that could be signatures of subcutaneous adipose depots that predict body weight loss.},
}

Humans
*Weight Loss
*Obesity/microbiology/genetics/metabolism
*DNA, Bacterial/genetics
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism
Female
Male
*Bariatric Surgery
Adult
Adipose Tissue/metabolism/microbiology
Middle Aged
Longitudinal Studies

@article {pmid39713824,
year = {2024},
author = {Karesh, WB},
title = {Shifting from wildlife disease threats to wildlife health.},
journal = {Revue scientifique et technique (International Office of Epizootics)},
volume = {Special Edition},
number = {},
pages = {141-144},
doi = {10.20506/rst.SE.3568},
pmid = {39713824},
issn = {0253-1933},
mesh = {Animals ; *Animals, Wild ; Humans ; Zoonoses/prevention & control ; Conservation of Natural Resources ; Animal Diseases/prevention & control/epidemiology ; },
abstract = {The evolution of wildlife disease management and surveillance, as documented in the World Organisation for Animal Health's Scientific and Technical Review, reflects a deepening understanding of the links between wildlife health, ecosystem integrity and human well-being. Early work, beginning with the World Assembly of Delegates in 1954, primarily focused on diseases like rabies. This focus expanded over time to include broader concerns such as the impacts of climate change, habitat loss and increased human-wildlife interactions on wildlife health. By the late 20th century, the emphasis had shifted towards improved practices for wildlife disease control and the development of advanced diagnostic methods and vaccines. Articles in the Review highlight the growing complexity of wildlife diseases and the need for holistic management strategies. The adoption in recent years of cutting-edge technologies like CRISPR-Cas systems and metagenomics points to a future of more proactive and integrated approaches to wildlife disease management. There is still a need to address not just the consequences of wildlife diseases but also their anthropogenic drivers. The latest perspectives advocate for nature-based solutions, expanded partnerships and systems-level thinking to effectively tackle 21st-century challenges in wildlife and biodiversity conservation.},
}

Animals
*Animals, Wild
Humans
Zoonoses/prevention & control
Conservation of Natural Resources
Animal Diseases/prevention & control/epidemiology

@article {pmid39713101,
year = {2024},
author = {Zhou, Q and Yang, J and Feng, Y and Yang, Z and Wang, Y and Zhang, Z and Zhang, T and Liu, W and Xu, Y and Yang, Y and Huang, J},
title = {Analysis of the effects of Bacillus velezensis HJ-16 inoculation on tobacco leaves based on multi-omics methods.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {12},
number = {},
pages = {1493766},
pmid = {39713101},
issn = {2296-4185},
abstract = {In this study, a strain isolated from the surface of flue-cured tobacco leaves, identified as Bacillus velezensis HJ-16, was applied in the solid-state fermentation of tobacco leaves. This strain, known for producing thermally stable enzymes, including amylase, cellulase, and protease, significantly improved the sensory qualities of tobacco, enhancing aromatic intensity, density, and softness, while reducing irritation. Whole-genome sequencing and functional annotation revealed that B. velezensis HJ-16 possesses a single circular chromosome containing genes associated with enzyme production and metabolic activities, particularly in carbohydrate metabolism and amino acid metabolism. Untargeted metabolomics analysis identified significant changes in non-volatile metabolites induced by fermentation. These metabolites were enriched in pathways related to flavonoid biosynthesis, alkaloid biosynthesis, aromatic amino acid metabolism, lipid metabolism, and carbon metabolism. Metagenomic analysis showed that Bacillus became the dominant genus on the tobacco leaf surface following inoculation with B. velezensis HJ-16, altering the microbial community composition, reducing diversity and evenness, and enhancing microbial metabolic activity. These findings underscore the potential of B. velezensis HJ-16 as a biotechnological tool to improve tobacco leaf quality.},
}

@article {pmid39712896,
year = {2024},
author = {Son, SH and Kang, MG and Kang, A and Kang, Y and Kim, K and Kwak, MJ and Song, M and Kim, Y},
title = {Gut microbiome and metabolome library construction based on age group using short-read and long-read sequencing techniques in Korean traditional canine species Sapsaree.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1486566},
pmid = {39712896},
issn = {1664-302X},
abstract = {This study investigated age-related changes in the gut microbiota and metabolome of Sapsaree dogs through metagenomic and metabolomic analyses. Using Illumina (short-read) and Nanopore (long-read) sequencing technologies, we identified both common and unique bacterial genera in the dogs across different age groups. In metagenomic analysis, Firmicutes were predominant at the family level. At the genus level, Lactobacillus, Streptococcus, Romboutsia, and Clostridium XI were the most abundant, and the bacterial genera typically considered beneficial were less prevalent in senior dogs, whereas the genera associated with pathogenicity were more abundant. These findings suggest age-related shifts in gut microbiota composition. Metabolomic analysis showed distinct clustering of metabolites based on the age group, with changes in metabolite profiles correlating with metagenomic findings. Although Illumina and Nanopore methods provided distinctive results, the genera detected by both methods exhibited similar trends across all age groups in Sapsaree dogs. These findings highlight the relationship between ages, metabolite profiles and gut microbiota composition in dogs, suggesting the need for further research to explore this relation in greater depth.},
}

@article {pmid39712641,
year = {2024},
author = {Shalini, TS and Prathiviraj, R and Senthilraja, P},
title = {Metagenomic analysis and bioactive profiling of kombucha fermentation: antioxidant, antibacterial activities, and molecular docking insights into gastric cancer therapeutics.},
journal = {Toxicology research},
volume = {13},
number = {6},
pages = {tfae224},
pmid = {39712641},
issn = {2045-452X},
abstract = {Kombucha is fermented and produced with a biofilm called a symbiotic culture of bacteria and yeast, which is drunk all over the world for its beneficial effects on human health and energy levels. The metagenomic study of kombucha frequently detected microorganisms in proteobacteria, firmicutes, and actinobacteria. And also, yeast and fungi are Ascomycota and Basidiomycota is present in green leaf and sugarcane juice fermented kombucha. The kombucha extracts' biological activities were assessed using pH, total phenolic content, antioxidant, antibacterial, and anticancer activity. Fermentation may enhance biological activity and the generation of bioactive substances. These results showed the pH -3.1 ± 0.2 and TPC -0.721 μg/mL of gallic acid equivalent. The antioxidant radicals scavenging activity of kombucha was evaluated by DPPH, ABTS, H2O2 and TAC. The bioactive chemicals identified by FT-IR and HR-LC/MS analysis of Kombucha totaled 45 components. The identified compounds were further move on to perform molecular docking study against gastric cancer target proteins 4H9M, 2DQ7 and 1TVO are binding with Nequinate compounds showing best LibDock scores 105.12, 114.49, and 108.97. So, this study suggests that knowledge can potentially active bioactive compounds are present in kombucha and it's stimulated the mechanism of gastrointestinal transit. Additionally, the metagenomic analysis gives strength to understand the bacterial and fungal distribution and its molecular mechanism from Kombucha.},
}

@article {pmid39712493,
year = {2024},
author = {Liu, HH and Lin, TT and Zhang, QJ and Zhang, L and Fang, JY and Hu, L},
title = {Effect of Helicobacter pylori-related chronic gastritis on gastrointestinal microorganisms and brain neurotransmitters in mice.},
journal = {Frontiers in pharmacology},
volume = {15},
number = {},
pages = {1472437},
pmid = {39712493},
issn = {1663-9812},
abstract = {The effects of Helicobacter pylori (Hp)-related chronic gastritis on gastrointestinal microorganisms or brain neurotransmitters are not fully understood. Here, this study selected SPF C57BL/6 mice to set up a Hp-related chronic gastritis experiment group and a blank control group, and used omics to explore the specific effects of Hp-related chronic gastritis on gastrointestinal microorganisms and brain neurotransmitters in mice. The Tyramine (TyrA) content in the female experiment group's brain was considerably reduced compared to the female control group (p < 0.01), and TyrA was strongly correlated with 13 gastrointestinal microorganisms with significant differences, such as Acinetobacter_baumannii (p < 0.05). The His content in the male experiment group's brain was significantly higher than that in the male control group (p < 0.05), and His was strongly correlated with four gastrointestinal microorganisms with significant differences, such as Acinetobacter_baumannii (p < 0.05). The Levodopa (DOPA) content in the female control group's brain was significantly lower than that in the male control group (p < 0.05), and DOPA was strongly correlated with 19 gastrointestinal microorganisms with significant differences, such as Achromobacter_xylosoxidans (p < 0.05). The contents of L-Glutamine (Gln), L-Glutamine (GABA), Noradrenaline hydrochloride (NE), and Adrenaline hydrochloride (E) in the female experiment group's brain were significantly lower than those in the male experiment group (p < 0.05), and Gln, GABA, NE, and E were strongly correlated with 41, 28, 40, and 33 gastrointestinal microorganisms with significant differences (p < 0.05), respectively. These results indicate that Hp-related chronic gastritis could affect gastrointestinal microorganisms and brain neurotransmitters in mice with certain gender differences, and the changes in brain neurotransmitters might be related to the changes in gastrointestinal microorganisms.},
}

@article {pmid39711694,
year = {2024},
author = {Sehgal, N and Pajuelo, MJ and Gilman, RH and Pickering, AJ and Earl, AM and Worby, CJ and Nadimpalli, ML},
title = {Effects of commonly used antibiotics on children's developing gut microbiomes and resistomes in peri-urban Lima, Peru.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.13.24317790},
pmid = {39711694},
abstract = {BACKGROUND: The effects of antibiotic use on children's gut microbiomes and resistomes are not well characterized in middle-income countries, where pediatric antibiotic consumption is exceptionally common. We characterized the effects of antibiotics commonly used by Peruvian children (i.e., amoxicillin, azithromycin, cefalexin, sulfa-trimethoprim) on gut diversity, genera, and antibiotic resistance gene (ARG) abundance from 3-16 months.

METHODS: This study included 54 children from a prospective cohort of enteric infections in peri-urban Lima, 2016-2019. Stool collected at 3, 6, 7, 9, 12, and 16 months underwent DNA extraction and short-read metagenomic sequencing. We profiled the taxonomy of stool metagenomes and assessed ARG abundance by aligning reads to the ResFinder database. We used daily surveillance data (40,662 observations) to tabulate the number of antibiotic courses consumed in the 30 days prior to stool sampling. Using linear mixed models, the association of recent antibiotic use with species richness, diversity, gut genera, and ARG abundance over time was examined.

RESULTS: Most children were vaginally delivered (73%), received breastmilk almost daily over the study period, and belonged to socioeconomically diverse households. Amoxicillin, azithromycin, cefalexin, and sulfa-trimethoprim did not impact gut diversity or genera abundance. Azithromycin use significantly impacted ARGs from the macrolide, aminoglycoside, and folate pathway antagonist classes. Amoxicillin use significantly increased total ARGs. Antibiotics' effects on ARGs appeared to be independent of gut microbiome changes.

CONCLUSION: Common antibiotics like amoxicillin and azithromycin may be key drivers of the gut resistome but not the microbiome during early childhood in this setting with frequent breastfeeding.},
}

@article {pmid39711517,
year = {2024},
author = {Long, L and Xu, XL and Duan, YF and Long, L and Chen, JY and Yin, YH and Zhu, YG and Huang, Q},
title = {Extracellular Vesicles Are Prevalent and Effective Carriers of Environmental Allergens in Indoor Dust.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c10056},
pmid = {39711517},
issn = {1520-5851},
abstract = {The global incidence of allergic diseases is rising and poses a substantial threat to human health. Allergenic proteins released by various allergenic species play a critical role in the pathogenesis of allergic diseases and have been widely detected in the environmental matrix. However, the release, presence and interaction of environmental allergens with human body remain to be elucidated. In this study, we reported the widespread of allergen-harboring extracellular vesicles (EVs) in indoor dust from 75 households across five provinces in China. Particle size and abundance of EVs were correlated with specific environmental factors. EVs showed long persistence and high resistance to environmental stress. Metagenomics and metaproteomics data revealed that most indoor allergenic species released allergens within the EVs into dust. A higher abundance of allergenic species and their derived EVs was observed in urban areas compared to rural areas. ELISA confirmed the allergenic activity of the EV-associated allergens. Allergens are common components and even markers of EVs, as evidenced by the data compilation of various allergenic species. The proportion of EV-associated allergens varied across species. EVs facilitated allergen entry into epithelial cells. Intranasally administered EVs can be rapidly transported to the lungs and gastrointestinal tract. EV-associated allergens exhibited higher allergenicity compared with non-EV allergens. Our findings elucidate a vesicle pathway through which environmental allergens are released, persist, and trigger allergic responses within EVs.},
}

@article {pmid39711113,
year = {2025},
author = {Olivares, C and Ruppé, E and Ferreira, S and Corbel, T and Andremont, A and de Gunzburg, J and Guedj, J and Burdet, C},
title = {A modelling framework to characterize the impact of antibiotics on the gut microbiota diversity.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2442523},
doi = {10.1080/19490976.2024.2442523},
pmid = {39711113},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; *Feces/microbiology ; *Bacteria/classification/genetics/drug effects/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; Adult ; Ceftazidime/pharmacology/administration & dosage ; Male ; Moxifloxacin/pharmacology/administration & dosage ; Drug Combinations ; Ceftriaxone/pharmacology/administration & dosage ; Female ; Azabicyclo Compounds/pharmacology/administration & dosage ; Biodiversity ; Young Adult ; Healthy Volunteers ; Piperacillin, Tazobactam Drug Combination ; },
abstract = {Metagenomic sequencing deepened our knowledge about the role of the intestinal microbiota in human health, and several studies with various methodologies explored its dynamics during antibiotic treatments. We compared the impact of four widely used antibiotics on the gut bacterial diversity. We used plasma and fecal samples collected during and after treatment from healthy volunteers assigned to a 5-day treatment either by ceftriaxone (1 g every 24 h through IV route), ceftazidime/avibactam (2 g/500 mg every 8 h through IV route), piperacillin/tazobactam (1 g/500 mg every 8 h through IV route) or moxifloxacin (400 mg every 24 h through oral route). Antibiotic concentrations were measured in plasma and feces, and bacterial diversity was assessed by the Shannon index from 16S rRNA gene profiling. The relationship between the evolutions of antibiotic fecal exposure and bacterial diversity was modeled using non-linear mixed effects models. We compared the impact of antibiotics on gut microbiota diversity by simulation, using various reconstructed pharmacodynamic indices. Piperacillin/tazobactam was characterized by the highest impact in terms of intensity of perturbation (maximal [IQR] loss of diversity of 27.3% [1.9; 40.0]), while moxifloxacin had the longest duration of perturbation, with a time to return to 95% of baseline value after the last administration of 13.2 d [8.3; 19.1]. Overall, moxifloxacin exhibited the highest global impact, followed by piperacillin/tazobactam, ceftazidime/avibactam and ceftriaxone. Their AUC between day 0 and day 42 of the change of diversity indices from day 0 were, respectively, -13.2 Shannon unit.day [-20.4; -7.9], -10.9 Shannon unit.day [-20.4; -0.6] and -10.1 Shannon unit.day [-18.3; -4.6]. We conclude that antibiotics alter the intestinal diversity to varying degrees, both within and between antibiotics families. Such studies are needed to help antibiotic stewardship in using the antibiotics with the lowest impact on the intestinal microbiota.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Anti-Bacterial Agents/pharmacology/administration & dosage
*Feces/microbiology
*Bacteria/classification/genetics/drug effects/isolation & purification
*RNA, Ribosomal, 16S/genetics
Adult
Ceftazidime/pharmacology/administration & dosage
Male
Moxifloxacin/pharmacology/administration & dosage
Drug Combinations
Ceftriaxone/pharmacology/administration & dosage
Female
Azabicyclo Compounds/pharmacology/administration & dosage
Biodiversity
Young Adult
Healthy Volunteers
Piperacillin, Tazobactam Drug Combination

@article {pmid39710721,
year = {2024},
author = {Zhou, N and Chen, W and Xia, L and Li, M and Ye, H and Lv, C and Chen, Y and Cheng, Z and Park, TJ and Ho, PL and Gao, X and Guo, X and Zhao, H and Cao, H and Zhu, Y},
title = {Metagenomic insights into the resistome, mobilome, and virulome of dogs with diverse lifestyles.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {76},
pmid = {39710721},
issn = {2524-4671},
support = {No. 2020-01//Shanghai Jiao Tong University Integrated Innovation Fund/ ; No. 32170141//National Natural Science Foundation of China/ ; No. 20-365//China Medical Board/ ; No.19201901//Health and Medical Research Fund/ ; 2024YFE0199000//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Dogs-whether pets, rural, or stray-exhibit distinct living styles that influence their fecal microbiota and resistomes, yet these dynamics remain underexplored. This study aimed to analyze and compare the fecal microbiota and resistomes of three groups of dogs (37 pets, 20 rural, and 25 stray dogs) in Shanghai, China.

