@article {pmid39045130,
year = {2024},
author = {Li, J and Zhou, J and Tan, Y and Hu, C and Meng, Q and Gao, J and Xing, L},
title = {Clinical characteristics and risk factors for mortality in pneumonia-associated acute respiratory distress syndrome patients: a single center retrospective cohort study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1396088},
pmid = {39045130},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; Male ; Risk Factors ; Female ; Middle Aged ; Aged ; *Respiratory Distress Syndrome/mortality ; *High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Intensive Care Units ; Adult ; Pneumonia/mortality ; },
abstract = {BACKGROUND: Pathogenic diversity may have contributed to the high mortality of pneumonia-associated acute respiratory distress syndrome (p-ARDS). Metagenomics next-generation sequencing (mNGS) serves as a valuable diagnostic tool for early pathogen identification. However, its clinical utility in p-ARDS remains understudied. There are still limited researches on the etiology, clinical characteristics and risk factors for 28-day mortality in p-ARDS patients.

METHODS: A single center retrospective cohort study of 75 p-ARDS patients was conducted. Patients were categorized into survival and deceased groups based on their 28-day outcomes. A comprehensive clinical evaluation was conducted, including baseline characteristics, laboratory indicators, outcomes and pathogen identification by mNGS and traditional microbiological testing. We then evaluated the diagnostic value of mNGS and identified clinical characteristics and risk factors for 28-day mortality in p-ARDS.

RESULT: The overall ICU mortality was 26.67%, and the 28-day mortality was 57.33%, with 32 cases (42.67%) in the survival group, and 43 cases (57.33%) in the deceased group. Patients in the deceased group were older than those in the survival group (68(59,73) years vs. 59(44,67) years, P=0.04). The average lengths of ICU and hospital stay were 9(5,13) days and 14(7,21) days, respectively. The survival group had longer lengths of ICU and hospital stay (ICU: 11(7,17) days and hospital: 17(9,27) days) compared to the deceased group (ICU: 8(4,11) days and hospital: 12(6,19) days) (P<0.05). Survival patients exhibited lower Acute Physiology and Chronic Health Evaluation (APACHE) II score on the 3rd and 7th days, higher lymphocyte counts, higher CD3[+] and CD8[+] T cell counts compared to deceased patients (P<0.05). Multivariate logistic regression analysis identified age, APACHE II scores on 3rd and 7th days, CD8[+] T cell count and length of ICU as independent risk factors for 28-day mortality in p-ARDS patients. mNGS demonstrated a significantly higher overall pathogen detection rate (70/75, 93.33%) compared to the traditional method (50/75, 66.67%, P=0.022). The average turnaround time (TAT) for mNGS was significantly shorter at 1(1,1) day compared to 4(3,5) days for the traditional method (P<0.001).

CONCLUSION: Metagenome next-generation sequencing can be used as a valuable tool for identifying pathogens in p-ARDS, reducing diagnostic time and improving accuracy. Early application of mNGS alongside traditional methods is recommended for p-ARDS. Furthermore, older age, higher APACHE II scores, lower lymphocyte counts and lymphocyte subset counts were associated with increased mortality in p-ARDS patients, highlighting the importance of timely assessment of immune status and disease severity, especially in elderly.},
}

Humans
Retrospective Studies
Male
Risk Factors
Female
Middle Aged
Aged
*Respiratory Distress Syndrome/mortality
*High-Throughput Nucleotide Sequencing
Metagenomics/methods
Intensive Care Units
Adult
Pneumonia/mortality

@article {pmid39045110,
year = {2024},
author = {Pan, Y and Qian, J and Wang, G and Zhao, H},
title = {Infective Endocarditis Caused by Streptococcus Sinensis in a Patient with Bioprosthetic Aortic Valve: A Case Report and Literature Review.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {2957-2964},
pmid = {39045110},
issn = {1178-6973},
abstract = {BACKGROUND: Infective endocarditis caused by Streptococcus sinensis is exceedingly rare, with only limited cases reported. Here, we present the first documented case of prosthetic valve endocarditis attributed to Streptococcus sinensis.

CASE PRESENTATION: A 40-year-old Chinese female was admitted with a 45-day history of intermittent fever. The presumed diagnosis was a pulmonary infection and antibiotic therapies failed to alleviate her symptoms. On admission, infective endocarditis was suspected, considering the history of aortic valve replacement and recent dental procedure without prophylactic antibiotics. Transesophageal echocardiography disclosed a 3-millimeter vegetation in the prosthetic aortic valve, and metagenomic next-generation sequencing and mass spectrometry identified Streptococcus sinensis. The patient was diagnosed with infective endocarditis. Antibiotic treatments resulted in temporary clinical improvements, although fluctuations in temperature and inflammatory markers led to multiple attempts at antibiotic therapies. At last, the patient underwent an elective aortic valve replacement with a favorable prognosis.

CONCLUSION: In this case, we demonstrated prosthetic valve endocarditis caused by Streptococcus sinensis, which is an extremely rare pathogen. All reported endocarditis cases caused by Streptococcus sinensis were reviewed and summarized. Most of these patients had rheumatic heart diseases or congenital heart diseases. Antibiotic prophylaxis is important for high-risk procedures. Timely identification of the bacterium is crucial for diagnosis and treatment. Overall, infective endocarditis caused by this bacterium had a good prognosis.},
}

@article {pmid39045107,
year = {2024},
author = {Luo, W and Lin, X and Chen, Y and Luo, W and Zhang, H},
title = {Metagenomic Next-Generation Sequencing for Accurate Diagnosis of Pneumocystis jirovecii Pneumonia: A Comparative Study with Traditional Methods.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {2965-2974},
pmid = {39045107},
issn = {1178-6973},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a high-throughput sequencing technique that identifies a wide array of pathogens directly from clinical specimens. This study evaluates the diagnostic value of mNGS in Pneumocystis jirovecii pneumonia (PJP) and compares its efficacy with traditional detection methods, including Grocott's Methenamine Silver (GMS) staining, serum (1-3)-β-D-Glucan (BDG) testing, and Lactate Dehydrogenase (LDH) testing.

METHODS: Seventy-eight patients hospitalized between January 2022 and March 2023 with suspected pulmonary infections were included. Patients were eligible for mNGS if they exhibited symptoms such as fever, cough, dyspnea, or progressive hypoxemia, and met specific clinical criteria for PJP. Specimens obtained included bronchoalveolar lavage fluid, sputum, and peripheral blood. Positive rates and pathogen distributions detected by mNGS and traditional methods were compared.

RESULTS: In the PJP group, 25%, 37.5%, and 9.38% of patients had solid organ tumors, corticosteroid use, and skin diseases, respectively, significantly higher than in the non-PJP group. The sensitivity and specificity of mNGS were both 100%, significantly higher than those of serum BDG (sensitivity 50%, specificity 81.8%) and LDH (sensitivity 9.3%, specificity 91.3%). Significant differences in microbial composition between the PJP and Non-PJP groups were observed. mNGS detected multiple mixed pathogens in 96.88% of PJP cases, with 68.75% exhibiting mixed bacterial and viral infections. Notably, 71% of patients improved following antibacterial treatment based on mNGS results.

CONCLUSION: mNGS technology shows superior sensitivity and specificity in diagnosing PJP and guides precise treatment for complex pulmonary infections.},
}

@article {pmid39044955,
year = {2024},
author = {Perez-Restrepo, LS and Ciuoderis, K and Usuga, J and Moreno, I and Vargas, V and Arévalo-Arbelaez, AJ and Berg, MG and Cloherty, GA and Hernández-Ortiz, JP and Osorio, JE},
title = {Mayaro Virus as the cause of Acute Febrile Illness in the Colombian Amazon Basin.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1419637},
pmid = {39044955},
issn = {1664-302X},
abstract = {INTRODUCTION: Mayaro Fever (MF) is a tropical disease caused by the Mayaro virus (MAYV), with outbreaks documented in Latin America.

METHODS: A hospital-based fever surveillance in Leticia, Colombian Amazon, collected sera from 1,460 patients aged 5-89 between December 2020 and April 2023.

RESULTS: Dengue and malaria were the main diagnoses (19.4 and 5.8%, respectively), leaving 71.4% of cases unidentified after testing. Metagenomic sequencing and real-time RT-qPCR testing identified MAYV in two patients (25-year-old male and an 80-year-old female) exhibiting typical symptoms, of MF including rash, joint pain, and fever. Phylogenetics analysis of these two viruses revealed a close relationship to Peruvian strains within the MAYV D genotype.

DISCUSSION: The study of AFI in Leticia, Colombia, identified dengue as prevalent, with malaria, COVID-19, Influenza, and Zika viruses also detected. Despite extensive testing, most cases remained unexplained until metagenomic sequencing revealed MAYV, previously unseen in Colombia but known in neighboring countries.

CONCLUSION: This study presents the first near full-length genomes of MAYV in Colombia, highlighting the need for further seroprevalence studies and enhanced surveillance to understand and control the spread of the virus in the region.},
}

@article {pmid39044948,
year = {2024},
author = {Han, N and Peng, X and Zhang, T and Qiang, Y and Li, X and Zhang, W},
title = {Temporal dynamics and species-level complexity of Prevotella spp. in the human gut microbiota: implications for enterotypes and health.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1414000},
pmid = {39044948},
issn = {1664-302X},
abstract = {The concept of "enterotypes" in microbiome research has attracted substantial interest, particularly focusing on the abundance of Prevotella spp. in the human gut. In this study, the intricate dynamics of Prevotella spp. in the human gut microbiota was investigated, based on the metagenomic method. First, 239 fecal samples from individuals across four regions of China revealed a bimodal distribution, highlighting the abundance and variability in Prevotella spp. within the Chinese population. Second, the longitudinal cohort study included 184 fecal samples from 52 time points collected from seven individuals who demonstrated either the outbreaks or disappearances of Prevotella spp., emphasizing the transient nature of Prevotella abundance levels and suggesting shifts in Prevotella "enterotypes." Furthermore, a turnover of the dominant Prevotella spp. was observed, indicating the potential presence of diverse subtypes of Prevotella enterotype. Notably, the genomic analysis demonstrated the persistence of specific Prevotella strains within individuals over extended periods, highlighting the enduring presence of Prevotella in the human gut. In conclusion, by integrating the temporal and geographical scales in our research, we gained deeper insights into the dynamics of Prevotella, emphasizing the importance of considering the dynamics at the time and species level in gut microbiota studies and their implications on human health.},
}

@article {pmid39044909,
year = {2024},
author = {Moumen, B and Samba-Louaka, C and Kimpamboudi, VAM and Boumba, AM and Ngoma, HS and Samba-Louaka, A},
title = {Metagenomic data from gutter water in the city of Pointe-Noire, Republic of Congo.},
journal = {Data in brief},
volume = {55},
number = {},
pages = {110655},
pmid = {39044909},
issn = {2352-3409},
abstract = {After Amazonia, the Congo Basin represents the second-largest tropical rainforest area in the world. This basin harbours remarkable biodiversity, yet much of its microbiological diversity within its waters, soils, and populations remains largely unexplored and undiscovered. While many initiatives to characterize global biodiversity are being undertaken, few are conducted in Africa and none of them concern the Congo Basin specifically in urban areas. In this context, we assessed the microbial diversity present in gutter water in the city of Pointe-Noire, Congo. This town has interesting characteristics as the population density is high and it is located between the Atlantic Ocean and the forest of Mayombe in Central Africa. The findings illuminate the microbial composition of surface water in Pointe-Noire. The dataset allows the identification of putative new bacteria through the assembly of 81 meta-genome-assembled genomes. It also serves as a valuable primary resource for assessing the presence of antibiotic-resistant genes, offering a useful tool for monitoring risks by public health authorities.},
}