RESULTS: Metagenomic analysis revealed substantial differences in fecal microbial composition and metabolic activities among the dog groups. Pet dogs displayed the lowest microbial diversity. Using Shapley Additive Explanations (SHAP), an interpretable machine learning approach, Ligilactobacillus emerged as the most diverse genus, with significantly higher SHAP values in stray dogs, suggesting enhanced adaptability to more variable and less controlled environments. Across all samples, 587 antibiotic resistance genes (ARGs) were identified, conferring resistance to 14 antibiotic classes. A striking observation was the detection of mcr-1 in one pet dog, indicating a potential public health risk. The floR gene was identified as a key differentiator in resistance profiles, particularly in pet and rural dogs, likely due to antibiotic exposure in their environments.

CONCLUSION: This study provides the first comprehensive assessment of fecal microbiota and resistome variations among dogs with different lifestyles, revealing a less resilient microbiome and heightened antimicrobial resistance in pet dogs, which could have public health implications.},
}

@article {pmid39710261,
year = {2024},
author = {Guerreiro, JF and Pires, AJ and Nunes, M and Esteves, A and Chambel, L and Pascoal, P and Pereira, M and Fangueiro, D and Tavares, L and Dias, R and Bexiga, R and Oliveira, M},
title = {Biochar supplementation affects the microbiome of recycled manure solids for cow bedding: a metagenomic analysis.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25616},
pmid = {39710261},
issn = {1525-3198},
abstract = {The widespread use of Recycled Manure Solids (RMS) as cow bedding material is not without risks, since cattle manure may act as a vehicle for pathogenic and antimicrobial resistant bacteria dissemination. Thus, our aim was to evaluate RMS-supplemented with a pine biochar produced in Portugal as a new cow bedding material, since the use of biochar has been shown to have the potential to mitigate the impact of relevant bacterial species when added to animal manure microbiota. Our experimental setup consisted on fresh RMS samples that were collected on a commercial dairy farm and placed in naturally-ventilated containers for a total of 4 groups: 1-non-supplemented RMS; 2-RMS supplemented with 2.5% (wt/wt) of biochar; 3-RMS supplemented with 5% (wt/wt) of biochar; and 4-RMS supplemented with 10% (wt/wt) of biochar. Sampling was performed at 4 different incubation times (0, 5, 15 and 30 d) and in 2 distinct seasons: April-May (humid season) and June-July (dry season). The resulting 32 samples were subjected to DNA extraction and their microbiome profile determined through complete 16S rDNA gene sequencing using Nanopore next-generation sequencing. We observed that biochar supplementation clearly altered the microbiome of RMS, which was reflected in changes in populations' diversity and their relative abundance of relevant pathogenic bacteria. In particular, we found that long-term storage (30 d) was more beneficial than short-term storage, an effect that was more evident for samples supplemented with 2.5% or 5% biochar. In both seasons, those concentrations of biochar led to a decrease in the levels of several mastitis-causing agents (Enterobacteriaceae, streptococci, enterococci and staphylococci). In addition, we also observed a reduction in the levels of Salmonella spp. and Gram-positive bacilli in the biochar-supplemented samples. Unexpectedly, however, those same conditions yielded an increase in the abundance of Brucella spp., a group which includes important infectious agents, highlighting the need for a deeper evaluation of the impact of biochar supplementation of RMS to ensure the future safe and sustainable use of this environmental-friendly resource in animal production.},
}

@article {pmid39710013,
year = {2024},
author = {He, B and Xu, S and Mary Schooling, C and Leung, GM and Ho, JWK and Yeung, SLA},
title = {Gut microbiome and obesity in late adolescence: a case-control study in "Children of 1997" birth cohort.},
journal = {Annals of epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.annepidem.2024.12.009},
pmid = {39710013},
issn = {1873-2585},
abstract = {PURPOSE: Although the gut microbiome is important in human health, its relation to adolescent obesity remains unclear. Here we assessed the associations of the gut microbiome with adolescent obesity in a case-control study.

METHODS: In the "Children of 1997" birth cohort, participants with and without obesity at ~17.4 years were 1:1 matched on sex, physical activity, parental education and occupation (n=312). Fecal gut microbiome composition and pathways were assessed via shotgun metagenomic sequencing. The association of microbiota species with obesity was evaluated using conditional logistic regression. We explored the association of the obesity-relevant species with adolescent metabolomics using multivariable linear regression, and causal relationships with type 2 diabetes using Mendelian randomization analysis.

RESULTS: Gut microbiota in the adolescents with obesity exhibited lower richness (p=0.031) and evenness (p=0.014) compared to controls. Beta diversity revealed differences in the microbiome composition in two groups (p=0.034). Lower relative abundance of Clostridium spiroforme, Clostridium phoceensis and Bacteroides uniformis were associated with higher obesity risk (q<0.15). Lower Bacteroides uniformis was associated with higher branched-chain amino acid, potentially contributing to higher type 2 diabetes risk.

CONCLUSION: Adolescents with obesity had a distinct gut microbiota profile compared to the controls, possibly linked to metabolic pertubation and related diseases.},
}

@article {pmid39709811,
year = {2024},
author = {Chi, C and Zheng, Y and Shi, Y and Lyu, C and Jiang, X and Zhang, Y and Wang, C},
title = {Harmless treatment of cyanide tailings by functional bacteria: Degradation of cyanide and the secondary pollutant ammonia nitrogen.},
journal = {Journal of hazardous materials},
volume = {485},
number = {},
pages = {136939},
doi = {10.1016/j.jhazmat.2024.136939},
pmid = {39709811},
issn = {1873-3336},
abstract = {The eco-friendly treatment of cyanide tailings (CT) using microorganisms is a cost-effective and promising technology. However, this process often generates the secondary pollutants, such as ammonia nitrogen (NH4[+]-N), which can adversely impacts the surrounding environment. The accumulation of NH4[+]-N is also toxic to cyanide-degrading microorganisms, presenting a significant challenge in achieving simultaneous cyanide degradation and NH4[+]-N mitigation. In this study, a group of functional bacteria CG305-1 with the ability to degrade cyanide and perform nitrification and denitrification was successfully enriched for the first time and used to treat CT by in situ microbial drenching technology. Results demonstrated that the total cyanide (CNT) concentration in the leaching solution decreased from 49.96 ± 1.51 mg/L to 0.19 ± 1.11 mg/L. NH4[+]-N was degraded to 0.25 ± 0.18 mg/L, and nitrate nitrogen (NO3[-]-N) was reduced to 0.41 ± 0.20 mg/L. Furthermore, CNT in the CT leachate was reduced to 0.94 ± 0.11 mg/L, meeting the storage standard for CT leachate (CNT < 5 mg/L). The potential synergistic microbial degradation mechanisms were elucidated through Scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and Metagenomic sequencing. This study provides significant insights into green and sustainable methods for the harmless treatment of CT.},
}

@article {pmid39709798,
year = {2024},
author = {Wang, RX and Zhou, HB and Gao, JX and Bai, WF and Wang, J and Bai, YC and Jiang, SY and Chang, H and Shi, SL},
title = {Metagenomics and metabolomics to investigate the effect of Amygdalus mongolica oil on intestinal microbiota and serum metabolites in rats.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {136},
number = {},
pages = {156335},
doi = {10.1016/j.phymed.2024.156335},
pmid = {39709798},
issn = {1618-095X},
abstract = {BACKGROUND: Renal fibrosis (RF) is an inevitable consequence of multiple manifestations of progressive chronic kidney diseases (CKDs). Mechanism of Amygdalus mongolica (Maxim.) in the treatment of RF needs further investigation.

PURPOSE: The study further investigated the potential mechanism of A. mongolica in the treatment of RF.

METHODS: A rat model of RF was induced by unilateral ureteral obstruction (UUO), followed by treatment with varying dosages of A. mongolica oil for 4 weeks. Body weight was measured weekly. We detected serum levels of interleukin (IL)-6, IL-1β, type Ⅲ procollagen (Col-Ⅲ), type IV collagen (Col-Ⅳ), laminin (LN), hyaluronidase (HA), and tissue levels of albumin (ALB), blood urea nitrogen (BUN), creatinine (Cre), superoxide dismutase (SOD), malondialdehyde (MDA), and hydroxyproline (HYP). Shotgun metagenomics analyzed the composition of the intestinal microbiota. High-performance liquid chromatography coupled with a quadrupole-exactive mass spectrometer (HPLC-Q-Exactive-MS) monitored changes in metabolite levels in serum and gut. Multiple reaction monitoring-mass spectrometry (MRM-MS) determined the levels of amino acids in serum.

RESULTS: A. mongolica oil significantly alleviated indicators related to RF (p < 0.05). A. mongolica oil reduced the ratio of Firmicutes to Bacteroidetes and restored the balance of intestinal microbiota in rats with RF. A. mongolica oil modulated levels of metabolites in gut content and serum. It regulated 11 metabolic pathways including arachidonic acid metabolism. Targeted metabolomics of amino acids showed that 17 amino acids were significantly changed by A. mongolica oil, including L-glycine, L-serine and L-glutamine.

CONCLUSION: A. mongolica oil regulates intestinal microbiota and metabolites, restoring amino acid metabolism to treat RF.},
}

@article {pmid39709651,
year = {2024},
author = {Cheng, E and Hung, SC and Lin, TY},
title = {Association of trimethylamine N-oxide and metabolites with kidney function decline in patients with chronic kidney disease.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {44},
number = {},
pages = {239-247},
doi = {10.1016/j.clnu.2024.12.001},
pmid = {39709651},
issn = {1532-1983},
abstract = {BACKGROUND: Trimethylamine N-oxide (TMAO) is a gut microbial metabolite derived from dietary l-carnitine and choline. High plasma TMAO levels are associated with cardiovascular disease and overall mortality, but little is known about the associations of TMAO and related metabolites with the risk of kidney function decline among patients with chronic kidney disease (CKD).

METHODS: We prospectively followed 152 nondialysis patients with CKD stages 3-5 and measured plasma TMAO and related metabolites (trimethylamine [TMA], choline, carnitine, and γ-butyrobetaine) via liquid chromatography‒mass spectrometry. An estimated glomerular filtration rate (eGFR) slope >3 ml/min/per 1.73 m[2] per year was defined as a rapid decline. We performed logistic regression to determine the probability of rapid or slow eGFR decline, with each metabolite as the main predictor. The gut microbiota was profiled via whole metagenomic sequencing.

RESULTS: The participants had a median age of 66 years, 41.4 % were women, 39.5 % had diabetes, and the median eGFR was 23 mL/min/1.73 m[2]. A rapid decrease in the eGFR occurred in 65 patients (42.8 %) over a median follow-up of 3.3 years. After adjustment for baseline eGFR, proteinuria, and clinical factors, plasma TMAO levels were independently associated with increased odds of rapid eGFR decline (odds ratio, 2.42; 95 % CI, 1.36-4.32), whereas plasma TMA, choline, carnitine, and γ-butyrobetaine levels were not. Patients who exhibited rapid eGFR decline had a distinct gut microbial composition characterized by increased α-diversity and an abundance of TMA-producing bacteria, including those of the genera Desulfovibrio and Collinsella tanakaei, as well as increased expression of the TMA-producing enzymes bbuA and cutC.

CONCLUSION: Our findings suggest the relevance of plasma TMAO in the progression of kidney disease among patients with CKD.},
}

@article {pmid39709594,
year = {2025},
author = {Smith, MZ and York, M and Townsend, KS and Martin, LM and Gull, T and Coghill, LM and Ericsson, AC and Johnson, PJ},
title = {Effects of orally administered clioquinol on the fecal microbiome of horses.},
journal = {Journal of veterinary internal medicine},
volume = {39},
number = {1},
pages = {e17276},
doi = {10.1111/jvim.17276},
pmid = {39709594},
issn = {1939-1676},
mesh = {Animals ; Horses ; *Feces/microbiology ; *Clioquinol/pharmacology/administration & dosage ; Female ; Male ; Administration, Oral ; Prospective Studies ; Gastrointestinal Microbiome/drug effects ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; },
abstract = {BACKGROUND: Whereas restoration of fecal consistency after treatment with clioquinol for chronic diarrhea and free fecal water syndrome has been attributed to its antiprotozoal properties, actions of clioquinol on the colonic bacterial microbiota have not been investigated.

OBJECTIVES: Characterize the dynamics of fecal microbial diversity before, during, and after PO administration of clioquinol to healthy horses.

STUDY DESIGN: Experimental prospective cohort study using a single horse group.

METHODS: Eight healthy adult horses received PO clioquinol (10 g, daily) for 7 days. Feces were obtained daily for 7 days before, during, and after conclusion of treatment, and again 3 months later. Libraries of 16S rRNA V4 region amplicons generated from fecal DNA were sequenced using the Illumina sequencing platform. Bioinformatic analysis was undertaken with QIIME2 and statistical analyses included analysis of variance (ANOVA) and permutational multivariate ANOVA (PERMANOVA).

RESULTS: The richness and composition of the fecal microbiome was altered after administration of clioquinol, reaching a maximum effect by the fifth day of administration. Changes included a 90% decrease in richness, and compensatory expansion of facultative anaerobes including Streptococcaceae, Enterococcaceae, and Enterobacteriaceae. Multiple horses had Salmonella cultured from feces.

MAIN LIMITATIONS: Limitations including lack of control group and modest sample size are obviated by robust longitudinal study design and strong effect size associated with drug exposure.

CONCLUSIONS: Clioquinol has broad-spectrum antibacterial effects on the fecal microbiome of horses, but spares certain bacterial families including several pathogens and pathobionts. Clioquinol should be used with caution in horses, in an environment free of contamination with fecal pathogens.},
}

Animals
Horses
*Feces/microbiology
*Clioquinol/pharmacology/administration & dosage
Female
Male
Administration, Oral
Prospective Studies
Gastrointestinal Microbiome/drug effects
RNA, Ribosomal, 16S/genetics
Cohort Studies

@article {pmid39709451,
year = {2024},
author = {Mushraf, S and Chawla, K and Fayaz, SMA and Mathew, AJ and Reddy, GPK and Kappettu Gadahad, MR and Shenoy, PA and Devi, V and Adiga, S and Nayak, V},
title = {Exploring the effects of probiotics on olanzapine-induced metabolic syndrome through the gut microbiota.},
journal = {Gut pathogens},
volume = {16},
number = {1},
pages = {77},
pmid = {39709451},
issn = {1757-4749},
abstract = {BACKGROUND: Maintaining gut microbial homeostasis is crucial for human health, as imbalances in the gut microbiota (GM) can lead to various diseases, including metabolic syndrome (MS), exacerbated by the use of antipsychotic medications such as olanzapine (OLZ). Understanding the role of the GM in OLZ-induced MS could lead to new therapeutic strategies. This study used metagenomic analysis to explore the impact of OLZ on the GM composition and examined how probiotics can mitigate its adverse effects in a rat model. Changes in weight, blood pressure, and lipid levels, which are key parameters defining MS, were assessed. Additionally, this study investigated serotonin, dopamine, and histopathological changes to explore their possible link with the microbiota-gut-brain axis (MGBA).

RESULTS: OLZ had an antagonistic effect on serotonin and dopamine receptors, and it was consistently found to alter the composition of the GM, with an increase in the relative abundance (RA) of the Firmicutes/Bacteroidetes phyla ratio and TM7 genera, indicating that the anticommonsal action of OLZ affects appetite and energy expenditure, contributing to obesity, dyslipidemia and increased blood pressure, which are core components of MS. Hepatic steatosis and intestinal damage in OLZ-treated rat tissues further indicate its role in MS. Conversely, the administration of probiotics, either alone or in combination with OLZ, was found to mitigate these OLZ-induced symptoms of MS by altering the GM composition. These alterations included increases in the abundances of the taxa Bacteroidetes, Actinobacteria, Prevotella, Blautia, Bacteroides, Bacteroidales, and Ruminococcaceae and a decrease in Firmicute abundance. These changes helped maintain gut barrier integrity and modulated neurotransmitter levels, suggesting that probiotics can counteract the adverse metabolic effects of OLZ by restoring the GM balance. Moreover, this study highlights the modulation of the MGBA by OLZ as a potential mechanism through which probiotics modulate serotonin and dopamine levels, influencing metabolic health.

CONCLUSION: These findings emphasise the significant impact of OLZ on the GM and its contribution to MS. These findings suggest that interventions targeting the GM, such as probiotics, could mitigate the metabolic side effects of OLZ. Future research should focus on developing integrative treatment approaches that consider the health of the gut microbiome in managing antipsychotic-induced adverse effects.},
}

@article {pmid39709449,
year = {2024},
author = {Dos Santos, SJ and Copeland, C and Macklaim, JM and Reid, G and Gloor, GB},
title = {Vaginal metatranscriptome meta-analysis reveals functional BV subgroups and novel colonisation strategies.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {271},
pmid = {39709449},
issn = {2049-2618},
support = {20170705//Weston Family Foundation/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; *Vaginosis, Bacterial/microbiology ; *Microbiota/genetics ; *Transcriptome ; *Bacteria/genetics/classification/isolation & purification ; Biofilms/growth & development ; Metagenomics/methods ; },
abstract = {BACKGROUND: The application of '-omics' technologies to study bacterial vaginosis (BV) has uncovered vast differences in composition and scale between the vaginal microbiomes of healthy and BV patients. Compared to amplicon sequencing and shotgun metagenomic approaches focusing on a single or few species, investigating the transcriptome of the vaginal microbiome at a system-wide level can provide insight into the functions which are actively expressed and differential between states of health and disease.