@article {pmid39044605,
year = {2024},
author = {Xu, H and Zhang, J and Wang, F and Chen, Y and Chen, H and Feng, Y and Hou, G and Zi, J and Zhang, M and Zhou, J and Deng, L and Lin, L and Zhang, X and Liu, S},
title = {Integration of metagenomics and metaproteomics in the intestinal lavage fluids benefits construction of discriminative model and discovery of biomarkers for HBV liver diseases.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e2400002},
doi = {10.1002/pmic.202400002},
pmid = {39044605},
issn = {1615-9861},
support = {2023YFC3402900//National Key Research and Development Program of China/ ; 2022YFA1304500//National Key Research and Development Program of China/ ; 2020YFE0202200//National Key Research and Development Program of China/ ; },
abstract = {Intestinal lavage fluid (IVF) containing the mucosa-associated microbiota instead of fecal samples was used to study the gut microbiota using different omics approaches. Focusing on the 63 IVF samples collected from healthy and hepatitis B virus-liver disease (HBV-LD), a question is prompted whether omics features could be extracted to distinguish these samples. The IVF-related microbiota derived from the omics data was classified into two enterotype sets, whereas the genomics-based enterotypes were poorly overlapped with the proteomics-based one in either distribution of microbiota or of IVFs. There is lack of molecular features in these enterotypes to specifically recognize healthy or HBV-LD. Running machine learning against the omics data sought the appropriate models to discriminate the healthy and HBV-LD IVFs based on selected genes or proteins. Although a single omics dataset is basically workable in such discrimination, integration of the two datasets enhances discrimination efficiency. The protein features with higher frequencies in the models are further compared between healthy and HBV-LD based on their abundance, bringing about three potential protein biomarkers. This study highlights that integration of metaomics data is beneficial for a molecular discriminator of healthy and HBV-LD, and reveals the IVF samples are valuable for microbiome in a small cohort.},
}

@article {pmid39044261,
year = {2024},
author = {Ma, S and Yin, Y and Guo, Y and Yao, C and Xu, S and Luo, Q and Yin, G and Wang, S and Wang, Q and Chen, H and Wang, R and Jin, L and Liang, G and Wang, H},
title = {The plasma viral communities associate with clinical profiles in a large-scale haematological patients cohort.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {137},
pmid = {39044261},
issn = {2049-2618},
mesh = {Humans ; Male ; Female ; *DNA Viruses/isolation & purification/genetics ; Middle Aged ; *Virus Diseases/blood/virology ; Adult ; *Hematologic Diseases/complications/blood ; *RNA Viruses/isolation & purification ; Virome ; Aged ; Torque teno virus/isolation & purification/genetics ; Cohort Studies ; Herpesvirus 4, Human/genetics/isolation & purification ; Young Adult ; },
abstract = {BACKGROUND: Haematological patients exhibit immune system abnormalities that make them susceptible to viral infections. Understanding the relationship between the virome in the blood plasma of haematological patients and their clinical characteristic is crucial for disease management. We aimed to explore the presence of viral pathogens and identify close associations between viral infections and various clinical features.

RESULTS: A total of 21 DNA viruses and 6 RNA viruses from 12 virus families were identified from 1383 patients. Patients with haematological diseases exhibited significantly higher diversity, prevalence, and co-detection rates of viral pathogens. During fever episodes, pathogen detection was notably higher, with Epstein-Barr virus (EBV) and Mucorales infections being the most probable culprits for fever symptoms in non-haematological patients. The detection rate of torque teno virus (TTV) significantly increases in haematological patients after transplantation and during primary lung infections. Additionally, TTV-positive patients demonstrate significantly higher absolute neutrophil counts, while C-reactive protein and procalcitonin levels are notably lower. Furthermore, TTV, cytomegalovirus, and parvovirus B19 (B19V) were found to be more prevalent in non-neutropenic patients, while non-viral pathogenic infections, such as Gram-negative bacteria and Mucorales, were more common in neutropenic patients. Pegivirus C (HPgV-C) infection often occurred post-transplantation, regardless of neutropenia. Additionally, some viruses such as TTV, B19V, EBV, and HPgV-C showed preferences for age and seasonal infections.

CONCLUSIONS: Analysis of the plasma virome revealed the susceptibility of haematological patients to plasma viral infections at specific disease stages, along with the occurrence of mixed infections with non-viral pathogens. Close associations were observed between the plasma virome and various clinical characteristics, as well as clinical detection parameters. Understanding plasma virome aids in auxiliary clinical diagnosis and treatment, enabling early prevention to reduce infection rates in patients and improve their quality of life. Video Abstract.},
}

Humans
Male
Female
*DNA Viruses/isolation & purification/genetics
Middle Aged
*Virus Diseases/blood/virology
Adult
*Hematologic Diseases/complications/blood
*RNA Viruses/isolation & purification
Virome
Aged
Torque teno virus/isolation & purification/genetics
Cohort Studies
Herpesvirus 4, Human/genetics/isolation & purification
Young Adult

@article {pmid39044244,
year = {2024},
author = {Glendinning, L and Jia, X and Kebede, A and Oyola, SO and Park, JE and Park, W and Assiri, A and Holm, JB and Kristiansen, K and Han, J and Hanotte, O},
title = {Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {138},
pmid = {39044244},
issn = {2049-2618},
mesh = {Animals ; *Chickens/microbiology ; Ethiopia ; *Altitude ; *Bacteria/classification/genetics/isolation & purification ; Gastrointestinal Microbiome/genetics ; Metagenome ; Cecum/microbiology ; Microbiota ; Biodiversity ; Phylogeny ; },
abstract = {BACKGROUND: Scavenging indigenous village chickens play a vital role in sub-Saharan Africa, sustaining the livelihood of millions of farmers. These chickens are exposed to vastly different environments and feeds compared to commercial chickens. In this study, we analysed the caecal microbiota of 243 Ethiopian village chickens living in different altitude-dependent agro-ecologies.

RESULTS: Differences in bacterial diversity were significantly correlated with differences in specific climate factors, topsoil characteristics, and supplemental diets provided by farmers. Microbiota clustered into three enterotypes, with one particularly enriched at high altitudes. We assembled 9977 taxonomically and functionally diverse metagenome-assembled genomes. The vast majority of these were not found in a dataset of previously published chicken microbes or in the Genome Taxonomy Database.

CONCLUSIONS: The wide functional and taxonomic diversity of these microbes highlights their importance in the local adaptation of indigenous poultry, and the significant impacts of environmental factors on the microbiota argue for further discoveries in other agro-ecologies. Video Abstract.},
}

Animals
*Chickens/microbiology
Ethiopia
*Altitude
*Bacteria/classification/genetics/isolation & purification
Gastrointestinal Microbiome/genetics
Metagenome
Cecum/microbiology
Microbiota
Biodiversity
Phylogeny

@article {pmid39044043,
year = {2024},
author = {Táncsics, A and Bedics, A and Banerjee, S and Soares, A and Baka, E and Probst, AJ and Kriszt, B},
title = {Stable-isotope probing combined with amplicon sequencing and metagenomics identifies key bacterial benzene degraders under microaerobic conditions.},
journal = {Biologia futura},
volume = {},
number = {},
pages = {},
pmid = {39044043},
issn = {2676-8607},
support = {FK 134439//National Research, Development and Innovation Office/ ; K 146358//National Research, Development and Innovation Office/ ; 899667//Horizon 2020/ ; },
abstract = {The primary aim of the present study was to reveal the major differences between benzene-degrading bacterial communities evolve under aerobic versus microaerobic conditions and to reveal the diversity of those bacteria, which can relatively quickly degrade benzene even under microaerobic conditions. For this, parallel aerobic and microaerobic microcosms were set up by using groundwater sediment of a BTEX-contaminated site and [13]C labelled benzene. The evolved total bacterial communities were first investigated by 16S rRNA gene Illumina amplicon sequencing, followed by a density gradient fractionation of DNA and a separate investigation of "heavy" and "light" DNA fractions. Results shed light on the fact that the availability of oxygen strongly determined the structure of the degrading bacterial communities. While members of the genus Pseudomonas were overwhelmingly dominant under clear aerobic conditions, they were almost completely replaced by members of genera Malikia and Azovibrio in the microaerobic microcosms. Investigation of the density resolved DNA fractions further confirmed the key role of these two latter genera in the microaerobic degradation of benzene. Moreover, analysis of a previously acquired metagenome-assembled Azovibrio genome suggested that benzene was degraded through the meta-cleavage pathway by this bacterium, with the help of a subfamily I.2.I-type catechol 2,3-dioxygenase. Overall, results of the present study implicate that under limited oxygen availability, some potentially microaerophilic bacteria play crucial role in the aerobic degradation of aromatic hydrocarbons.},
}

@article {pmid39043813,
year = {2024},
author = {Yuan, L and Zhu, XY and Lai, LM and Chen, Q and Liu, Y and Zhao, R},
title = {Clinical application and evaluation of metagenomic next-generation sequencing in pathogen detection for suspected central nervous system infections.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16961},
pmid = {39043813},
issn = {2045-2322},
support = {grant number 2021B723//Science and Technology Program of Jiangxi Traditional Chinese Medicine/ ; SKJP220212485//the Natural Science Foundation of Jiangxi Province/ ; 82260085//the National Natural Science Fund of China/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Central Nervous System Infections/diagnosis/microbiology/virology ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; Adult ; Retrospective Studies ; Aged ; Sensitivity and Specificity ; Adolescent ; Young Adult ; Child ; Child, Preschool ; Metagenome ; },
abstract = {Central nervous system Infections (CNSIs) is a disease characterized by complex pathogens, rapid disease progression, high mortality rate and high disability rate. Here, we evaluated the clinical value of metagenomic next generation sequencing (mNGS) in the diagnosis of central nervous system infections and explored the factors affecting the results of mNGS. We conducted a retrospective study to compare mNGS with conventional methods including culture, smear and etc. 111 suspected CNS infectious patients were enrolled in this study, and clinical data were recorded. Chi-square test were used to evaluate independent binomial variables, taking p < 0.05 as statistically significant threshold. Of the 111 enrolled cases, 57.7% (64/111) were diagnosed with central nervous system infections. From these cases, mNGS identified 39.6% (44/111) true-positive cases, 7.2% (8/111) false-positive case, 35.1% (39/111) true-negative cases, and 18.0% (20/111) false-negative cases. The sensitivity and specificity of mNGS were 68.7% (44/64) and 82.9% (39/47), respectively. Compared with culture, mNGS provided a higher pathogen detection rate in CNSIs patients (68.7% (44/64) vs. 26.5% (17/64), p < 0.0001). Compared to conventional methods, positive percent agreement and negative percent agreement was 84.60% (44/52) and 66.1% (39/59) separately. At a species-specific read number (SSRN) ≥ 2, mNGS performance in the diagnosis of definite viral encephalitis and/or meningitis was optimal (area under the curve [AUC] 0.758, 95% confidence interval [CI] 0.663-0.854). In bacterial CNSIs patients with significant CSF abnormalities (CSF WBC > 300*10[6]/L), the positive rate of CSF mNGS is higher. To sum up, conventional microbiologic testing is insufficient to detect all neuroinvasive pathogens, and mNGS exhibited satisfactory diagnostic performance in CNSIs and with an overall detection rate higher than culture (p < 0.0001).},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Central Nervous System Infections/diagnosis/microbiology/virology
Male
Female
*Metagenomics/methods
Middle Aged
Adult
Retrospective Studies
Aged
Sensitivity and Specificity
Adolescent
Young Adult
Child
Child, Preschool
Metagenome

@article {pmid39043406,
year = {2024},
author = {Rolfe, RJ and Sheldon, SW and Kingry, LC and Petersen, JM and Maro, VP and Kinabo, GD and Saganda, W and Maze, MJ and Halliday, JEB and Nicholson, WL and Galloway, RL and Rubach, MP and Crump, JA},
title = {Metagenomic Detection of Bacterial Zoonotic Pathogens among Febrile Patients, Tanzania, 2007-2009[1].},
journal = {Emerging infectious diseases},
volume = {30},
number = {8},
pages = {1599-1608},
doi = {10.3201/eid3008.240529},
pmid = {39043406},
issn = {1080-6059},
mesh = {Humans ; Tanzania/epidemiology ; Adult ; Child, Preschool ; Adolescent ; *Metagenomics/methods ; *Fever/microbiology ; Male ; Female ; Animals ; Child ; *RNA, Ribosomal, 16S/genetics ; Young Adult ; Bacteria/genetics/classification/isolation & purification ; Bacterial Zoonoses/microbiology/epidemiology ; Bacterial Infections/microbiology/epidemiology/diagnosis ; Zoonoses/microbiology/epidemiology ; },
abstract = {Bacterial zoonoses are established causes of severe febrile illness in East Africa. Within a fever etiology study, we applied a high-throughput 16S rRNA metagenomic assay validated for detecting bacterial zoonotic pathogens. We enrolled febrile patients admitted to 2 referral hospitals in Moshi, Tanzania, during September 2007-April 2009. Among 788 participants, median age was 20 (interquartile range 2-38) years. We performed PCR amplification of V1-V2 variable region 16S rRNA on cell pellet DNA, then metagenomic deep-sequencing and pathogenic taxonomic identification. We detected bacterial zoonotic pathogens in 10 (1.3%) samples: 3 with Rickettsia typhi, 1 R. conorii, 2 Bartonella quintana, 2 pathogenic Leptospira spp., and 1 Coxiella burnetii. One other sample had reads matching a Neoerhlichia spp. previously identified in a patient from South Africa. Our findings indicate that targeted 16S metagenomics can identify bacterial zoonotic pathogens causing severe febrile illness in humans, including potential novel agents.},
}