RESULTS: We conducted a meta-analysis of vaginal metatranscriptomes from three studies, split into exploratory (n = 42) and validation (n = 297) datasets, accounting for the compositional nature of sequencing data and differences in scale between healthy and BV microbiomes. Conducting differential expression analyses on the exploratory dataset, we identified a multitude of strategies employed by microbes associated with states of health and BV to evade host cationic antimicrobial peptides (CAMPs); putative mechanisms used by BV-associated species to resist and counteract the low vaginal pH; and potential approaches to disrupt vaginal epithelial integrity so as to establish sites for adherence and biofilm formation. Moreover, we identified several distinct functional subgroups within the BV population, distinguished by genes involved in motility, chemotaxis, biofilm formation and co-factor biosynthesis. After defining molecular states of health and BV in the validation dataset using KEGG orthology terms rather than community state types, differential expression analysis confirmed earlier observations regarding CAMP resistance and compromising epithelial barrier integrity in healthy and BV microbiomes and also supported the existence of motile vs. non-motile subgroups in the BV population. These findings were independent of the enzyme classification system used (KEGG or EggNOG).

CONCLUSIONS: Our findings highlight a need to focus on functional rather than taxonomic differences when considering the role of microbiomes in disease and identify pathways for further research as potential BV treatment targets. Video Abstract.},
}

Humans
Female
*Vagina/microbiology
*Vaginosis, Bacterial/microbiology
*Microbiota/genetics
*Transcriptome
*Bacteria/genetics/classification/isolation & purification
Biofilms/growth & development
Metagenomics/methods

@article {pmid39708838,
year = {2024},
author = {Luo, Q and Zhang, S and Butt, H and Chen, Y and Jiang, H and An, L},
title = {PhyImpute and UniFracImpute: two imputation approaches incorporating phylogeny information for microbial count data.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
doi = {10.1093/bib/bbae653},
pmid = {39708838},
issn = {1477-4054},
support = {R01ES027013//National Institute of Health/ ; ARZT-1361620-H22-149//United States Department of Agriculture/ ; },
mesh = {*Phylogeny ; Algorithms ; Humans ; Computational Biology/methods ; Microbiota/genetics ; },
abstract = {Sequencing-based microbial count data analysis is a challenging task due to the presence of numerous non-biological zeros, which can impede downstream analysis. To tackle this issue, we introduce two novel approaches, PhyImpute and UniFracImpute, which leverage similar microbial samples to identify and impute non-biological zeros in microbial count data. Our proposed methods utilize the probability of non-biological zeros and phylogenetic trees to estimate sample-to-sample similarity, thus addressing this challenge. To evaluate the performance of our proposed methods, we conduct experiments using both simulated and real microbial data. The results demonstrate that PhyImpute and UniFracImpute outperform existing methods in recovering the zeros and empowering downstream analyses such as differential abundance analysis, and disease status classification.},
}

*Phylogeny
Algorithms
Humans
Computational Biology/methods
Microbiota/genetics

@article {pmid39708826,
year = {2024},
author = {Hu, Y and Zhang, ZY and Wang, F and Zhuang, K and Xu, X and Liu, DS and Fan, HZ and Yang, L and Jiang, K and Zhang, DK and Xu, L and Tang, JH and Liu, XM and He, C and Shu, X and Xie, Y and Lau, JYW and Zhu, Y and Du, YQ and Graham, DY and Lu, NH},
title = {Effects of amoxicillin dosage on cure rate, gut microbiota, and antibiotic resistome in vonoprazan and amoxicillin dual therapy for Helicobacter pylori: a multicentre, open-label, non-inferiority randomised controlled trial.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {100975},
doi = {10.1016/j.lanmic.2024.100975},
pmid = {39708826},
issn = {2666-5247},
abstract = {BACKGROUND: Vonoprazan and amoxicillin (VA) dual therapy as a mainstream Helicobacter pylori regimen has gained momentum worldwide, but the optimum dosages remain unclear. We aimed to compare the efficacy and safety of VA dual therapy with 2 g amoxicillin or 3 g amoxicillin, and to assess the short-term effects of therapy on the gut microbiota and antibiotic resistome.

METHODS: We conducted an open-label, non-inferiority randomised controlled trial at 12 centres in China. Individuals infected with H pylori, aged 18-70 years, and without previous eradication therapy were recruited. Participants were randomly assigned at a 1:1 ratio (block size of six) to receive vonoprazan (20 mg twice a day) with either low-dose amoxicillin (1 g twice a day; LVA therapy) or high-dose amoxicillin (1 g three times a day; HVA therapy) for 14 days. Gastric biopsies were collected before treatment for detection of antibiotic resistance. Stool samples were collected at baseline, week 2, and week 8-10 for shotgun metagenomic sequencing. The primary outcome was the eradication rate of H pylori, assessed by [13]C urea breath test, in both intention-to-treat and per-protocol analyses. Secondary outcomes were adverse events, adherence, antibiotic resistance, and alterations to the gut microbiota and antibiotic resistome. The margin used to establish non-inferiority was -0·10. The trial was registered with ClinicalTrials.gov, NCT05649709.

FINDINGS: Between Feb 13, 2023, and Jan 25, 2024, 504 patients (204 [40%] male and 300 [60%] female; mean age 43 years [SD 13]) were randomly assigned to LVA therapy or HVA therapy (n=252 in each group). No infections were resistant to amoxicillin. The H pylori eradication rate was 85·3% (215 of 252; 95% CI 80·4 to 89·2) in the LVA group and 86·5% (218 of 252; 81·7 to 90·2) in the HVA group in the intention-to-treat analysis (p=0·70) and 88·8% (213 of 240; 84·1 to 92·2) and 92·4% (218 of 236; 88·3 to 95·1), respectively, in the per-protocol analysis (p=0·18). The efficacy of LVA was non-inferior to HVA in the intention-to-treat analysis (risk difference -1·2%, 95% CI -7·3 to 4·9, p=0·0022) and the per-protocol analysis (-3·6%, -9·0 to 1·7, p=0·0085). 31 (12%) patients in the LVA group and 43 (17%) patients in the HVA group reported adverse events. Adherence to therapy was 97% in the LVA group and 96% in the HVA group. The diversity of gut microbiota decreased after treatment but was restored to baseline at week 8-10 in both groups. The abundance of beta-lactam-related resistance genes was increased at week 2 after treatment, and was restored to pretreatment level at week 8-10 for the LVA group but not the HVA group.

INTERPRETATION: LVA dual therapy was effective and non-inferior to HVA dual therapy as first-line treatment of H pylori infection and showed a non-lasting effect on the abundance of beta-lactam-related resistance genes. High amoxicillin dosage (eg, 3 g per day) is not required to achieve high cure rates with vonoprazan dual therapy.

FUNDING: National Natural Science Foundation of China, Project for Academic and Technical Leaders of Major Disciplines in Jiangxi Province, and Key Research and Development Program of Jiangxi Province.},
}

@article {pmid39708657,
year = {2024},
author = {Ren, Y and Sun, J and Mao, X},
title = {Protein degradation mechanisms during refrigerated storage of gazami crab (Portunus trituberculatus) at endogenous and microbial-derived enzyme levels.},
journal = {Food chemistry},
volume = {469},
number = {},
pages = {142449},
doi = {10.1016/j.foodchem.2024.142449},
pmid = {39708657},
issn = {1873-7072},
abstract = {During storage, the proteins of gazami crab (Portunus trituberculatus) are prone to hydrolysis into amino acids and biogenic amines, in which enzymes play a critical role. However, studies exploring spoilage mechanisms from the perspective of enzymes are limited. This study identified 84 endogenous and 52 microbial-derived proteolytic enzymes and peptidases by proteomics and metagenomics. There are 7 endogenous amino acid deaminases, primarily degrade glutamate and aspartate. Additionally, 25 amino acid deaminases of microbial origin were identified, which mainly degrade serine. The formation of biogenic amines involved 14 enzymes, all of which were microbial in origin, primarily synthesizing putrescine from arginine. The main microbial contributors to these enzymes were Photobacterium, Vibrio, and Aliivibrio, accounting for 63.87 %, 15.51 %, and 8.69 % at the end of refrigeration, respectively. This study provides insights into the mechanisms of quality deterioration in gazami crab during refrigeration, from the perspectives of metabolic enzymes and microbial activity.},
}

@article {pmid39708598,
year = {2024},
author = {Sun, D and Shi, X and Shen, Y and Liu, Y and Luo, S and Jin, Y and Zhai, W and Liu, L and Deng, Z and Sun, C and Liu, D and Yang, X and Xie, Y and Krüger-Haker, H and Wu, C and Schwarz, S and Shen, J and Chen, Y and Ma, S and Wang, Y},
title = {Comparative efficacy of anaerobic digestion systems in removing antimicrobial resistance genes from swine wastewater.},
journal = {Journal of hazardous materials},
volume = {485},
number = {},
pages = {136868},
doi = {10.1016/j.jhazmat.2024.136868},
pmid = {39708598},
issn = {1873-3336},
abstract = {Swine farm wastewater is a major reservoir of antimicrobial resistance genes (ARGs). Anaerobic digestion (AD), widely implemented in farms, has been extensively studied for ARG removal. However, a comparative study on ARG removal efficiency across the four principal AD systems - up-flow anaerobic sludge blanket (UASB), continuous stirred tank reactor (CSTR), buried biogas digester (BBD), and septic tank (SPT) - is lacking. Herein, we employed metagenomic sequencing, ultra-performance liquid chromatography-tandem mass spectrometry, as well as atomic absorption spectrometry/atomic fluorescence spectrophotometry, and revealed that UASB and CSTR achieved higher removal efficiencies for both ARGs (67% and 57%) and antibiotic residues (100% and 90%) compared to BBD and SPT. Acinetobacter, Escherichia, Pseudomonas and Streptococcus were the primary ARG hosts, comprising over 65% of the total abundance in influent samples. UASB and CSTR systems demonstrated superior removal efficiencies for both mobile genetic elements (MGEs) and antibiotic residues, both of which had essential impacts on ARG profiles. In addition, heavy metals might contribute to variation in ARGs through horizontal gene transfer. Collectively, the variation in microbial communities and better removal of both MGEs and antibiotic residues contribute to the remarkable ARG removal efficiency of UASB and CSTR, therefore, advocating for the widespread adoption of these two AD systems in swine farms.},
}

@article {pmid39708450,
year = {2024},
author = {Gao, B and Chen, L and Wu, L and Zhang, S and Zhao, S and Mo, Z and Chen, Z and Tu, P},
title = {Association between microplastics and the functionalities of human gut microbiome.},
journal = {Ecotoxicology and environmental safety},
volume = {290},
number = {},
pages = {117497},
doi = {10.1016/j.ecoenv.2024.117497},
pmid = {39708450},
issn = {1090-2414},
abstract = {As an integral part of humans, the gut microbiome plays a significant role in the physiological and pathological processes of the host, and dysbiosis of the gut microbiome is linked to various diseases. The impact of microplastics on the diversity and composition of human gut microbiome has been reported previously. However, effects of microplastics on the functionality of the gut microbiome in humans have not been well studied. In the present study, concentrations of microplastics in human blood were detected through pyrolysis-gas chromatography/mass spectrometry in 39 adults. Five types of microplastics were found in human blood, including polyvinyl chloride, polyethylene, polypropylene, polystyrene, and polyamide 66. Shotgun metagenomic sequencing was further employed to analyze the metagenomes of the human stool samples and fecal samples from mice exposed to microplastics. Associations were found between microplastics and microbial species, as well as microbial genes encoding invasion-related virulence factors, quorum sensing, autoinducer and transporter system, and microplastic biodegradation enzymes. The findings are of significance to improve the understanding of functional changes in the gut microbiome associated with microplastic exposure, as well as raising awareness regarding the health risks of microplastics in the human population.},
}

@article {pmid39707929,
year = {2024},
author = {Shahzaib, M and Muaz, M and Zubair, MH and Kayani, MUR},
title = {MiCK: a database of gut microbial genes linked with chemoresistance in cancer patients.},
journal = {Database : the journal of biological databases and curation},
volume = {2024},
number = {},
pages = {},
doi = {10.1093/database/baae124},
pmid = {39707929},
issn = {1758-0463},
mesh = {Humans ; *Neoplasms/genetics/drug therapy ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Neoplasm/genetics ; *Databases, Genetic ; },
abstract = {Cancer remains a global health challenge, with significant morbidity and mortality rates. In 2020, cancer caused nearly 10 million deaths, making it the second leading cause of death worldwide. The emergence of chemoresistance has become a major hurdle in successfully treating cancer patients. Recently, human gut microbes have been recognized for their role in modulating drug efficacy through their metabolites, ultimately leading to chemoresistance. The currently available databases are limited to knowledge regarding the interactions between gut microbiome and drugs. However, a database containing the human gut microbial gene sequences, and their effect on the efficacy of chemotherapy for cancer patients has not yet been developed. To address this challenge, we present the Microbial Chemoresistance Knowledgebase (MiCK), a comprehensive database that catalogs microbial gene sequences associated with chemoresistance. MiCK contains 1.6 million sequences of 29 gene types linked to chemoresistance and drug metabolism, curated manually from recent literature and sequence databases. The database can support downstream analysis as it provides a user-friendly web interface for sequence search and download functionalities. MiCK aims to facilitate the understanding and mitigation of chemoresistance in cancers by serving as a valuable resource for researchers. Database URL: https://microbialchemreskb.com/.},
}

Humans
*Neoplasms/genetics/drug therapy
*Gastrointestinal Microbiome/genetics
*Drug Resistance, Neoplasm/genetics
*Databases, Genetic

@article {pmid39708135,
year = {2024},
author = {Martiniuc, C and Taveira, I and Abreu, F and Cabral, AS and Paranhos, R and Seldin, L and Jurelevicius, D},
title = {Insights into the dynamics and evolution of Rummeliibacillus stabekisii prophages in extreme environments: from Antarctic soil to spacecraft floors.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {1},
pages = {10},
pmid = {39708135},
issn = {1433-4909},
mesh = {Antarctic Regions ; *Extreme Environments ; *Prophages/genetics ; *Soil Microbiology ; Spacecraft ; Evolution, Molecular ; Lysogeny ; Bacillaceae/genetics/virology/isolation & purification ; },
abstract = {Since prophages can play a multifaceted role in bacterial evolution, this study aims to characterize the virome of Rummeliibacillus stabekisii, a bacterium isolated from different environments, including Antarctic soil and NASA spacecraft floors. From the analyses, it was found that the Antarctic strain, PP9, had the largest number of prophages, including intact ones, indicating potential benefits for survival in adverse conditions. In contrast, other strains harbored predominantly degenerate prophages, suggesting a dynamic process of gene gain and loss during evolution. Furthermore, strain PP9 exhibited polylysogeny, a strategy capable of increasing its competitive advantage by providing a broader spectrum of defensive mechanisms. In addition, evidence demonstrates that prophage regions in PP9 act as hotspots for recombination events, favoring the insertion of different phages and possible antimicrobial resistance genes. Finally, lytic cycle induction experiments revealed at least two intact prophages active in PP9. In this way, understanding the interaction between viruses and bacteria can provide valuable information about microbial evolution and adaptation in extreme environments, such as Antarctica.},
}

Antarctic Regions
*Extreme Environments
*Prophages/genetics
*Soil Microbiology
Spacecraft
Evolution, Molecular
Lysogeny
Bacillaceae/genetics/virology/isolation & purification

@article {pmid39707568,
year = {2024},
author = {Yang, X and Yuan, R and Yang, S and Dai, Z and Di, N and Yang, H and He, Z and Wei, M},
title = {A salt-tolerant growth-promoting phyllosphere microbial combination from mangrove plants and its mechanism for promoting salt tolerance in rice.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {270},
pmid = {39707568},
issn = {2049-2618},
mesh = {*Oryza/microbiology/growth & development ; *Salt Tolerance ; *Plant Leaves/microbiology ; Microbiota ; Rhizosphere ; Pantoea/genetics ; Soil Microbiology ; Bacillus/genetics/isolation & purification/physiology ; Bacteria/genetics/classification/isolation & purification ; Wetlands ; Rhizophoraceae/microbiology ; Quorum Sensing ; },
abstract = {BACKGROUND: Mangrove plants growing in the high salt environment of coastal intertidal zones colonize a variety of microorganisms in the phyllosphere, which have potential salt-tolerant and growth-promoting effects. However, the characteristics of microbial communities in the phyllosphere of mangrove species with and without salt glands and the differences between them remain unknown, and the exploration and the agricultural utilization of functional microbial resources from the leaves of mangrove plants are insufficient.

RESULTS: In this study, we examined six typical mangrove species to unravel the differences in the diversity and structure of phyllosphere microbial communities between mangrove species with or without salt glands. Our results showed that a combination of salt-tolerant growth-promoting strains of Pantoea stewartii A and Bacillus marisflavi Y25 (A + Y25) was constructed from the phyllosphere of mangrove plants, which demonstrated an ability to modulate osmotic substances in rice and regulate the expression of salt-resistance-associated genes. Further metagenomic analysis revealed that exogenous inoculation with A + Y25 increased the rice rhizosphere's specific microbial taxon Chloroflexi, thereby elevating microbial community quorum sensing and ultimately enhancing ionic balance and overall microbial community function to aid salt resistance in rice.