Humans
Tanzania/epidemiology
Adult
Child, Preschool
Adolescent
*Metagenomics/methods
*Fever/microbiology
Male
Female
Animals
Child
*RNA, Ribosomal, 16S/genetics
Young Adult
Bacteria/genetics/classification/isolation & purification
Bacterial Zoonoses/microbiology/epidemiology
Bacterial Infections/microbiology/epidemiology/diagnosis
Zoonoses/microbiology/epidemiology

@article {pmid39043353,
year = {2024},
author = {Thacharodi, A and Hassan, S and Ahmed, ZHT and Singh, P and Maqbool, M and Meenatchi, R and Pugazhendhi, A and Sharma, A},
title = {The ruminant gut microbiome vs enteric methane emission: The essential microbes may help to mitigate the global methane crisis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119661},
doi = {10.1016/j.envres.2024.119661},
pmid = {39043353},
issn = {1096-0953},
abstract = {Ruminants release enteric methane into the atmosphere, significantly increasing greenhouse gas emissions and degrading the environment. A common focus of traditional mitigation efforts is on dietary management and manipulation, which may have limits in sustainability and efficacy, exploring the potential of essential microorganisms as a novel way to reduce intestinal methane emissions in ruminants; a topic that has garnered increased attention in recent years. Fermentation and feed digestion are significantly aided by essential microbes found in the rumen, such as bacteria, fungi, and archaea. The practical implications of the findings reported in various studies conducted on rumen gut concerning methane emissions may pave the way to understanding the mechanisms of CH4 production in the rumen to enhance cattle feed efficiency and mitigate CH4 emissions from livestock. This review discussed using essential bacteria to reduce intestinal methane emissions in ruminants. It investigates how particular microbial strains or consortia can alter rumen fermentation pathways to lower methane output while preserving the health and productivity of animals. We also describe the role of probiotics and prebiotics in managing methane emissions using microbial feed additives, some recent studies involving microbial interventions have been discussed. The use of new methods involving functional metagenomics and meta-transcriptomics for exploring the rumen microbiome structure has been highlighted. This review also emphasizes the challenges faced in altering the gut microbiome and future directions in this area.},
}

@article {pmid39043311,
year = {2024},
author = {Wang, X and Li, J and Wang, D and Sun, C and Zhang, X and Zhao, J and Teng, J and Wang, Q},
title = {Unveiling microplastic's role in nitrogen cycling: metagenomic insights from estuarine sediment microcosms.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {124591},
doi = {10.1016/j.envpol.2024.124591},
pmid = {39043311},
issn = {1873-6424},
abstract = {Marine microplastics (MPs) pollution, with rivers as a major source, leads to MPs accumulation in estuarine sediments, which are also nitrogen cycling hotspots. However, the impact of MPs on nitrogen cycling in estuarine sediments has rarely been documented. In this study, we conducted microcosm experiment to investigate the effects of commonly encountered polyethylene (PE) and polystyrene (PS) MPs, with two MPs concentrations (0.3% and 3% wet sediment weight) based on environmental concentration considerations and dose-response effects, on sediment dissolved oxygen (DO) diffusion capacity and microbial communities using microelectrode system and metagenomic analysis respectively. The results indicated that high concentrations of PE-MPs inhibited DO diffusion during the mid-phase of the experiment, an effect that dissipated in the later stages. Metagenomic analysis revealed that MP treatments reduced the relative abundance of dominant microbial colonies in the sediments. The PCoA results demonstrated that MPs altered the microbial community structure, particularly evident under high concentration PE-MPs treatments. Functional analysis related to the nitrogen cycle suggested that PS-MPs promoted the nitrification, denitrification, and DNRA processes, but inhibited the ANRA process, while PE-MPs had an inhibitory effect on the nitrate reduction process and the ANRA process. Additionally, the high concentration of PE-MPs treatment significantly stimulated the abundance of genus (Bacillus) by 34.1% and genes (lip, pnbA) by 100-187.5% associated with plastic degradation, respectively. Overall, in terms of microbial community structure and the abundance of nitrogen cycling functional genes, PE- and PS- MPs exhibit both similarities and differences in their impact on nitrogen cycling. Our findings highlight the complexity of MP effects on nitrogen cycling in estuarine sediments and high concentrations of PE-MP stimulated plastic-degrading genus and genes.},
}

@article {pmid39043054,
year = {2024},
author = {Perdomo, A and Calle, A},
title = {Assessment of microbial communities in a dairy farm from a food safety perspective.},
journal = {International journal of food microbiology},
volume = {423},
number = {},
pages = {110827},
doi = {10.1016/j.ijfoodmicro.2024.110827},
pmid = {39043054},
issn = {1879-3460},
abstract = {Microbial communities associated with dairy farm operations have a significant influence on food safety, dairy product quality, and animal health. This study aimed to create a microbial mapping at a dairy farm to learn about their bacterial diversity, distribution, and potential dissemination pathways. The investigation included the detection of key zoonotic pathogens, enumeration of Staphylococcus aureus and Escherichia coli as indicators of typical bacterial loads in a dairy production environment, and a microbiome analysis using metagenomics. A total of 160 samples (environmental, udder swabs, feed, feces, raw milk, and water) were collected during winter (N = 80) and spring (N = 80). In winter, Cronobacter spp. were detected in four feed and two water samples; L. monocytogenes was identified in two samples, one from feces and one from a cattle mat; E. coli O157:H7 was found in two feed samples. On the other hand, during spring, Cronobacter spp. were present in four feed samples and one hallway drain, with only one feed sample testing positive for E. coli O157:H7, while L. monocytogenes was absent during the spring season. Regarding microbial counts, there was no significant difference between the two seasons (p = 0.068) for S. aureus; however, a significant difference (p = 0.025) was observed for E. coli. Environmental microbiome analysis showed the presence of Proteobacteria (46.0 %) and Firmicutes (27.2 %) as the dominant phyla during both seasons. Moraxellaceae (11.8 %) and Pseudomonadaceae (10.62 %) were notable during winter, while Lactobacillaceae (13.0 %) and Enterobacteriaceae (12.6 %) were prominent during spring. These findings offer valuable insights into microbial distribution within a dairy farm and potential risks to animal and human health through environmental cross-contamination.},
}