CONCLUSIONS: This study advances our understanding of the mutualistic and symbiotic relationships between mangrove species and their phyllosphere microbial communities. It offers a paradigm for exploring agricultural beneficial microbial resources from mangrove leaves and providing the potential for applying the salt-tolerant bacterial consortium to enhance crop adaptability in saline-alkaline land. Video Abstract.},
}

*Oryza/microbiology/growth & development
*Salt Tolerance
*Plant Leaves/microbiology
Microbiota
Rhizosphere
Pantoea/genetics
Soil Microbiology
Bacillus/genetics/isolation & purification/physiology
Bacteria/genetics/classification/isolation & purification
Wetlands
Rhizophoraceae/microbiology
Quorum Sensing

@article {pmid39707567,
year = {2024},
author = {Feng, X and Xing, P and Tao, Y and Wang, X and Wu, QL and Liu, Y and Luo, H},
title = {Functional traits and adaptation of lake microbiomes on the Tibetan Plateau.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {264},
pmid = {39707567},
issn = {2049-2618},
support = {2023A1515012162//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2022M712195//the China Postdoctoral Science Foundation/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; U2102216//the National Natural Science Foundation of China/ ; 92251304//the National Natural Science Foundation of China/ ; 92251304//the National Natural Science Foundation of China/ ; AoE/M-403/16//the Hong Kong Research Grants Council Area of Excellence Scheme/ ; },
mesh = {*Lakes/microbiology ; Tibet ; *Microbiota/genetics ; *Phylogeny ; *Bacteria/classification/genetics ; Metagenome ; Salinity ; Climate Change ; Ecosystem ; Adaptation, Physiological ; },
abstract = {BACKGROUND: Tibetan Plateau is credited as the "Third Pole" after the Arctic and the Antarctic, and lakes there represent a pristine habitat ideal for studying microbial processes under climate change.

RESULTS: Here, we collected 169 samples from 54 lakes including those from the central Tibetan region that was underrepresented previously, grouped them to freshwater, brackish, and saline lakes, and generated a genome atlas of the Tibetan Plateau Lake Microbiome. This genomic atlas comprises 8271 metagenome-assembled genomes featured by having significant phylogenetic and functional novelty. The microbiomes of freshwater lakes are enriched with genes involved in recalcitrant carbon degradation, carbon fixation, and energy transformation, whereas those of saline lakes possess more genes that encode osmolyte transport and synthesis and enable anaerobic metabolism. These distinct metabolic features match well with the geochemical properties including dissolved organic carbon, dissolved oxygen, and salinity that distinguish between these lakes. Population genomic analysis suggests that microbial populations in saline lakes are under stronger functional constraints than those in freshwater lakes. Although microbiomes in the Tibet lakes, particularly the saline lakes, may be subject to changing selective regimes due to ongoing warming, they may also benefit from the drainage reorganization and metapopulation reconnection.

CONCLUSIONS: Altogether, the Tibetan Plateau Lake Microbiome atlas serves as a valuable microbial genetic resource for biodiversity conservation and climate research. Video Abstract.},
}

*Lakes/microbiology
Tibet
*Microbiota/genetics
*Phylogeny
*Bacteria/classification/genetics
Metagenome
Salinity
Climate Change
Ecosystem
Adaptation, Physiological

@article {pmid39707560,
year = {2024},
author = {Wang, H and Sun, C and Li, Y and Chen, J and Zhao, XM and Chen, WH},
title = {Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {260},
pmid = {39707560},
issn = {2049-2618},
support = {T2225015//National Natural Science Foundation of China/ ; 32070660//National Natural Science Foundation of China/ ; 2020YFA0712403//National Key Research and Development Program of China/ ; 2019YFA0905600//National Key Research and Development Program of China/ ; 82161138017//NNSF-VR Sino-Swedish Joint Research Programme/ ; },
mesh = {*Genome, Viral/genetics ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; *Feces/virology ; Metagenomics/methods ; Virome/genetics ; Viruses/genetics/classification ; Benchmarking ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Metagenome-assembled viral genomes have significantly advanced the discovery and characterization of the human gut virome. However, we lack a comparative assessment of assembly tools on the efficacy of viral genome identification, particularly across next-generation sequencing (NGS) and third-generation sequencing (TGS) data.

RESULTS: We evaluated the efficiency of NGS, TGS, and hybrid assemblers for viral genome discovery using 95 viral-like particle (VLP)-enriched fecal samples sequenced on both Illumina and PacBio platforms. MEGAHIT, metaFlye, and hybridSPAdes emerged as the optimal choices for NGS, TGS, and hybrid datasets, respectively. Notably, these assemblers recovered distinct viral genomes, demonstrating a remarkable degree of complementarity. By combining individual assembler results, we expanded the total number of nonredundant high-quality viral genomes by 4.83 ~ 21.7-fold compared to individual assemblers. Among them, viral genomes from NGS and TGS data have the least overlap, indicating the impact of data type on viral genome recovery. We also evaluated four binning methods, finding that CONCOCT incorporated more unrelated contigs into the same bins, while MetaBAT2, AVAMB, and vRhyme balanced inclusiveness and taxonomic consistency within bins.

CONCLUSIONS: Our findings highlight the challenges in metagenome-driven viral discovery, underscoring tool limitations. We advocate for combined use of multiple assemblers and sequencing technologies when feasible and highlight the urgent need for specialized tools tailored to gut virome assembly. This study contributes essential insights for advancing viral genome research in the context of gut metagenomics. Video Abstract.},
}

*Genome, Viral/genetics
Humans
*High-Throughput Nucleotide Sequencing/methods
*Gastrointestinal Microbiome/genetics
*Metagenome/genetics
*Feces/virology
Metagenomics/methods
Virome/genetics
Viruses/genetics/classification
Benchmarking
Sequence Analysis, DNA/methods

@article {pmid39707557,
year = {2024},
author = {Santamarina-García, G and Yap, M and Crispie, F and Amores, G and Lordan, C and Virto, M and Cotter, PD},
title = {Shotgun metagenomic sequencing reveals the influence of artisanal dairy environments on the microbiomes, quality, and safety of Idiazabal, a raw ewe milk PDO cheese.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {262},
pmid = {39707557},
issn = {2049-2618},
support = {IT1568-22//Eusko Jaurlaritza/ ; IT1568-22//Eusko Jaurlaritza/ ; IT1568-22//Eusko Jaurlaritza/ ; PIF19/31//Euskal Herriko Unibertsitatea/ ; },
mesh = {*Cheese/microbiology ; Animals ; *Milk/microbiology ; *Microbiota ; *Metagenomics ; Sheep/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Female ; Dairying ; Food Microbiology ; Metagenome ; },
abstract = {BACKGROUND: Numerous studies have highlighted the impact of bacterial communities on the quality and safety of raw ewe milk-derived cheeses. Despite reported differences in the microbiota among cheese types and even producers, to the best of our knowledge, no study has comprehensively assessed all potential microbial sources and their contributions to any raw ewe milk-derived cheese, which could suppose great potential for benefits from research in this area. Here, using the Protected Designation of Origin Idiazabal cheese as an example, the impact of the environment and practices of artisanal dairies (including herd feed, teat skin, dairy surfaces, and ingredients) on the microbiomes of the associated raw milk, whey, and derived cheeses was examined through shotgun metagenomic sequencing.

RESULTS: The results revealed diverse microbial ecosystems across sample types, comprising more than 1300 bacterial genera and 3400 species. SourceTracker analysis revealed commercial feed and teat skin as major contributors to the raw milk microbiota (45.6% and 33.5%, respectively), being a source of, for example, Lactococcus and Pantoea, along with rennet contributing to the composition of whey and cheese (17.4% and 41.0%, respectively), including taxa such as Streptococcus, Pseudomonas_E or Lactobacillus_H. Functional analysis linked microbial niches to cheese quality- and safety-related metabolic pathways, with brine and food contact surfaces being most relevant, related to genera like Brevibacterium, Methylobacterium, or Halomonas. With respect to the virulome (virulence-associated gene profile), in addition to whey and cheese, commercial feed and grass were the main reservoirs (related to, e.g., Brevibacillus_B or CAG-196). Similarly, grass, teat skin, or rennet were the main contributors of antimicrobial resistance genes (e.g., Bact-11 or Bacteriodes_B). In terms of cheese aroma and texture, apart from the microbiome of the cheese itself, brine, grass, and food contact surfaces were key reservoirs for hydrolase-encoding genes, originating from, for example, Lactococcus, Lactobacillus, Listeria or Chromohalobacter. Furthermore, over 300 metagenomic assembled genomes (MAGs) were generated, including 60 high-quality MAGs, yielding 28 novel putative species from several genera, e.g., Citricoccus, Corynebacterium, or Dietzia.

CONCLUSION: This study emphasizes the role of the artisanal dairy environments in determining cheese microbiota and, consequently, quality and safety. Video Abstract.},
}

*Cheese/microbiology
Animals
*Milk/microbiology
*Microbiota
*Metagenomics
Sheep/microbiology
*Bacteria/classification/genetics/isolation & purification
Female
Dairying
Food Microbiology
Metagenome

@article {pmid39707511,
year = {2024},
author = {Ma, X and Hu, X and Liu, K and Wang, W and Jia, W and Gao, H and Lu, M and Liu, J and Chen, Y and Ma, Y and Li, Y and Nie, Y},
title = {Spatiotemporal differences induced changes in the structure and function of the gut microbiota in an endangered ungulate.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {74},
pmid = {39707511},
issn = {2524-4671},
support = {32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; },
abstract = {The composition and function of animal gut microbiota are shaped by various factors, among which diet is one of the major factors. Diet is affected by seasonal shifts and geographical differences, which in turn impact the host's nutritional levels. To adapt to these environmental changes, the gut microbiome often produces matching responses. Understanding the relationships among the environment, diet, host and the gut microbiome is helpful for exploring the environmental adaptation of wildlife. Here, we chose wild sika deer (Cervus nippon), which is composed natural allopatric populations, to explore how the environment shapes the gut microbiome and affects the relationship between microbiota composition and function and the mutual adaptation of the seasonal living environment to seasonal dietary changes. To this purpose we used DNA metabarcoding, 16S RNA gene amplification sequencing, metagenomic shotgun sequencing and nutritional analyses to comprehensively examine the relationships among the forage plant, nutrient status and host gut microbiome. Our analyses showed spatiotemporal differences in diet between the Tiebu and Hunchun regions, which ultimately led to varying intakes of protein, cellulose, and soluble sugar. The microbiome composition and function showed unique characteristics in each group, and significant differences were detected at the gene level for the protein absorption and metabolism pathway, the carbohydrate metabolic absorption pathway, and cellulase enzyme function, which are related to nutrition. We also found differences in the pathogenic bacteria and resistance mechanisms genes of the gut microbiota in different groups. Our results showed that the gut microbiome of allopatric populations adapts to changes in food composition and nutrition in different seasons and areas to help the host cope with spatiotemporal changes in the living environment. At the same time, varying levels of human activity can have potential health impacts on wild animals.},
}

@article {pmid39707494,
year = {2024},
author = {Li, C and Liu, K and Gu, C and Li, M and Zhou, P and Chen, L and Sun, S and Li, X and Wang, L and Ni, W and Li, M and Hu, S},
title = {Gastrointestinal jumbo phages possess independent synthesis and utilization systems of NAD.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {268},
pmid = {39707494},
issn = {2049-2618},
mesh = {*Bacteriophages/genetics/classification/isolation & purification ; Animals ; *Genome, Viral/genetics ; *NAD/metabolism ; *Phylogeny ; Humans ; Gastrointestinal Microbiome ; Swine ; Sheep ; Metagenomics ; Horses ; Cattle ; Bacteria/virology/genetics ; Deer/virology ; DNA Replication ; },
abstract = {BACKGROUND: Jumbo phages, phages with genomes > 200 kbp, contain some unique genes for successful reproduction in their bacterial hosts. Due to complex and massive genomes analogous to those of small-celled bacteria, how jumbo phages complete their life cycle remains largely undefined.

RESULTS: In this study, we assembled 668 high-quality jumbo phage genomes from over 15 terabytes (TB) of intestinal metagenomic data from 955 samples of 5 animal species (cow, sheep, pig, horse, and deer). Within them, we obtained a complete genome of 716 kbp in length, which is the largest phage genome so far reported in the gut environments. Interestingly, 174 out of the 668 jumbo phages were found to encode all genes required for the synthesis of NAD[+] by the salvage pathway or Preiss-Handler pathway, referred to as NAD-jumbo phage. Besides synthesis genes of NAD[+], these NAD-jumbo phages also encode at least 15 types of NAD[+]-consuming enzyme genes involved in DNA replication, DNA repair, and counterdefense, suggesting that these phages not only have the capacity to synthesize NAD[+] but also redirect NAD[+] metabolism towards phage propagation need in hosts. Phylogenetic analysis and environmental survey indicated NAD-jumbo phages are widely present in the Earth's ecosystems, including the human gut, lakes, salt ponds, mine tailings, and seawater.

CONCLUSION: In summary, this study expands our understanding of the diversity and survival strategies of phages, and an in-depth study of the NAD-jumbo phages is crucial for understanding their role in ecological regulation. Video Abstract.},
}

*Bacteriophages/genetics/classification/isolation & purification
Animals
*Genome, Viral/genetics
*NAD/metabolism
*Phylogeny
Humans
Gastrointestinal Microbiome
Swine
Sheep
Metagenomics
Horses
Cattle
Bacteria/virology/genetics
Deer/virology
DNA Replication

@article {pmid39707478,
year = {2024},
author = {He, Z and Hou, Y and Li, Y and Bei, Q and Li, X and Zhu, YG and Liesack, W and Rillig, MC and Peng, J},
title = {Increased methane production associated with community shifts towards Methanocella in paddy soils with the presence of nanoplastics.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {259},
pmid = {39707478},
issn = {2049-2618},
mesh = {*Methane/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Oryza/microbiology ; Microbiota ; Polyethylene ; Soil Pollutants ; Metagenomics ; Archaea/metabolism/genetics/classification ; Carbon/metabolism ; Plastics ; },
abstract = {BACKGROUND: Planetary plastic pollution poses a major threat to ecosystems and human health in the Anthropocene, yet its impact on biogeochemical cycling remains poorly understood. Waterlogged rice paddies are globally important sources of CH4. Given the widespread use of plastic mulching in soils, it is urgent to unravel whether low-density polyethylene (LDPE) will affect the methanogenic community in flooded paddy soils. Here, we employed a combination of process measurements, short-chain and long-chain fatty acid (SCFAs and LCFAs) profiling, Fourier-transform ion cyclotron resonance mass spectrometry, quantitative PCR, metagenomics, and mRNA profiling to investigate the impact of LDPE nanoplastics (NPs) on dissolved organic carbon (DOC) and CH4 production in both black and red paddy soils under anoxic incubation over a 160-day period.

RESULTS: Despite significant differences in microbiome composition between the two soil types, both exhibited similar results to NPs exposure. NPs induced a change in DOC content and CH4 production up to 1.8-fold and 10.1-fold, respectively. The proportion of labile dissolved organic matter decreased, while its recalcitrance increased. Genes associated with the degradation of complex carbohydrates and aromatic carbon were significantly enriched. The elevated CH4 production was significantly correlated to increases in both the PCR-quantified mcrA gene copy numbers and the metagenomic methanogen-to-bacteria abundance ratio. Notably, the latter was linked to an enrichment of the hydrogenotrophic methanogenesis pathway. Among 391 metagenome-assembled genomes (MAGs), the abundance of several Syntrophomonas and Methanocella MAGs increased concomitantly, suggesting that the NPs treatments stimulated the syntrophic oxidation of fatty acids. mRNA profiling further identified Methanosarcinaceae and Methanocellaceae to be the key players in the NPs-induced CH4 production.

CONCLUSIONS: The specific enrichment of Syntrophomonas and Methanocella indicates that LDPE NPs stimulate the syntrophic oxidation of LCFAs and SCFAs, with Methanocella acting as the hydrogenotrophic methanogen partner. Our findings enhance the understanding of how LDPE NPs affect the methanogenic community in waterlogged paddy soils. Given the importance of this ecosystem, our results are crucial for elucidating the mechanisms that govern carbon fluxes, which are highly relevant to global climate change.},
}

*Methane/metabolism
*Soil Microbiology
*Soil/chemistry
*Oryza/microbiology
Microbiota
Polyethylene
Soil Pollutants
Metagenomics
Archaea/metabolism/genetics/classification
Carbon/metabolism
Plastics

@article {pmid39707381,
year = {2024},
author = {Elton, L and Williams, A and Ali, S and Heaphy, J and Pang, V and Commins, L and O'Brien, C and Yetiş, Ö and Caine, E and Ward, I and Muzslay, M and Yui, S and Karia, K and Shore, E and Rofael, S and Mack, DJF and McHugh, TD and Wey, EQ},
title = {Tracing the transmission of carbapenem-resistant Enterobacterales at the patient: ward environmental nexus.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {23},
number = {1},
pages = {108},
pmid = {39707381},
issn = {1476-0711},
mesh = {Humans ; *Enterobacteriaceae Infections/microbiology/transmission ; *Carbapenem-Resistant Enterobacteriaceae/genetics/isolation & purification/drug effects ; *Wastewater/microbiology ; *beta-Lactamases/genetics ; *Whole Genome Sequencing ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Microbial Sensitivity Tests ; Cross Infection/microbiology/transmission ; Bacterial Proteins/genetics ; Enterobacter/genetics/drug effects/isolation & purification ; },
abstract = {INTRODUCTION: Colonisation and infection with Carbapenem-resistant Enterobacterales (CRE) in healthcare settings poses significant risks, especially for vulnerable patients. Genomic analysis can be used to trace transmission routes, supporting antimicrobial stewardship and informing infection control strategies. Here we used genomic analysis to track the movement and transmission of CREs within clinical and environmental samples.

METHODS: 25 isolates were cultured from clinical patient samples or swabs, that tested positive for OXA-48-like variants using the NG-Test® CARBA-5 test and whole genome sequenced (WGS) using Oxford Nanopore Technologies (ONT). 158 swabs and 52 wastewater samples were collected from the ward environment. 60 isolates (matching clinical isolate genera; Klebsiella, Enterobacter, Citrobacter and Escherichia) were isolated from the environmental samples using selective agar. Metagenomic sequencing was undertaken on 36 environmental wastewater and swab samples.

RESULTS: 21/25 (84%) clinical isolates had > 1 blaOXA gene and 19/25 (76%) harboured > 1 blaNDM gene. Enterobacterales were most commonly isolated from environmental wastewater samples 27/52 (51.9%), then stick swabs 5/43 (11.6%) and sponge swabs 5/115 (4.3%). 11/60 (18%) environmental isolates harboured > 1 blaOXA gene and 1.9% (1/60) harboured blaNDM-1. blaOXA genes were found in 2/36 (5.5%) metagenomic environmental samples.

CONCLUSIONS: Potential for putative patient-patient and patient-ward transmission was shown. Metagenomic sampling needs optimization to improve sensitivity.},
}

Humans
*Enterobacteriaceae Infections/microbiology/transmission
*Carbapenem-Resistant Enterobacteriaceae/genetics/isolation & purification/drug effects
*Wastewater/microbiology
*beta-Lactamases/genetics
*Whole Genome Sequencing
Anti-Bacterial Agents/pharmacology
Carbapenems/pharmacology
Microbial Sensitivity Tests
Cross Infection/microbiology/transmission
Bacterial Proteins/genetics
Enterobacter/genetics/drug effects/isolation & purification

@article {pmid39707302,
year = {2024},
author = {Zhang, N and Zhang, X and Guo, Y and Zheng, Y and Gai, W and Yang, Z},
title = {Clinical and metagenomic predicted antimicrobial resistance in pediatric critically ill patients with infectious diseases in a single center of Zhejiang.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {23},
number = {1},
pages = {107},
pmid = {39707302},
issn = {1476-0711},
support = {2021YFC2701800, 2021YFC2701801//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Critical Illness ; Female ; Male ; Retrospective Studies ; Child, Preschool ; Child ; Infant ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; China ; *Intensive Care Units, Pediatric ; Drug Resistance, Bacterial/genetics ; Metagenomics ; Microbial Sensitivity Tests ; High-Throughput Nucleotide Sequencing ; Communicable Diseases/drug therapy/microbiology ; Adolescent ; Prognosis ; Bacteria/genetics/drug effects/classification/isolation & purification ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) poses a significant threat to pediatric health; therefore, precise identification of pathogens as well as AMR is imperative. This study aimed at comprehending antibiotic resistance patterns among critically ill children with infectious diseases admitted to pediatric intensive care unit (PICU) and to clarify the impact of drug-resistant bacteria on the prognosis of children.

METHODS: This study retrospectively collected clinical data, identified pathogens and AMR from 113 children's who performed metagenomic next-generation sequencing for pathogen and antibiotic resistance genes identification, and compared the clinical characteristic difference and prognostic effects between children with and without AMR detected.

RESULTS: Based on the presence or absence of AMR test results, the 113 patients were divided into Antimicrobial resistance test positive group (AMRT+, n = 44) and Antimicrobial resistance test negative group (AMRT-, n = 69). Immunocompromised patients (50% vs. 28.99%, P = 0.0242) and patients with underlying diseases (70.45% vs. 40.58%, P = 0.0019) were more likely to develop resistance to antibiotics. Children in the AMRT + group showed significantly increased C-reaction protein, score of pediatric sequential organ failure assessment and pediatric risk of mortality of children and longer hospital stay and ICU stay in the AMRT + group compared to the AMRT+- group (P < 0.05). Detection rate of Gram-negative bacteria was significantly higher in the AMRT + group rather than Gram-positive bacteria (n = 45 vs. 31), in contrast to the AMRT- group (n = 10 vs. 36). Cephalosporins, β-lactams/β-Lactamase inhibitors, carbapenems and sulfonamides emerged as the most common types of drug resistance in children. Resistance rates to these antibiotics exhibited considerable variation across common pathogens, including Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii.

CONCLUSIONS: The development of drug resistance in bacteria will significantly affect the prognosis of patients. The significant differences in drug resistance of common pathogenic bacteria indicate that identification of drug resistance is important for the rational use of antibiotics and patient prognosis.},
}

Humans
*Critical Illness
Female
Male
Retrospective Studies
Child, Preschool
Child
Infant
*Anti-Bacterial Agents/pharmacology/therapeutic use
China
*Intensive Care Units, Pediatric
Drug Resistance, Bacterial/genetics
Metagenomics
Microbial Sensitivity Tests
High-Throughput Nucleotide Sequencing
Communicable Diseases/drug therapy/microbiology
Adolescent
Prognosis
Bacteria/genetics/drug effects/classification/isolation & purification

@article {pmid39707301,
year = {2024},
author = {Shan, X and Li, Z and Dong, L},
title = {A case of pneumonia caused by infection with Tropheryma whipplei complicated by cryptococcus during treatment with a Janus kinase inhibitor: a case report.},
journal = {BMC pulmonary medicine},
volume = {24},
number = {1},
pages = {625},
pmid = {39707301},
issn = {1471-2466},
mesh = {Humans ; Male ; Adult ; *Cryptococcosis/drug therapy/diagnosis/microbiology ; *Tropheryma/isolation & purification ; *Janus Kinase Inhibitors/therapeutic use/adverse effects ; *Whipple Disease/drug therapy/diagnosis/complications ; Tomography, X-Ray Computed ; Cryptococcus/isolation & purification ; Pyrimidines/therapeutic use ; Opportunistic Infections/microbiology/drug therapy/diagnosis ; Anti-Bacterial Agents/therapeutic use ; Bronchoalveolar Lavage Fluid/microbiology ; },
abstract = {This report describes the case of a 41-year-old male patient complaining of a hacking cough. The patient was treated with a Janus kinase (JAK) inhibitor for psoriasis. Blood tests revealed mild lymphopenia and high levels of serum cryptococcal antigen. Chest computed tomography revealed infection in the lower lobe of the left lung. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid revealed Tropheryma whipplei. Tropheryma whipplei and Cryptococcus antimicrobial therapies were sequentially administered. During follow-up, the patient showed clinical and radiographic improvement. Tropheryma whipplei is an opportunistic Gram-positive rod-shaped bacterium belonging to the family Actinomycetes. Lung involvement is an unusual but classic manifestation of Whipple's disease. This is the first report of pneumonia caused by infection with Tropheryma whipplei complicated by Cryptococcus. To our knowledge, this is the first case report of Tropheryma whipplei infection following the use of JAK inhibitors. Clinicians should be aware of opportunistic infections that can occur during treatment with JAK inhibitors.},
}

Humans
Male
Adult
*Cryptococcosis/drug therapy/diagnosis/microbiology
*Tropheryma/isolation & purification
*Janus Kinase Inhibitors/therapeutic use/adverse effects
*Whipple Disease/drug therapy/diagnosis/complications
Tomography, X-Ray Computed
Cryptococcus/isolation & purification
Pyrimidines/therapeutic use
Opportunistic Infections/microbiology/drug therapy/diagnosis
Anti-Bacterial Agents/therapeutic use
Bronchoalveolar Lavage Fluid/microbiology

@article {pmid39707169,
year = {2024},
author = {Carrasco-Villanueva, M and Wang, C and Wei, C},
title = {Identification of diversity-generating retroelements in host-associated and environmental genomes: prevalence, diversity, and roles.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1227},
pmid = {39707169},
issn = {1471-2164},
support = {2023YFF1001600//National Key Research and Development Program of China/ ; 32170643//National Natural Science Foundation of China/ ; 20ZR1428200, 22ZR1433600//Natural Science Foundation of Shanghai Municipality/ ; },
mesh = {*Retroelements ; *Phylogeny ; Humans ; *Genetic Variation ; Bacteria/genetics/classification ; Metagenome ; Archaea/genetics ; RNA-Directed DNA Polymerase/genetics ; },
abstract = {BACKGROUND: The diversity-generating retroelements (DGRs) are a family of genetic elements that can produce mutations in target genes often related to ligand-binding functions, which possess a C-type lectin (CLec) domain that tolerates massive variations. They were first identified in viruses, then in bacteria and archaea from human-associated and environmental genomes. This DGR mechanism represents a fast adaptation of organisms to ever- changing environments. However, their existence, phylogenetic and structural diversity, and functions in a wide range of environments are largely unknown.

RESULTS: Here we present a study of DGR systems based on metagenome-assembled genomes (MAGs) from host-associated, aquatic, terrestrial and engineered environments. In total, we identified 861 non-redundant DGR-RTs and ~ 5.7% are new. We found that microbes associated with human hosts harbor the highest number of DGRs and also exhibit a higher prevalence of DGRs. After normalizing with genome size and including more genome data, we found that DGRs occur more frequently in organisms with smaller genomes. Overall, we identified nine main clades in the phylogenetic tree of reverse transcriptases (RTs), some comprising specific phyla and cassette architectures. We identified 38 different cassette patterns and 6 of them were shown in at least 10 DGRs, showing differences in terms of the numbers, arrangements, and orientations of their components. Finally, most of the target genes were related to ligand-binding and signaling functions, but we discovered a few cases in which the VRs were situated in domains different from the CLec.

CONCLUSIONS: Our research sheds light on the widespread prevalence of DGRs within environments and taxa, and supports the DGR phylogenetic divergence in different organisms. These variations might also occur in their structures since some cassette architectures were common in specific underrepresented phyla. In addition, we suggest that VRs could be found in domains different to the CLec, which should be further explored for organisms in scarcely studied environments.},
}

*Retroelements
*Phylogeny
Humans
*Genetic Variation
Bacteria/genetics/classification
Metagenome
Archaea/genetics
RNA-Directed DNA Polymerase/genetics

@article {pmid39706917,
year = {2024},
author = {Chang, WS and Harvey, E and Mahar, JE and Firth, C and Shi, M and Simon-Loriere, E and Geoghegan, JL and Wille, M},
title = {Improving the reporting of metagenomic virome-scale data.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1687},
pmid = {39706917},
issn = {2399-3642},
mesh = {*Virome/genetics ; *Metagenomics/methods ; Humans ; Animals ; *Viruses/genetics/classification ; Metagenome ; Genome, Viral ; },
abstract = {Over the last decade metagenomic sequencing has facilitated an increasing number of virome-scale studies, leading to an exponential expansion in understanding of virus diversity. This is partially driven by the decreasing costs of metagenomic sequencing, improvements in computational tools for revealing novel viruses, and an increased understanding of the key role that viruses play in human and animal health. A central concern associated with this remarkable increase in the number of virome-scale studies is the lack of broadly accepted "gold standards" for reporting the data and results generated. This is of particular importance for animal virome studies as there are a multitude of nuanced approaches for both data presentation and analysis, all of which impact the resulting outcomes. As such, the results of published studies can be difficult to contextualise and may be of reduced utility due to reporting deficiencies. Herein, we aim to address these reporting issues by outlining recommendations for the presentation of virome data, encouraging a transparent communication of findings that can be interpreted in evolutionary and ecological contexts.},
}

*Virome/genetics
*Metagenomics/methods
Humans
Animals
*Viruses/genetics/classification
Metagenome
Genome, Viral

@article {pmid39706308,
year = {2024},
author = {Wang, Z and Jiang, C and Nnorom, MA and Avignone-Rossa, C and Yang, K and Guo, B},
title = {Multi-faceted effects and mechanisms of granular activated carbon to enhance anaerobic ammonium oxidation (anammox) for nitrogen removal from wastewater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132001},
doi = {10.1016/j.biortech.2024.132001},
pmid = {39706308},
issn = {1873-2976},
abstract = {Nitrogen removal via anammox is efficient but challenged by their slow growth. Adding granular activated carbon (GAC) increased the total nitrogen removal rate to 66.99 g-N/m[3]/day, compared to 50.00 g-N/m[3]/day in non-GAC reactor. Both reactors dominated by Candidatus Brocadia (non-GAC: 36.25 %, GAC: 35.5 %) but GAC improved specific anammox activity. Functional metabolic profiling from metagenomic analysis unveiled that GAC enhanced pathways associated with electron shuttle production, potentially promoting intra/extracellular electron transfer. In nitrogen metabolism, GAC is indicated to facilitate anammox N2H4 synthesis process, and inhibit nitrification and full denitrification processes, functioned by Nitrosomonas and Castellaniella which are more abundant in the non-GAC reactor. GAC also enhanced dissimilatory nitrate reduction to ammonium and partial denitrification processes, providing anammox with NH4[+]/NO, which was conducted by Anaerolineae members (29.7 % in GAC-reactor and 7.8 % in non-GAC reactor sludge). This research illuminated the intricate microbial nitrogen cycling networks affected by GAC in anammox systems.},
}

@article {pmid39706307,
year = {2024},
author = {Zhang, B and Liu, J and Cai, C and Zhou, Y},
title = {Membrane photobioreactor for biogas capture and conversion - Enhanced microbial interaction in biofilm.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131999},
doi = {10.1016/j.biortech.2024.131999},
pmid = {39706307},
issn = {1873-2976},
abstract = {The urgency to mitigate greenhouse gas emissions has driven interest in sustainable biogas utilization. This study investigates a 1 L enclosed membrane photobioreactor (MPBR) using a microalgae-methanotroph coculture for biogas capture. Operating with a hydraulic and solid retention time of 7 days and a biogas loading rate of 2.7 L /day, the introduction of gas membrane module increased CO2-C and CH4-C uptake rates by 12 % and 50 %, respectively. Biofilm formation on the membrane surface enhanced system performance, with imaging analyses revealing methanotroph predominantly located near the membrane surface and photosynthetic microorganisms distributed throughout. Metagenomic analysis showed shifts in key metabolic pathways, including increased abundance of soluble methane monooxygenase genes and enhanced vitamin B synthesis in the biofilm. These findings highlight the spatial organization and metabolic interactions in methanotroph-microalgae coculture system, providing insights into the role of membrane-induced biofilms in improving MPBR performance for sustainable biogas utilization.},
}

@article {pmid39706000,
year = {2024},
author = {Zhang, X and Huang, Z and Zhong, Z and Li, Q and Bian, F},
title = {Forest management impacts on soil phosphorus cycling: Insights from metagenomics in Moso bamboo plantations.},
journal = {Journal of environmental management},
volume = {373},
number = {},
pages = {123735},
doi = {10.1016/j.jenvman.2024.123735},
pmid = {39706000},
issn = {1095-8630},
abstract = {Bamboo forests are crucial ecosystems and provide essential ecological and economic services in both tropical and subtropical regions. Soil phosphorus (P), a vital nutrient for plant growth, is fundamental to the productivity and health of bamboo forests. However, the microbial mechanisms through which management practices affect soil P processes in bamboo forests remain poorly understood. This study employed metagenomics to examine alterations in microbial P cycling in Moso bamboo plantations under three distinct management conditions. The results revealed that intensive management (M2, annual fertilization, selective harvesting, and understory vegetation removal) significantly increased soil inorganic P (Pi) by 61.76% and 87.39% compared to extensive management (M1, selective bamboo trunk and shoot harvesting every two years) and non-management (M0), respectively, while decreasing soil organic P (Po) by 50.41% and 41.05%. Forest management significantly altered the bacterial communities: Firmicutes, WPS-2, and Acidobacteriales were represented in M2, Xanthobacteraceae in M1, and Chloroflexi AD3, Acidothermus, and Subgroup_2 in M0. M2 significantly increased the community-level habitat niche breadth and weakened the deterministic process of bacterial community assembly relative to M1 and M0 (p ≤ 0.05). Furthermore, functional metagenomics showed that the total abundance of genes related to Po mineralization, P transportation, and P regulation was significantly lower (p ≤ 0.05) in M2 than in M0 and M1. pstA, pstB, and pstC were more abundant in M2 (p ≤ 0.05), whereas phnN, phnI, phnG, phoA, phoD, phnC, phnD, and phnE were more abundant in M1 (p ≤ 0.05), and phnF was significantly abundant in M0 (p ≤ 0.05). A partial least squares path model indicated that soil bacterial community and P cycling genes had direct effects on Pi and Po, respectively. These findings enhance our understanding of the links between forest management practices and P cycling, providing insights for improving soil functionality and nutrient balance.},
}