@article {pmid39042309,
year = {2024},
author = {Hussan, H and Ali, MR and Lyo, V and Webb, A and Pietrzak, M and Zhu, J and Choueiry, F and Li, H and Cummings, BP and Marco, ML and Medici, V and Clinton, SK},
title = {Bariatric Surgery Is Associated with Lower Concentrations of Fecal Secondary Bile Acids and Their Metabolizing Microbial Enzymes: A Pilot Study.},
journal = {Obesity surgery},
volume = {},
number = {},
pages = {},
pmid = {39042309},
issn = {1708-0428},
support = {R35GM133510/GM/NIGMS NIH HHS/United States ; },
abstract = {INTRODUCTION: Excess body fat elevates colorectal cancer risk. While bariatric surgery (BRS) induces significant weight loss, its effects on the fecal stream and colon biology are poorly understood. Specifically, limited data exist on the impact of bariatric surgery (BRS) on fecal secondary bile acids (BA), including lithocholic acid (LCA), a putative promotor of colorectal carcinogenesis.

METHODS: This cross-sectional case-control study included 44 patients with obesity; 15 pre-BRS (controls) vs. 29 at a median of 24.1 months post-BRS. We examined the fecal concentrations of 11 BA by liquid chromatography and gene abundance of BA-metabolizing bacterial enzymes through fecal metagenomic sequencing. Differences were quantified using non-parametric tests for BA levels and linear discriminant analysis (LDA) effect size (LEfSe) for genes encoding BA-metabolizing enzymes.

RESULTS: Total fecal secondary BA concentrations trended towards lower levels post- vs. pre-BRS controls (p = 0.07). Individually, fecal LCA concentrations were significantly lower post- vs. pre-BRS (8477.0 vs. 11,914.0 uM/mg, p < 0.008). Consistent with this finding, fecal bacterial genes encoding BA-metabolizing enzymes, specifically 3-betahydroxycholanate-3-dehydrogenase (EC 1.1.1.391) and 3-alpha-hydroxycholanate dehydrogenase (EC 1.1.1.52), were also lower post- vs. pre-BRS controls (LDA of - 3.32 and - 2.64, respectively, adjusted p < 0.0001). Post-BRS fecal BA concentrations showed significant inverse correlations with weight loss, a healthy diet quality, and increased physical activity.

CONCLUSIONS: Concentrations of LCA, a secondary BA, and bacterial genes needed for BA metabolism are lower post-BRS. These changes can impact health and modulate the colorectal cancer cascade. Further research is warranted to examine how surgical alterations and the associated dietary changes impact bile acid metabolism.},
}

@article {pmid39042247,
year = {2024},
author = {Çalık Koç, G and Rezaei, F and Kahraman Ilıkkan, Ö and Bağdat, EŞ},
title = {Effect of seed priming with polyethylene glycol, distilled water, and sorbitol on physical, chemical quality parameters, and nodule microbiota of lentil.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {39042247},
issn = {1678-4405},
support = {21/07//Baskent Üniversitesi/ ; },
abstract = {The aim of this study was to investigate the effects of different seed priming solutions on physical and chemical quality parameters of lentils as well as nodule bacterial diversity before sowing. Therefore, lentil seeds were treated with polyethylene glycol (PEG 6000) (15%), sorbitol (6%), and distilled water, and none pretreated lentils (Lens culinaris) were used as control. The seeds were kept in these solutions for 24 h, then dried on toweling paper for 24 h, and used for the experiment. For nodule microbiota analysis, the plant root was divided into two equal parts, upper and lower, according to the root length and all nodules were collected from each region. According to the results, it was observed that emergence and flowering started late in the control compared to other seed priming treatments. Sorbitol application was found to provide advantages in terms of germination and seedling development. PEG and distilled water (DW) treatments showed an increase in total phenolic component activity; however, no significant change was observed in DPPH radical scavenging activity. Amplicon-based metagenomic analysis revealed that sorbitol and distilled water were the seed priming solutions altering the species diversity, especially Rhizobium sp. as the genus. In the comparison of samples taken from different parts of the root nodules, more Rhizobium sp. as a genus and Rhizobium leguminosarum as the species were found in the nodules collected from the top of the root. According to the overall results of lentil pod, lentil plant, and microbiota, sorbitol and DW can be considered to be a good priming solutions.},
}

@article {pmid39042190,
year = {2024},
author = {Saket, P and Joshi, A and Yadav, AK and Bala, K},
title = {Exploring the potential of graphite material in an unplanted electroactive wetland for the remediation of synthetic wastewater containing azo dye.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {39042190},
issn = {1614-7499},
support = {NASF/CA- 6031/2017-18 (GAP-303)//Indian Council of Agricultural Research/ ; MLP-037//Council of Scientific and Industrial Research, India/ ; MLP-059//Council of Scientific and Industrial Research, India/ ; DST/TMD-EWO/WTI/2K19/EWFH/2019/109 (GAP-340)]//department of science and technology, India/ ; },
abstract = {The current study was conducted to understand the sole role of graphite as a substrate material in a dual-chambered baffled electroactive wetland (EW) in the treatment of Methyl red dye-containing wastewater. The results obtained were compared with conventional gravel-based unplanted dual-chambered constructed wetlands (CW) at a lab scale. The highest dye decolorisation and COD removal efficiency achieved was 92.88 ± 1.6% and 95.78 ± 4.1%, respectively, in the electro-active wetland. Dissolved oxygen (DO) and pH conditions were appropriately maintained in both the microcosms because of separated aerobic and anaerobic chambers. UV-vis and gas chromatography-mass spectroscopy analysis revealed the production of by-products like 4-amino benzoic and N- N dimethyl phenyl-diamine of MR in microcosms and revealed further mineralisation of by-products in the aerobic zone of electroactive-wetland. Higher root growth of Cicer aerietinum and Vigna radiata was observed in the presence of effluents of baffled electroactive wetlands compared to constructed wetland, indicating a decrease in phytotoxicity. Metagenomic analysis revealed the abundance of potential microbes for MR and organic matter removal from phylum Proteobacteria, Firmicutes, Bacteroidetes, and Euryarchaeota. A batch adsorption study revealed a higher adsorption capability of graphite material in comparison to gravel. Hence, this study demonstrated that graphite is an appropriate substrate in electroactive wetland in facilitating microbial attachments and enhancing dye degradation, in addition to exhibiting superior adsorption quality.},
}