@article {pmid39705954,
year = {2024},
author = {Basile, A and Riggio, FP and Tescari, M and Chebbi, A and Sodo, A and Bartoli, F and Imperi, F and Caneva, G and Visca, P},
title = {Metagenome-resolved functional traits of Rubrobacter species implicated in rosy discoloration of ancient frescoes in two Georgian Cathedrals.},
journal = {The Science of the total environment},
volume = {958},
number = {},
pages = {178135},
doi = {10.1016/j.scitotenv.2024.178135},
pmid = {39705954},
issn = {1879-1026},
abstract = {Pink biofilm formation on stone monuments and mural paintings poses serious harm to cultural heritage preservation. Pink biofilms are globally widespread and recalcitrant to eradication, often causing recurrences after restoration. Yet, the ecological drivers of pink biofilm formation and the metabolic functions sustaining the growth of pigment-producing biodeteriogens remain unclear. In this study, a combined approach integrating physicochemical investigations, scanning electron microscopy, 16S rRNA sequence-based analysis of the prokaryotic community, metagenomic deep sequencing, and metabolic profiling, was applied to determine the etiology of rosy discoloration of ancient frescoes in the Gelati and the Martvili Cathedrals (Georgia). Martvili samples showed greater diversity than Gelati samples, though Actinomycetota predominated in both samples. Rubrobacter-related sequences were detected in all sampling sites, showing an overwhelming abundance in Gelati samples. Reconstruction of metagenome-assembled genomes (MAGs) and phylogenetic analyses highlighted significant intra-genus diversity for Rubrobacter-related sequences, most of which could not be assigned to any formally described Rubrobacter species. Metabolic profiling of the Gelati metagenomes suggests that carbon-fixing autotrophic bacteria and proteinaceous substances in the plaster could contribute to sustaining the chemoorganotrophic members of the community. Complete pathways for β-carotene and bacterioruberin synthesis were identified in Rubrobacter MAGs, consistent with the Raman spectroscopy-based detection of these pigments in fresco samples. Gene clusters for the synthesis of secondary metabolites endowed with antibiotic activity were predicted from the annotation of Rubrobacter MAGs, along with genes conferring resistance to several antimicrobials and biocides. In conclusion, genome-resolved metagenomics provided robust evidence of a causal relationship between contamination by Rubrobacter-related carotenoid-producing bacteria and the rosy discoloration of Georgian frescoes, with relevant implications for rational biodeteriogen-targeted restoration strategies.},
}

@article {pmid39705480,
year = {2024},
author = {Lu, S and Sun, L and Cao, L and Zhao, M and Guo, Y and Li, M and Duan, S and Zhai, Y and Zhang, X and Wang, Y and Gai, W and Cui, X},
title = {Analysis of lung microbiota in pediatric pneumonia patients using BALF metagenomic next-generation sequencing: A retrospective observational study.},
journal = {Medicine},
volume = {103},
number = {51},
pages = {e40860},
doi = {10.1097/MD.0000000000040860},
pmid = {39705480},
issn = {1536-5964},
support = {202139//Clinical Medical peronnel training programs/ ; },
mesh = {Humans ; Retrospective Studies ; Male ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Child, Preschool ; Child ; *Lung/microbiology ; *Microbiota/genetics ; Infant ; Metagenomics/methods ; Severity of Illness Index ; Pneumonia/microbiology ; Pneumonia, Mycoplasma/microbiology/diagnosis ; },
abstract = {The contribution of the lung microbiota to pneumonia in children of varying severity remains poorly understood. This study utilized metagenomic next-generation sequencing (mNGS) technology to elucidate the characteristics of lung microbiota and their association with disease severity. This retrospective study analyzed bronchoalveolar lavage fluid (BALF) mNGS data of 92 children diagnosed with pneumonia between January 2021 and July 2022. A comparative analysis of the lung microbiota was conducted between the severe pneumonia (SP) (n = 44) and non-severe pneumonia (NSP) (n = 48) groups. Compared to conventional microbiological tests (CMT), mNGS had a higher positivity rate in etiology detection (68% vs 100%). In the NSP group, the predominant type of infection was Mycoplasma pneumoniae single infection, whereas in the SP group, the main type involved a combination of M pneumoniae and bacterial infection. The top 3 identified microbial taxa in both the groups were M pneumoniae, Rothia mucilaginosa, and Schaalia odontolyticus. Although there were no significant differences in the α and β diversity of the lung microbiota between the SP and NSP groups, the abundance of M pneumoniae was higher in the SP group (P = .053). Spearman analysis indicated a highly significant positive correlation between the abundance of Prevotella melaninogenica and M pneumoniae (P < .001). Our analysis identified an association between M pneumoniae infections and disease severity. This study provides a foundation for a better understanding of the pathogenesis of pediatric pneumonia and the relationship between microorganisms.},
}

Humans
Retrospective Studies
Male
Female
*Bronchoalveolar Lavage Fluid/microbiology
*High-Throughput Nucleotide Sequencing/methods
Child, Preschool
Child
*Lung/microbiology
*Microbiota/genetics
Infant
Metagenomics/methods
Severity of Illness Index
Pneumonia/microbiology
Pneumonia, Mycoplasma/microbiology/diagnosis

@article {pmid39705298,
year = {2024},
author = {Oliveira, V and Cleary, DFR and Polónia, ARM and Huang, YM and Rocha, U and Voogd, NJ and Gomes, NCM},
title = {Unravelling a Latent Pathobiome Across Coral Reef Biotopes.},
journal = {Environmental microbiology},
volume = {26},
number = {12},
pages = {e70008},
doi = {10.1111/1462-2920.70008},
pmid = {39705298},
issn = {1462-2920},
support = {VH-NG-1248 Micro "BigData"//Helmholtz Young Investigator Grant/ ; MNPH 104403//Marine National Parks Headquarter, Taiwan/ ; MOST 105-2621-B-346-002//Ministry of Science and Technology, Taiwan/ ; DOI: 10.54499/DL57/2016/CP1482/CT0109//Foundation for Science and Technology/ ; PTDC/BIA29/MIC/6473/2014 - POCI-01-0145-FEDER-01//Foundation for Science and Technology/ ; SFRH/BPD/117563/2016//Foundation for Science and Technology/ ; UIDP/50017/2020 + UIDB/50017/2020 + LA/P/0094/2020//Foundation for Science and Technology/ ; },
mesh = {*Coral Reefs ; Animals ; *Anthozoa/microbiology ; *Bacteria/genetics/classification ; *Microbiota ; Virulence Factors/genetics ; },
abstract = {Previous studies on disease in coral reef organisms have neglected the natural distribution of potential pathogens and the genetic factors that underlie disease incidence. This study explores the intricate associations between hosts, microbial communities, putative pathogens, antibiotic resistance genes (ARGs) and virulence factors (VFs) across diverse coral reef biotopes. We observed a substantial compositional overlap of putative bacterial pathogens, VFs and ARGs across biotopes, consistent with the 'everything is everywhere, but the environment selects' hypothesis. However, flatworms and soft corals deviated from this pattern, harbouring the least diverse microbial communities and the lowest diversity of putative pathogens and ARGs. Notably, our study revealed a significant congruence between the distribution of putative pathogens, ARGs and microbial assemblages across different biotopes, suggesting an association between pathogen and ARG occurrence. This study sheds light on the existence of this latent pathobiome, the disturbance of which may contribute to disease onset in coral reef organisms.},
}

*Coral Reefs
Animals
*Anthozoa/microbiology
*Bacteria/genetics/classification
*Microbiota
Virulence Factors/genetics

@article {pmid39705278,
year = {2024},
author = {Kanyerezi, S and Guerfali, FZ and Anzaku, AA and Babaleye, OA and Calvert-Joshua, T and Nguinkal, JA and Amoo, OP and Atri, C and Khan, W and Saleh, I and Nisar, MI and Kasambula, AS and Morapedi, K and Mboowa, G},
title = {Wastewater metagenomics in Africa: Opportunities and challenges.},
journal = {PLOS global public health},
volume = {4},
number = {12},
pages = {e0004044},
pmid = {39705278},
issn = {2767-3375},
abstract = {The advent of metagenomics has dramatically expanded our understanding of microbial communities, particularly through the study of wastewater, which serves as a rich source of microbial data. In Africa, wastewater metagenomics presents unparalleled opportunities for public health monitoring, antimicrobial resistance (AMR) tracking, and the discovery of new microbial species and functions. Utilizing high-throughput sequencing (HTS) technologies, this method allows for direct analysis of nucleic acids from wastewater samples, providing a cost-effective and comprehensive approach for pathogen surveillance. The potential of wastewater metagenomics in Africa is vast. It can revolutionize public health monitoring by acting as an early warning system for infectious disease outbreaks, offering near real-time data to shape effective responses. This is especially critical in densely populated urban areas with poor sanitation, where the risk of disease spread is high. Moreover, this approach enables the detection of emerging pathogens and insights into environmental health. However, the implementation of wastewater metagenomics in Africa faces several challenges. These include variability in wastewater composition due to differing local customs, limited infrastructure for sequencing and data analysis, and a shortage of bioinformatics expertise. Socio-political and ethical issues also complicate data sharing and the equitable distribution of benefits. To overcome these challenges, there is a need to enhance capacity through collaborative training, infrastructural development, and international partnerships. Investing and sustaining local genomics and bioinformatics infrastructure and expertise is crucial. Moreover, establishing robust data governance frameworks and engaging communities are essential for leveraging metagenomics to advance scientific knowledge and deliver tangible health and economic benefits. With strategic planning and collaboration, Africa can harness the transformative potential of wastewater metagenomics to improve disease surveillance, combat AMR, and foster scientific innovation, contributing significantly to sustainable development and improved quality of life.},
}

@article {pmid39704517,
year = {2024},
author = {Agudelo-Romero, P and Caparros-Martin, JA and Sharma, A and Saladié, M and Sly, PD and Stick, SM and O'Gara, F and , },
title = {Virome assembly reveals draft genomes of native Pseudomonas phages isolated from a paediatric bronchoalveolar lavage sample.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0103024},
doi = {10.1128/mra.01030-24},
pmid = {39704517},
issn = {2576-098X},
abstract = {We present lung virome data recovered through shotgun metagenomics in bronchoalveolar lavage fluid from an infant with cystic fibrosis, who tested positive for Stenotrophomonas maltophilia infection. Using a bioinformatic pipeline for virus characterization in shotgun metagenomic data, we identified five viral contigs representing Pseudomonas phages classified as Caudoviricetes.},
}

@article {pmid39703701,
year = {2024},
author = {Jia, X and Li, Q and Yang, X and Li, D and Jin, Z},
title = {Comparative analysis of the gut microbiota composition and diversity in Erinaceus amurensis from the Wandashan Mountain range area based on metagenomics.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1479352},
pmid = {39703701},
issn = {1664-302X},
abstract = {This study aimed to preliminarily explore the composition and diversity of intestinal bacteria in Erinaceus amurensis during breeding period, aiding in the field rescue and population conservation efforts of Erinaceus amurensis. This also provides foundational data for further research on the prevention and screening of Emerging Zoonotic Infectious Diseases and the experimental animalization of wild Erinaceus amurensis. Between April and July 2023, we collected 13 fresh fecal samples from Erinaceus amurensis at the Sishan Forest Farm in Jidong County, Heilongjiang Province, situated within the Wandashan Mountain range. Utilizing metagenomic sequencing technology, we conducted a comparative analysis of the gut microbiota composition and diversity in wild Erinaceus amurensis across different genders and between adult and fetal individuals within the same habitat. Our results revealed significant differences (P < 0.01) in the classification and diversity of gut microbiota between genders and between adult and fetal Erinaceus amurensis. Specifically, the dominant bacterial groups in the gut of Erinaceus amurensis were Pseudomonas, Proteobacteria, and Enterobacteriaceae. In male and female Erinaceus amurensis, the dominant bacterial groups were Pseudomonas, Bacteroides, and Firmicutes, with variations in bacterial abundance and diversity. While male and female Erinaceus amurensis exhibited similar microbial compositions, they displayed significant differences in specific bacterial classifications. The dominant bacterial group in fetal Erinaceus amurensis was Proteobacteria, which demonstrated lower diversity and abundance compared to the adult group. Furthermore, the types and abundance of pathogenic or opportunistic pathogens in the gut of fetal Erinaceus amurensis and male Erinaceus amurensis were higher than those in female Erinaceus amurensis. The analysis of experimental results indicates that Erinaceus amurensis in this region either have or are at risk of developing inflammation related to the intestinal and urinary tracts, as well as skin-related issues. Consequently, it is advised that forestry and wildlife conservation personnel in this area prioritize treatment against these specific pathogens when conducting rescue operations for Erinaceus amurensis in the wild.},
}

@article {pmid39703432,
year = {2024},
author = {Zhao, J and Pierre Both, J and Konstantinidis, KT},
title = {Approximate nearest neighbor graph provides fast and efficient embedding with applications for large-scale biological data.},
journal = {NAR genomics and bioinformatics},
volume = {6},
number = {4},
pages = {lqae172},
pmid = {39703432},
issn = {2631-9268},
abstract = {Dimension reduction (DR or embedding) algorithms such as t-SNE and UMAP have many applications in big data visualization but remain slow for large datasets. Here, we further improve the UMAP-like algorithms by (i) combining several aspects of t-SNE and UMAP to create a new DR algorithm; (ii) replacing its rate-limiting step, the K-nearest neighbor graph (K-NNG), with a Hierarchical Navigable Small World (HNSW) graph; and (iii) extending the functionality to DNA/RNA sequence data by combining HNSW with locality sensitive hashing algorithms (e.g. MinHash) for distance estimations among sequences. We also provide additional features including computation of local intrinsic dimension and hubness, which can reflect structures and properties of the underlying data that strongly affect the K-NNG accuracy, and thus the quality of the resulting embeddings. Our library, called annembed, is implemented, and fully parallelized in Rust and shows competitive accuracy compared to the popular UMAP-like algorithms. Additionally, we showcase the usefulness and scalability of our library with three real-world examples: visualizing a large-scale microbial genomic database, visualizing single-cell RNA sequencing data and metagenomic contig (or population) binning. Therefore, annembed can facilitate DR for several tasks for biological data analysis where distance computation is expensive or when there are millions to billions of data points to process.},
}

@article {pmid39703404,
year = {2024},
author = {Huang, K and Zhang, X and Xiong, N and Sun, L and Zhao, X and Zhou, K and Wu, J},
title = {First metagenomic sequencing for the analysis of microbial community populations of adults and pupae of Melophagus ovinus in Xinjiang, China.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1462772},
pmid = {39703404},
issn = {2297-1769},
abstract = {INTRODUCTION: Melophagus ovinus, a parasite on the body surface of sheep, directly attacks the host through biting and sucking blood and may also transmit pathogens in the process. There are currently only a few studies on the microbial composition of M. ovinus, while there are no such studies on pupae.

METHODS: In this study, samples AT-1 to AT-4 each contained four M. ovinus individuals, while sample AT-5 comprised four M. ovinus pupae, all used for metagenomic sequencing and analysis. Melophagus ovinus adults and pupae were collected from four regions in Xinjiang, China. DNA was extracted from the samples, amplified, and sequenced using the Illumina Novaseq 6000 System; finally, the sequencing data were analyzed using molecular biology software.