@article {pmid39041354,
year = {2024},
author = {Wang, X and Xu, H and Qin, L and Wang, H and Jiang, Y and Liu, H and Zhang, M and Pang, R and Wu, W and Li, W},
title = {Metagenomic next-generation sequencing of cerebrospinal fluid reveals etiological and microbiological features in patients with various central nervous system infections.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {38},
number = {14},
pages = {e23812},
doi = {10.1096/fj.202400792R},
pmid = {39041354},
issn = {1530-6860},
support = {SBGJ2018077//Health Commission of Henan Province ()/ ; },
mesh = {Humans ; Male ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Adult ; *Metagenomics/methods ; Aged ; *Central Nervous System Infections/cerebrospinal fluid/microbiology/diagnosis ; Adolescent ; Biomarkers/cerebrospinal fluid ; Child ; Young Adult ; Cerebrospinal Fluid/microbiology ; Aged, 80 and over ; Child, Preschool ; Metagenome ; },
abstract = {The application of metagenomic next-generation sequencing (mNGS) in pathogens detection of cerebrospinal fluid (CSF) is limited because clinical, microbiological, and biological information are not well connected. We analyzed the 428 enrolled patients' clinical features, pathogens diagnostic efficiency of mNGS in CSF, microbial community structure and composition in CSF, and correlation of microbial and clinical biomarkers in CSF. General characteristics were unspecific but helpful in formulating a differential diagnosis. CSF mNGS has a higher detection rate (34.6%) compared to traditional methods (5.4%). mNGS detection rate was higher when the time from onset to CSF collection was ≤20 days, the CSF leukocytes count was >200 × 10[6]/L, the CSF protein concentration was >1.3 g/L, or CSF glucose concentration was ≤2.5 mmol/L in non-postoperative bacterial CNS infections (CNSi). CSF was not strictly a sterile environment, and the potential pathogens may contribute to the dysbiosis of CSF microbiome. Furthermore, clinical biomarkers were significantly relevant to CNS pathogens. Clinical data are helpful in choosing a proper opportunity to obtain an accurate result of mNGS, and can speculate whether the mNGS results are correct or not. Our study is a pioneering study exploring the CSF microbiome in different CNSIs.},
}

Humans
Male
Female
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
Adult
*Metagenomics/methods
Aged
*Central Nervous System Infections/cerebrospinal fluid/microbiology/diagnosis
Adolescent
Biomarkers/cerebrospinal fluid
Child
Young Adult
Cerebrospinal Fluid/microbiology
Aged, 80 and over
Child, Preschool
Metagenome

@article {pmid39041196,
year = {2024},
author = {Tan, S and Liu, L and Jiao, JY and Li, MM and Hu, CJ and Lv, AP and Qi, YL and Li, YX and Rao, YZ and Qu, YN and Jiang, HC and Soo, RM and Evans, PN and Hua, ZS and Li, WJ},
title = {Exploring the origins and evolution of oxygenic and anoxygenic photosynthesis in deeply branched Cyanobacteriota.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msae151},
pmid = {39041196},
issn = {1537-1719},
abstract = {Cyanobacteriota, the sole prokaryotes capable of oxygenic photosynthesis (OxyP), occupy a unique and pivotal role in Earth's history. While the notion that OxyP may have originated from Cyanobacteriota is widely accepted, its early evolution remains elusive. Here, by using both metagenomics and metatranscriptomics, we explore 36 metagenome-assembled genomes (MAGs) from hot spring ecosystems, belonging to two deep-branching cyanobacterial orders: Thermostichales and Gloeomargaritales. Functional investigation reveals that Thermostichales encode the crucial thylakoid membrane biogenesis protein, Vipp1. Based on the phylogenetic results, we infer that the evolution of the thylakoid membrane predates the divergence of Thermostichales from other cyanobacterial groups and that Thermostichales may be the most ancient lineage known to date to have inherited this feature from their common ancestor. Apart from OxyP, both lineages are potentially capable of sulfide-driven anoxygenic photosynthesis (AnoxyP) by linking sulfide oxidation to the photosynthetic electron transport chain. Unexpectedly, this AnoxyP capacity appears to be an acquired feature, as the key gene sqr was horizontally transferred from later-evolved cyanobacterial lineages. The presence of two D1 protein variants in Thermostichales suggests the functional flexibility of photosystems, ensuring their survival in fluctuating redox environments. Furthermore, all MAGs feature streamlined phycobilisomes with a preference for capturing longer-wavelength light, implying a unique evolutionary trajectory. Collectively, these results reveal the photosynthetic flexibility in these early-diverging cyanobacterial lineages, shedding new light on the early evolution of Cyanobacteriota and their photosynthetic processes.},
}

@article {pmid39041015,
year = {2024},
author = {Brame, JE and Liddicoat, C and Abbott, CA and Cando-Dumancela, C and Fickling, NW and Robinson, JM and Breed, MF},
title = {Urban sports fields support higher levels of soil butyrate and butyrate-producing bacteria than urban nature parks.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e70057},
pmid = {39041015},
issn = {2045-7758},
abstract = {Butyrate-producing bacteria colonise the gut of humans and non-human animals, where they produce butyrate, a short-chain fatty acid with known health benefits. Butyrate-producing bacteria also reside in soils and soil bacteria can drive the assembly of airborne bacterial communities (the aerobiome). Aerobiomes in urban greenspaces are important reservoirs of butyrate-producing bacteria as they supplement the human microbiome, but soil butyrate producer communities have rarely been examined in detail. Here, we studied soil metagenome taxonomic and functional profiles and soil physicochemical data from two urban greenspace types: sports fields (n = 11) and nature parks (n = 22). We also developed a novel method to quantify soil butyrate and characterised the in situ activity of butyrate-producing bacteria. We show that soil butyrate was higher in sports fields than nature parks and that sports fields also had significantly higher relative abundances of the terminal butyrate production genes buk and butCoAT than nature parks. Soil butyrate positively correlated with buk gene abundance (but not butCoAT). Soil moisture (r = .50), calcium (r = -.62), iron (ρ = .54), ammonium nitrogen (ρ = .58) and organic carbon (r = .45) had the strongest soil abiotic effects on soil butyrate concentrations and iron (ρ = .56) and calcium (ρ = -.57) had the strongest soil abiotic effects on buk read abundances. Overall, our findings contribute important new insights into the role of sports fields as key exposure reservoirs of butyrate producing bacteria, with important implications for the provision of microbiome-mediated human health benefits via butyrate.},
}