RESULTS AND DISCUSSION: From all samples, a total of 32 phyla, comprising 372 genera and 1,037 species, were detected. The highest microbial diversity was observed in Kuqa City (AT-2) and Qira County (AT-4). Pupae exhibited 40 unique microbial genera (AT-5) but did not have the highest microbial diversity. Proteobacteria was the dominant phylum in all samples. The dominant genera included Bartonella, Wolbachia, Pseudomonas, and Arsenophonus. This is the first study to report most of the bacteria (e.g., Pseudomonas versuta and Arsenophonus nasoniae), fungi (e.g., Saitoella complicata), viruses (e.g., Orf virus and Wolbachia phage WO), and protozoa (e.g., Trypanosoma theileri and Babesia bigemina) in M. ovinus. This study has enriched the microbial diversity data of M. ovinus, and the pathogens it carries may pose a threat to public health safety and the economy of related industries, necessitating further research to develop effective biological control strategies.},
}

@article {pmid39702789,
year = {2024},
author = {Kaur, S and Patel, BCK and Collen, A and Malhotra, R},
title = {The microbiome and the eye: a new era in ophthalmology.},
journal = {Eye (London, England)},
volume = {},
number = {},
pages = {},
pmid = {39702789},
issn = {1476-5454},
abstract = {The human microbiome has progressively been recognised for its role in various disease processes. In ophthalmology, complex interactions between the gut and distinct ocular microbiota within each structure and microenvironment of the eye has advanced our knowledge on the multi-directional relationships of these ecosystems. Increasingly, studies have shown that modulation of the microbiome can be achieved through faecal microbiota transplantation and synbiotics producing favourable outcomes for ophthalmic diseases. As ophthalmologists, we are obliged to educate our patients on measures to cultivate a healthy gut microbiome through a range of holistic measures. Further integrative studies combining microbial metagenomics, metatranscriptomics and metabolomics are necessary to fully characterise the human microbiome and enable targeted therapeutic interventions.},
}

@article {pmid39702650,
year = {2024},
author = {Vriend, EMC and Galenkamp, H and Herrema, H and Nieuwdorp, M and van den Born, BH and Verhaar, BJH},
title = {Machine learning analysis of sex and menopausal differences in the gut microbiome in the HELIUS study.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {152},
pmid = {39702650},
issn = {2055-5008},
support = {189235//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 09150182010020/ZONMW_/ZonMw/Netherlands ; 101141346/ERC_/European Research Council/International ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; Female ; *Machine Learning ; Male ; Middle Aged ; *Menopause ; Aged ; Sex Factors ; Metagenomics/methods ; Adult ; Cohort Studies ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; },
abstract = {Sex differences in the gut microbiome have been examined previously, but results are inconsistent, often due to small sample sizes. We investigated sex and menopausal differences in the gut microbiome in a large multi-ethnic population cohort study, including 5166 participants. Using machine learning models, we revealed modest associations between sex and menopausal status, and gut microbiota composition (AUC 0.61-0.63). After adjustments for age, cardiovascular risk factors, and diet, a part of the associations of the highest-ranked gut microbes with sex were attenuated, but most associations remained significant. In contrast, most associations with menopausal status were driven by age and lost significance after adjustment. Using pathway analyses on metagenomic data, we identified sex differences in vitamin B6 synthesis and stachyose degradation pathways. Since some of sex differences in gut microbiome composition and function could not be explained by covariates, we recommend sex stratification in future microbiome studies.},
}

*Gastrointestinal Microbiome
Humans
Female
*Machine Learning
Male
Middle Aged
*Menopause
Aged
Sex Factors
Metagenomics/methods
Adult
Cohort Studies
Bacteria/classification/genetics/isolation & purification
Feces/microbiology

@article {pmid39702405,
year = {2024},
author = {Soufi, HH and Porch, R and Korchagina, MV and Abrams, JA and Schnider, JS and Carr, BD and Williams, MA and Louca, S},
title = {Taxonomic variability and functional stability across Oregon coastal subsurface microbiomes.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1663},
pmid = {39702405},
issn = {2399-3642},
mesh = {Oregon ; *Microbiota/genetics ; *Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Phylogeny ; Metagenomics/methods ; Biodiversity ; },
abstract = {The factors shaping microbial communities in marine subsurface sediments remain poorly understood. Here, we analyzed the microbiome of subsurface sediments within a depth range of 1.6-1.9 m, at 10 locations along the Oregon coast. We used metagenomics to reconstruct the functional structure and 16S rRNA gene amplicon sequencing to estimate the taxonomic composition of microbial communities, accompanied by physicochemical measurements. Functional community structure, in terms of the proportions of various gene groups, was remarkably stable across samples, despite the latter covering a region spanning over 300 km. In contrast, taxonomic composition was highly variable, especially at the level of amplicon sequence variants (ASVs) and operational taxonomic units (OTUs). Mantel correlation tests between compositional dissimilarities and geographic distances revealed only a moderate influence of distance on composition. Regression models predicting taxonomic dissimilarities and considering up to 20 physicochemical variables as predictors, almost always failed to select a significant predictor, suggesting that variation in local conditions does not explain the high taxonomic variability. Permutation null models of community assembly revealed that taxa tend to strongly segregate, i.e., exclude each other. We conclude that biological interactions are important drivers of taxonomic variation in subsurface sediments, and that this variation can decouple from functional structure.},
}

Oregon
*Microbiota/genetics
*Geologic Sediments/microbiology
*RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Phylogeny
Metagenomics/methods
Biodiversity

@article {pmid39702006,
year = {2024},
author = {Demirkan, A and van Dongen, J and Finnicum, CT and Westra, HJ and Jankipersadsing, S and Willemsen, G and Ijzerman, RG and Boomsma, DI and Ehli, EA and Bonder, MJ and Fu, J and Franke, L and Wijmenga, C and de Geus, EJC and Kurilshikov, A and Zhernakova, A},
title = {Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1224},
pmid = {39702006},
issn = {1471-2164},
mesh = {*DNA Methylation ; *Gastrointestinal Microbiome/genetics ; Humans ; *Epigenome ; *Genome-Wide Association Study ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; CpG Islands/genetics ; Middle Aged ; Adult ; Netherlands ; },
abstract = {Microbiome influences multiple human systems, but its effects on gene methylation is unknown. We investigated the relations between gene methylation in blood and the abundance of common gut bacteria profiled by 16s rRNA gene sequencing in two population-based Dutch cohorts: LifeLines-Deep (LLD, n = 616, discovery) and the Netherlands Twin Register (NTR, n = 296, replication). In LLD, we also explored microbial pathways using data generated by shotgun metagenomic sequencing (n = 683). Methylation in both cohorts was profiled in blood samples using the Illumina 450K array. Discovery and replication analysis identified two independent CpGs associated with the genus Eggerthella: cg16586104 (Pmeta-analysis = 3.21 × 10[-11]) and cg12234533 (Pmeta-analysis = 4.29 × 10[-10]). We also show that microbiome can mediate the effect of environmental factors on host gene methylation. In this first association study linking epigenome to microbiome, we found and replicated the associations of two CpGs to the abundance of genus Eggerthella and identified microbiome as a mediator of the exposome. These associations are observational and suggest further investigation in larger and longitudinal set-ups.},
}

*DNA Methylation
*Gastrointestinal Microbiome/genetics
Humans
*Epigenome
*Genome-Wide Association Study
Male
Female
RNA, Ribosomal, 16S/genetics
CpG Islands/genetics
Middle Aged
Adult
Netherlands

@article {pmid39701966,
year = {2024},
author = {Oskolkov, N and Sandionigi, A and Götherström, A and Canini, F and Turchetti, B and Zucconi, L and Mimmo, T and Buzzini, P and Borruso, L},
title = {Unraveling the ancient fungal DNA from the Iceman gut.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1225},
pmid = {39701966},
issn = {1471-2164},
mesh = {*DNA, Ancient/analysis ; Humans ; *DNA, Fungal/genetics ; Metagenomics/methods ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Mummies/microbiology ; Computational Biology/methods ; Fungi/genetics/classification ; },
abstract = {BACKGROUND: Fungal DNA is rarely reported in metagenomic studies of ancient samples. Although fungi are essential for their interactions with all kingdoms of life, limited information is available about ancient fungi. Here, we explore the possibility of the presence of ancient fungal species in the gut of Ötzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria).

METHODS: A robust bioinformatic pipeline has been developed to detect and authenticate fungal ancient DNA (aDNA) from muscle, stomach, small intestine, and large intestine samples.

RESULTS: We revealed the presence of ancient DNA associated with Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, which were abundant in the stomach and small intestine and absent in the large intestine and muscle samples.

CONCLUSION: We suggest that Ötzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they persisted in his gut after his death due to their adaptability to harsh and cold environments. This suggests the potential co-occurrence of ancient humans with opportunistic fungal species and proposes and validates a conservative bioinformatic approach for detecting and authenticating fungal aDNA in historical metagenomic samples.},
}

*DNA, Ancient/analysis
Humans
*DNA, Fungal/genetics
Metagenomics/methods
Gastrointestinal Microbiome/genetics
Gastrointestinal Tract/microbiology
Mummies/microbiology
Computational Biology/methods
Fungi/genetics/classification

@article {pmid39701896,
year = {2024},
author = {Haas, AL and Bradley, BT and Hanson, KE},
title = {Recent Developments in Culture-Independent Fungal Diagnostics.},
journal = {Infectious disease clinics of North America},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.idc.2024.11.004},
pmid = {39701896},
issn = {1557-9824},
abstract = {Culture-independent diagnostics for fungi potentially offer increased sensitivity and more rapid results relative to culture. Recent developments include new platforms for fungal cell wall antigen detection, commercially available targeted nucleic acid amplification tests, and the use of sequencing-based technologies for the detection and identification of a broad range of fungal pathogens. Although these tests are not without limitations, many more commercially available platforms now exist, and efforts to increase the standardization of laboratory-developed tests are ongoing. Additionally, implementation studies are beginning to delineate the optimal use cases for molecular diagnostics across a range of fungal diseases and at-risk populations.},
}

@article {pmid39701829,
year = {2024},
author = {McAlister, JS and Blum, MJ and Bromberg, Y and Fefferman, NH and He, Q and Lofgren, E and Miller, DL and Schreiner, C and Candan, KS and Szabo-Rogers, H and Reed, JM},
title = {An interdisciplinary perspective of the built-environment microbiome.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae166},
pmid = {39701829},
issn = {1574-6941},
abstract = {The built environment provides an excellent setting for interdisciplinary research on the dynamics of microbial communities. The system is simplified compared to many natural settings, and to some extent the entire environment can be manipulated, from architectural design to materials use, air flow, human traffic, and capacity to disrupt microbial communities through cleaning. Here we provide an overview of the ecology of the microbiome in the built environment. We address niche space and refugia, population and community (metagenomic) dynamics, spatial ecology within a building, including the major microbial transmission mechanisms, as well as evolution. We also address landscape ecology, connecting microbiomes between physically separated buildings. At each stage we pay particular attention to the actual and potential interface between disciplines, such as ecology, epidemiology, materials science, and human social behavior. We end by identifying some opportunities for future interdisciplinary research on the microbiome of the built environment.},
}

@article {pmid39701698,
year = {2024},
author = {Bao, YY and Li, MX and Gao, XX and Wei, WJ and Huang, WJ and Lin, LZ and Wang, H and Zheng, NN and Li, HK},
title = {[Astragalus polysaccharides improve adipose tissue aging in naturally aged mice via indole-3-lactic acid].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {49},
number = {22},
pages = {5998-6007},
doi = {10.19540/j.cnki.cjcmm.20240508.401},
pmid = {39701698},
issn = {1001-5302},
mesh = {Animals ; Mice ; *Aging/drug effects ; *Adipose Tissue/drug effects/metabolism ; *Polysaccharides/pharmacology ; *Indoles/pharmacology ; Male ; *Astragalus Plant/chemistry ; 3T3-L1 Cells ; Humans ; Adipocytes/drug effects/metabolism/cytology ; Mice, Inbred C57BL ; Cellular Senescence/drug effects ; Drugs, Chinese Herbal/pharmacology/administration & dosage ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Plant polysaccharides are effective components that widely present in traditional Chinese medicine(TCM), exhibiting rich biological activities. However, as most plant polysaccharides cannot be directly absorbed and utilized by the human digestive system, it is now believed that their mode of action mainly involves interaction with intestinal microbiota, leading to the production of functional small molecules. The efficacy of Astragalus polysaccharide(APS) is extensive, including weight loss, improvement of fatty liver, reduction of blood lipids, and enhancement of insulin sensitivity, which may also be related to the regulation of intestinal microbiota. Adipose tissue senescence is an important characteristic of the physiological aging process in the body, often occurring prior to the aging of other important organs. Its main features include the accumulation of senescent cells and exacerbation of inflammation within the tissue. Therefore, to explore the potential protective effects of APS on aging, the improvement of adipose tissue aging phenotype in naturally aging mice was observed using APS, and combined with metagenomic metabolomics, corresponding microbial metabolic functional molecules were identified. Furthermore, functional tests in cell aging models were conducted. The results showed that APS significantly improved the adipocyte aging characteristics of naturally aging mice: specifically reducing aging-induced adipocyte hypertrophy; decreasing the protein expression of aging markers cyclin-dependent kinase inhibitor p21(P21) and multiple tumor suppressor 1(P16); lowering the tissue inflammation reaction. Metagenomic metabolomic analysis of serum from mice in each group revealed that APS significantly increased the content of indole-3-lactic acid(ILA) in naturally aging mice. Further in vitro studies showed that ILA could improve the aging of 3T3-L1 mouse embryonic fibroblasts induced by bleomycin, reduce the protein expression of the aging marker P21, alleviate inflammation, and enhance the ability of preadipocytes to mature. Therefore, APS had the efficacy of protecting naturally aging mice, and its action may be related to the increase in the intestinal microbiota metabolite ILA. This study suggested that TCM may serve as an important entry point for explaining the mechanism of action of TCM by regulating intestinal microbiota and their functional metabolites.},
}

Animals
Mice
*Aging/drug effects
*Adipose Tissue/drug effects/metabolism
*Polysaccharides/pharmacology
*Indoles/pharmacology
Male
*Astragalus Plant/chemistry
3T3-L1 Cells
Humans
Adipocytes/drug effects/metabolism/cytology
Mice, Inbred C57BL
Cellular Senescence/drug effects
Drugs, Chinese Herbal/pharmacology/administration & dosage
Gastrointestinal Microbiome/drug effects

@article {pmid39701526,
year = {2024},
author = {Sinclair, KD},
title = {Developmental epigenetics: Understanding genetic and sexually dimorphic responses to parental diet and outcomes following assisted reproduction.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25811},
pmid = {39701526},
issn = {1525-3198},
abstract = {The developmental integrity and wellbeing of offspring are influenced by events that occur in utero, particularly around the time of conception. While extraneous factors such as environmental temperature and exposure to environmental chemicals can each have a bearing on these events, the epigenetic mechanisms that direct cellular differentiation during early development in ruminants are best described for studies which have investigated the effects of parental nutrition or pregnancy outcomes following assisted reproduction. In this article the case is made that the genetic constitution of an individual directs epigenetic responses to environmental stimuli, and consideration in this regard is also given to the origins of sexual dimorphism and mechanisms of germline intergenerational inheritance. These aspects are considered in the context of epigenetic modifications that take place during the normal course of gametogenesis and embryogenesis, and again following either dietary or procedural interventions such as embryo culture. A recurring feature of such interventions, irrespective of species, is that one carbon metabolic pathways are invariably disrupted, and this affects the provision of methyl groups for chromatin and RNA methylation. Inter-specific variation in how these pathways operate, both within the liver and in germ cells, indicates that ruminants may be particularly sensitive in this regard. Recent advances in genomic technologies should enable rapid progress in these areas. Knowledge gained can be integrated into breed improvement programs and used to tailor management practices to specific breeds and strains (including sexes) within breeds. Ultimately, consideration should be given to integrating metagenomics into analyses of genetic-directed epigenetic programming of animal development.},
}

@article {pmid39701375,
year = {2024},
author = {Corbett, GA and Corcoran, S and Feehily, C and Soldati, B and Rafferty, A and MacIntyre, DM and Cotter, PD and McAuliffe, FM},
title = {Preterm-birth-prevention with Lactobacillus Crispatus oral probiotics: Protocol for a double blinded randomised placebo-controlled trial (the PrePOP study).},
journal = {Contemporary clinical trials},
volume = {},
number = {},
pages = {107776},
doi = {10.1016/j.cct.2024.107776},
pmid = {39701375},
issn = {1559-2030},
abstract = {INTRODUCTION: Effective spontaneous preterm birth (sPTB) prevention is an urgent unmet clinical need. Vaginal depletion of Lactobacillus crispatus is linked to sPTB. This trial will investigate impact of an oral Lactobacillus spp. probiotic product containing an L. crispatus strain with other Lactobacilli spp., on the maternal vaginal and gut microbiome in pregnancies high-risk for sPTB.

METHODS: A double-blind, placebo-controlled, randomised trial will be performed at the National Maternity Hospital Dublin, Ireland. Inclusion criteria are women with history of sPTB or mid-trimester loss, cervical surgery (cone biopsy or two previous large-loop-excision-of-transformation-zone) or uterine anomaly. The intervention is oral supplementation for twelve weeks with probiotic or identical placebo. The probiotic will contains: ◦ 4 billion CFU Lactobacillus crispatus Lbv 88(2x10[9]CFU/Capsule) ◦ 4 billion CFU Lactobacillus rhamnosus Lbv 96(2x10[9]CFU/Capsule) ◦ 0.8 billion CFU Lactobacillus jensenii Lbv 116(0.4x10[9]CFU/Capsule) ◦ 1.2 billion CFU Lactobacillus gasseri Lbv 150(0.6x10[9]CFU/Capsule) Investigators and participants will be blinded to assignment.

RESULTS: The primary outcome is detectable L. crispatus in the vaginal microbiome after twelve weeks of treatment, measured using high-throughput DNA sequencing. A total of 126 women are required to detect a 25 % increase in detectable L. crispatus. Secondary outcomes include impact of intervention on the gut microbiome and metabolome, rate of sPTB and mid-trimester loss, neonatal outcomes and maternal morbidity.

CONCLUSIONS: This randomised trial will investigate ability of an oral probiotic containing L. crispatus to increase its abundance in the vaginal microbiome, both directly by horizontal transfer and indirectly via microbiome and metabolome of the gut.},
}

@article {pmid39701354,
year = {2024},
author = {Liu, J and Zhou, M and Zhou, L and Dang, R and Xiao, L and Tan, Y and Li, M and Yu, J and Zhang, P and Hernández, M and Lichtfouse, E},
title = {Methane production related to microbiota in dairy cattle feces.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120642},
doi = {10.1016/j.envres.2024.120642},
pmid = {39701354},
issn = {1096-0953},
abstract = {Methane (CH4) emission from livestock feces, led by ruminants, shows a profound impact on global warming. Despite this, we have almost no information on the syntrophy of the intact microbiome metabolisms, from carbohydrates to the one-carbon units, covering multiple stages of ruminant development. In this study, syntrophic effects of polysaccharide degradation and acetate-producing bacteria, and methanogenic archaea were revealed through metagenome-assembled genomes from water saturated dairy cattle feces. Although CH4 is thought to be produced by archaea, more edges, nodes, and balanced interaction types revealed by network analysis provided a closed bacteria-archaea network. The CH4 production potential and pathways were further evaluated through dynamic, thermodynamic and [13]C stable isotope analysis. The powerful CH4 production potential benefited from the metabolic flux: classical polysaccharides, soluble sugar (glucose, galactose, lactose), acetate, and CH4 produced via typical acetoclastic methanogenesis. In comparison, a cooperative model dominated by hydrogenotrophic methanogenic archaea presented a weak ability to generate CH4. Our findings comprehensively link carbon and CH4 metabolism paradigm to specific microbial lineages which are shaped related to developmental stages of the dairy cattle, directing influencing global warming from livestock and waste treatment.},
}

@article {pmid39700995,
year = {2024},
author = {Xu, X and Hao, Y and Cai, Z and Cao, Y and Jia, W and Zhao, J and White, JC and Ma, C},
title = {Nanoscale‑boron nitride positively alters rhizosphere microbial communities and subsequent cucumber (Cucumis sativa) growth: A metagenomic analysis.},
journal = {The Science of the total environment},
volume = {958},
number = {},
pages = {178115},
doi = {10.1016/j.scitotenv.2024.178115},
pmid = {39700995},
issn = {1879-1026},
abstract = {Boron (B) deficiency affects over 132 crop species globally, making effective B supplement crucial for enhancing agricultural yield and health. This study explores an innovative application of nanoscale boron nitride (nano-BN) as a sustainable solution for addressing B deficiency in crops. Cucumber seedlings were treated with different contents of nano-BN under greenhouse conditions and both B and N ionic treatments were set as comparisons. Results show that soil application of 10 mg/kg nano-BN achieved a remarkable 15.8 % increase in fresh weight compared to the control. Notably, nano-BN exhibited superior efficiency in providing essential micronutrients without inducing toxicity as compared to traditional ionic B sources. Phytohormone correlation analysis reveals that nano-BN application significantly enhances levels of indole-3-acetic acid (IAA) and cytokinins while reducing abscisic acid (ABA), fostering optimal plant growth conditions. Furthermore, increases in dissolved organic matter (DOM) and dissolved organic carbon (DOC) levels in the rhizosphere improve nutrient availability and promote beneficial microbial activity in the soil as affected by nano-BN. Metagenomics techniques were used to investigate the impact of nano-BN on soil carbon and nitrogen cycling, alongside its effects on the soil microbiome. The upregulation of genes associated with fermentation pathways as affected by nano-BN suggests the enhanced carbon cycling. Additionally, nano-BN upregulated a number of functional genes involved in nitrogen-based processes, leading to a significant increase in microorganisms harboring nitrogen-fixing genes, including Phenylobacterium, Novosphingobium, and Reyranella. Overall, these findings provide valuable insight into the application of nano-BN in agriculture to sustainably increase crop productivity and enhance the efficiency of carbon and nitrogen cycling.},
}

@article {pmid39700989,
year = {2024},
author = {Liu, F and Zeng, J and Ding, J and Wang, C and He, Z and Liu, Z and Shu, L},
title = {Microbially-driven phosphorus cycling and its coupling mechanisms with nitrogen cycling in mangrove sediments.},
journal = {The Science of the total environment},
volume = {958},
number = {},
pages = {178118},
doi = {10.1016/j.scitotenv.2024.178118},
pmid = {39700989},
issn = {1879-1026},
abstract = {The phosphorus (P) cycle plays a crucial role in the biogeochemical cycling of mangrove sediments. However, the diversity of microbially-driven P-cycling and its coupling with nitrogen (N)-cycling remain poorly understood. In this study, we used metagenomic approaches to investigate microbial P-cycling and its potential interactions with N-cycling in mangrove sediments. Our results revealed that pH, total carbon, and total nitrogen were key environmental factors influencing the diversity of P-cycling microbial communities. Phosphorus metabolic pathways differed among mangrove sediment depths. In surface sediments (0-5 cm), microbial communities primarily acquired readily available inorganic phosphorus, whereas, in deeper sediments (>60 cm), they hydrolyzed more persistent triphosphates, reabsorbed nucleotides, and sourced free phosphate, reflecting a shift in phosphorus transport modes. We also identified glutamate metabolism as a potential pathway linking P-cycling with N-cycling, with these functions co-occurring in both contigs and genomes. Additionally, the diversity of microbial communities associated with the P-cycling increased with sediment depth, suggesting that microbially-driven P-cycling diversifies as depth increases. This study provides new insights into P-cycling and its potential coupling with N-cycling through glutamate metabolism, its coupling with N-cycling through glutamate metabolism.},
}

@article {pmid39700951,
year = {2024},
author = {Gu, H and Hu, X and Zhang, J and Li, Y and Yu, Z and Liu, J and Sui, Y and Jin, J and Liu, X and Wang, G},
title = {Biogeographic patterns of viral communities, ARG profiles and virus-ARG associations in adjacent paddy and upland soils across black soil region.},
journal = {Journal of hazardous materials},
volume = {485},
number = {},
pages = {136909},
doi = {10.1016/j.jhazmat.2024.136909},
pmid = {39700951},
issn = {1873-3336},
abstract = {Biogeographic distribution of prokaryotic and eukaryotic communities has been extensively studied. Yet, our knowledge of viral biogeographic patterns, the corresponding driving factors and the virus-resistome associations is still limited. Here, using metagenomic analysis, we explored the viral communities and profiles of antibiotic resistance genes (ARGs) in 30 fields of paddy (rice soils, RS) and upland soils (corn soils, CS) at a regional scale across black soil region of Northeast China. Our finding revealed that viral communities displayed significant distance-decay relationships, and environmental variables largely dominated viral community patterns in agricultural soils. Compared to RS, viral community in CS harbored significantly higher viral α-diversity and distinct β-diversity, and exhibited a higher turnover along with environmental gradients and spatial distance. However, no clear latitudinal diversity gradient (LDG) pattern was observed in viral diversity over large-scale sampling for RS and CS, and heterogeneous distribution of soil viruses was well maintained over large-scale sampling. Soil pH was the important influential factor driving viral community, and the high soil nutrient levels negatively affected viral diversity. Uroviricota, Nucleocytoviricota and Artverviricota were the main viral phyla in agricultural soils, and virus-host linkages spanned 17 prokaryotic phyla, including Actinobacteriota and Proteobacteria. Besides, 2578 ARG subtypes were retrieved and conferred resistance to 27 types of antibiotics, in which multidrug was the predominant ARG type in Mollisols. Procrustes analysis showed the significant contribution of viral community to ARG profiles, which was more obvious in CS compared to RS. We identified 9.61 % and 11.4 % of soil viruses carried at least one ARG can infect multi-host in RS and CS. Furthermore, 43 and 77 complete viral metagenome-assembled genome (vMAG) were reconstructed in RS and CS, respectively. Notably, the lysogenic phages in RS contained 29.7 % of ARGs, a higher proportion than the 12.5 % found in CS. Overall, our study underscored the prevalent distribution of viral communities and ARG profiles at a large spatial scale, and the distinct ecological strategies of virus-ARG associations in adjacent paddy and upland soils.},
}

@article {pmid39700725,
year = {2024},
author = {Petersen, JF and Valk, LC and Verhoeven, MD and Nierychlo, MA and Singleton, CM and Dueholm, MKD and Nielsen, PH},
title = {Diversity and physiology of abundant Rhodoferax species in global wastewater treatment systems.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {1},
pages = {126574},
doi = {10.1016/j.syapm.2024.126574},
pmid = {39700725},
issn = {1618-0984},
abstract = {Wastewater treatment plants rely on complex microbial communities for bioconversion and removal of pollutants, but many process-critical species are still poorly investigated. One of these genera is Rhodoferax, an abundant core genus in wastewater treatment plants across the world. The genus has been associated with many metabolic traits such as iron reduction and oxidation and denitrification. We used 16S rRNA gene amplicon data to uncover the diversity and abundance of Rhodoferax species in Danish and global treatment plants. Publicly available metagenome-assembled genomes were analyzed based on phylogenomics to delineate species and assign taxonomies based on the SeqCode. The phylogenetic analysis of "Rhodoferax" revealed that species previously assigned to Rhodoferax in wastewater treatment plants should be considered as at least eight different genera, with five representing previously undescribed genera. Genome annotation showed potential for several key-bioconversions in wastewater treatment, such as nitrate reduction, carbohydrate degradation, and accumulations of various storage compounds. Iron oxidation and reduction capabilities were not predicted for abundant species. Species-resolved FISH-Raman was performed to gain an overview of the morphology and ecophysiology of selected taxa to clarify their potential role in global wastewater treatment systems. Our study provides a first insight into the functional and ecological characteristics of several novel genera abundant in global wastewater treatment plants, previously assigned to the Rhodoferax genus.},
}

@article {pmid39700724,
year = {2024},
author = {Mao, YL and Dong, XY and Tao, CQ and Wu, ZP and Shi, XW and Hou, J and Cui, HL},
title = {Natronorarus salvus gen. nov., sp. nov., Halalkalicoccus ordinarius sp. nov., and Halalkalicoccus salilacus sp. nov., halophilic archaea from a soda lake and two saline lakes, and proposal to classify the genera Halalkalicoccus and Natronorarus into Halalkalicoccaceae fam. nov. in the order Halobacteriales within the class Halobacteria.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {1},
pages = {126577},
doi = {10.1016/j.syapm.2024.126577},
pmid = {39700724},
issn = {1618-0984},
abstract = {Four novel halophilic archaeal strains CGA53[T], CG83[T], FCH27[T], and SEDH24 were isolated from a soda lake and two saline lakes in China, respectively. Strain CGA53[T] showed the highest 16S rRNA gene similarity (92.6%) to Salinilacihabitans rarus AD-4[T], and the other three strains were found to be related to Halalkalicoccus species with similarities of 97.6-98.3%. Metagenomic studies indicated that these four strains are low abundant inhabitants detected in these hypersaline environments, and only one MAG of Chagannuoer Soda Lake (CG) could be assigned to the genus Halalkalicoccus. Their growth occurred at 20-60 °C (optima, 42, 37, 37-42, and 35 °C), 0.9-5.1 M NaCl (optima, 3.9, 2.6, 3.5, and 3 M), and 0-1.0 M MgCl2 (optima, 0.5, 0.7, and 0.1) and pH 5.5-10.5 (optima, 9.0, 7.5, 7.0, and 7.0), respectively. Phylogenetic and phylogenomic analyses revealed that strains CG83[T], FCH27[T], and SEDH24 cluster with the current species of the genus Halalkalicoccus, and strain CGA53[T] forms an independent branch separated from this genus. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values among strains CGA53[T], CG83[T], FCH27[T], SEDH24, and the type species of the current genera within the class Halobacteria were 67.4-81.6%, 16.5-28.6% and 49.7-74.1%, respectively, clearly lower than the cutoff values for species demarcation. Strain CGA53[T] may represent a novel species of a new genus according to the cutoff value for genus demarcation of 65% AAI. Diverse differential phenotypic characteristics, such as nutrition, biochemical activities, antibiotic sensitivity, and H2S formation, were found among these four strains and Halalkalicoccus species. Genome-based classification supported that strains CGA53[T], CG83[T], FCH27[T], SEDH24, and the current species of Halalkalicoccus represent a novel family of the order Halobacteriales within the class Halobacteria.},
}

@article {pmid39700673,
year = {2024},
author = {Zhang, Z and Zhou, L and Li, H and Li, L and Liu, H},
title = {Diagnostic performance of metagenomic next-generation sequencing based on alveolar lavage fluid in unexplained lung shadows.},
journal = {Diagnostic microbiology and infectious disease},
volume = {111},
number = {3},
pages = {116651},
doi = {10.1016/j.diagmicrobio.2024.116651},
pmid = {39700673},
issn = {1879-0070},
abstract = {BACKGROUND: Unexplained lung shadows are challenging in respiratory medicine, with both infectious and non-infectious etiologies. Lung biopsy is definitive but invasive, prompting a need for non-invasive alternatives. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) is emerging as a promising diagnostic tool.

METHODS: We retrospectively analyzed 105 patients with unexplained lung shadows, collecting general information, mNGS results from BALF, and clinical diagnosis. We evaluated mNGS's diagnostic performance by comparing with final diagnosis.

RESULTS: mNGS showed good diagnostic performance in differentiating infectious from non-infectious causes. The specificity and accuracy for bacteria and fungi exceeded 90%, while the sensitivity and precision for fungi were lower than for bacteria. Atypical pathogens were frequently identified, especially in mixed infections.

CONCLUSIONS: mNGS of BALF is efficient in diagnosing infectious and non-infectious causes of unexplained lung shadows. While effective for bacteria and fungi detection, the sensitivity and precision for fungi are lower.},
}

@article {pmid39700412,
year = {2024},
author = {Duan, HN and Hearne, G and Polikar, R and Rosen, GL},
title = {The Naïve Bayes Classifier ++ for Metagenomic Taxonomic Classification-Query Evaluation.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btae743},
pmid = {39700412},
issn = {1367-4811},
abstract = {MOTIVATION: This study examines the query performance of the NBC ++ (Incremental Naive Bayes Classifier) program for variations in canonicality, k-mer size, databases, and input sample data size. We demonstrate that both NBC ++ and Kraken2 are influenced by database depth, with macro measures improving as depth increases. However, fully capturing the diversity of life, especially viruses, remains a challenge.

RESULTS: NBC ++ can competitively profile the superkingdom content of metagenomic samples using a small training database. NBC ++ spends less time training and can use a fraction of the memory than Kraken2 but at the cost of long querying time. Major NBC ++ enhancements include accommodating canonical k-mer storage (leading to significant storage savings) and adaptable and optimized memory allocation that accelerates query analysis and enables the software to be run on nearly any system. Additionally, the output now includes log-likelihood values for each training genome, providing users with valuable confidence information.

AVAILABILITY: Source code and Dockerfile are available at http://github.com/EESI/Naive_Bayes.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online, and databases are available at Zenodo records #11657719 and #11643985.},
}

@article {pmid39699489,
year = {2024},
author = {Souza, PJ and Fernandes, J and Coelho, TA and Cosentino, M and D'arc, M and Alves, PDG and Guterres, A and Vilar, EM and Lemos, ERS and Cordeiro-Estrela, P and Santos, AFA and Oliveira, RC},
title = {A newly bat-borne hantavirus detected in Seba's short-tailed bats (Carollia perspicillata) in the Brazilian Atlantic Rainforest.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {119},
number = {},
pages = {e240132},
doi = {10.1590/0074-02760240132},
pmid = {39699489},
issn = {1678-8060},
mesh = {Animals ; *Chiroptera/virology ; Brazil/epidemiology ; *Orthohantavirus/genetics/classification/isolation & purification ; *Phylogeny ; *Rainforest ; RNA, Viral/genetics/analysis ; Reverse Transcriptase Polymerase Chain Reaction ; Hantavirus Infections/veterinary/epidemiology/virology ; },
abstract = {BACKGROUND: Bat-borne hantaviruses have been identified worldwide but little is known about neotropical bats in the megadiverse biomes of the American continent. Although serological evidence has hinted at hantavirus circulation in Brazil, the scarce number of genomic detection represents a gap to understand viral diversity, prevalence, and ecology of bat-borne hantaviruses.

OBJECTIVE: We aim to investigate and evaluate the presence and prevalence of bat-borne hantavirus in the Brazilian Atlantic Forest.

METHODS: Here in, 97 lung and kidney tissue samples from bats captured in the Brazilian Atlantic Rainforest were submitted to hantavirus-specific nested reverse transcription-polymerase chain reaction (RT-PCR) targeted the hantaviral L segment and metagenomic analysis.

FINDINGS: Hantavirus RNA was detected in five tissue fragments of 20 Seba's short-tailed bats (Carollia perspicillata). Phylogenetic analysis, based on partial L-segment sequence using maximum likelihood method, demonstrated that the identified virus formed a monophyletic clade and a highly divergent bat-borne lineage comprising other recent strains found in the genus Carollia from South America.

MAIN CONCLUSIONS: Our findings suggest the presence of a novel bat-borne hantavirus in Brazil, tentatively named Mamanguape virus (MGPV). Additional genomic data will help to extend our knowledge about the classification of MGPV within the Hantaviridae family and the evolution origins of new world bat-borne hantaviruses.},
}

Animals
*Chiroptera/virology
Brazil/epidemiology
*Orthohantavirus/genetics/classification/isolation & purification
*Phylogeny
*Rainforest
RNA, Viral/genetics/analysis
Reverse Transcriptase Polymerase Chain Reaction
Hantavirus Infections/veterinary/epidemiology/virology