@article {pmid39040904,
year = {2024},
author = {Wang, C and Zhang, Y and Wang, S and Lv, X and Xu, J and Zhang, X and Yang, Q and Meng, F and Xu, B},
title = {Differential effects of domesticated and wild Capsicum frutescens L. on microbial community assembly and metabolic functions in rhizosphere soil.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1383526},
pmid = {39040904},
issn = {1664-302X},
abstract = {OBJECTIVE: Rhizosphere microorganisms play crucial roles in the growth and development of plants, disease resistance, and environmental adaptability. As the only wild pepper variety resource in China, domesticated Capsicum frutescens Linn. (Xiaomila) exhibits varying beneficial traits and affects rhizosphere microbial composition compared with its wild counterparts. In this study, we aimed to identify specific rhizosphere microbiome and metabolism patterns established during the domestication process.

METHODS: The rhizosphere microbial diversity and composition of domesticated and wild C. frutescens were detected and analyzed by metagenomics. Non-targeted metabolomics were used to explore the differences of metabolites in rhizosphere soil between wild and domesticated C. frutescens.

RESULTS: We found that the rhizosphere microbial diversity of domesticated variety was significantly different from that of the wild variety, with Massilia being its dominant bacteria. However, the abundance of certain beneficial microbes such as Gemmatimonas, Streptomyces, Rambibacter, and Lysobacter decreased significantly. The main metabolites identified in the wild variety included serylthreonine, deoxyloganic acid, vitamin C, among others. In contrast, those identified in the domesticated group were 4-hydroxy-l-glutamic acid and benzoic acid. Furthermore, the differentially enriched pathways were concentrated in tyrosine and tryptophan biosynthesis, histidine and purine-derived alkaloids biosynthesis, benzoic acid family, two-component system, etc.

CONCLUSION: This study revealed that C. frutescens established specific rhizosphere microbiota and metabolites during domestication, which has important significance for the efficient utilization of beneficial microorganisms in breeding and cultivation practices.},
}

@article {pmid39040894,
year = {2024},
author = {Feng, M and Zhang, J and Li, X and Wang, S and Li, Y and Dong, C},
title = {Case report: Suspected organizing pneumonia secondary to severe respiratory syncytial virus pneumonia in an elderly patient.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1394542},
pmid = {39040894},
issn = {2296-858X},
abstract = {Respiratory syncytial virus (RSV) usually causes acute respiratory tract infection in infants. In recent years, it has gradually become an important pathogen of lower respiratory tract infection in elderly people with an underlying disease. However, at present, the treatment of severe RSV pneumonia in adults is unclear, and organizing pneumonia (OP) after severe RSV infection has rarely been reported. We reported a 76-year-old man with multiple chronic heart and lung diseases who presented with fever, cough and progressive dyspnea. Finally, severe RSV pneumonia was diagnosed after his nasopharyngeal swabs and bronchoalveolar lavage metagenomic next-generation sequencing tests were positive for RSV. After combined treatment with oral ribavirin, intravenous immunoglobulin and corticosteroids, the patient's condition largely resolved, and he was discharged. However, when the corticosteroids were gradually tapered, the disease relapsed twice, and the patient experienced fever and aggravated dyspnea. Despite the lack of pathological evidence, we highly suspected organizing pneumonia secondary to severe RSV pneumonia based on the typical imaging manifestations and the clinical characteristics of a good response to corticosteroids. Finally, this patient was successfully treated with a course of corticosteroids and followed up for 14 months in total.},
}

@article {pmid39040893,
year = {2024},
author = {Ling, J and Liang, L and Liu, X and Wu, W and Yan, Z and Zhou, W and Jiang, Y and Kuang, L},
title = {Invasive Fusarium solani infection diagnosed by traditional microbial detection methods and metagenomic next-generation sequencing in a pediatric patient: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1322700},
pmid = {39040893},
issn = {2296-858X},
abstract = {Fusarium solani, as an opportunistic pathogen, can infect individuals with immunosuppression, neutropenia, hematopoietic stem cell transplantation (HSCT), or other high-risk factors, leading to invasive or localized infections. Particularly in patients following allogeneic HSCT, Fusarium solani is more likely to cause invasive or disseminated infections. This study focuses on a pediatric patient who underwent HSCT for severe aplastic anemia. Although initial blood cultures were negative, an abnormality was detected in the 1,3-β-D-glucan test (G test) post-transplantation. To determine the causative agent, blood samples were subjected to metagenomic next-generation sequencing (mNGS) and blood cultures simultaneously. Surprisingly, the results of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and mNGS differed slightly, with mNGS identifying Nectria haematonectria, while MALDI-TOF MS based on culture showed Fusarium solani. To clarify the results, Sanger sequencing was performed for further detection, and the results were consistent with those of MALDI-TOF MS. Since the accuracy of Sanger sequencing is higher than that of mNGS, the diagnosis was revised to invasive Fusarium solani infection. With advancements in technology, various detection methods for invasive fungi have been developed in recent years, such as mNGS, which has high sensitivity. While traditional methods may be time-consuming, they are important due to their high specificity. Therefore, in clinical practice, it is essential to utilize both traditional and novel detection methods in a complementary manner to enhance the diagnosis of invasive fungal infections.},
}

@article {pmid39040604,
year = {2024},
author = {Hasan, Z and Netherland, M and Hasan, NA and Begum, N and Yasmin, M and Ahmed, S},
title = {An insight into the vaginal microbiome of infertile women in Bangladesh using metagenomic approach.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1390088},
pmid = {39040604},
issn = {2235-2988},
mesh = {Humans ; Female ; *Vagina/microbiology ; *Metagenomics/methods ; *Infertility, Female/microbiology ; Adult ; *Microbiota/genetics ; Bangladesh ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Young Adult ; Lactobacillus/isolation & purification/genetics/classification ; Dysbiosis/microbiology ; Phylogeny ; },
abstract = {INTRODUCTION: The dysbiosis of vaginal microbiota is recognized as a potential underlying factor contributing to infertility in women. This study aimed to compare the vaginal microbiomes of infertile and fertile women to investigate their relationship with infertility.

METHODS: Metagenomic analysis was conducted on samples from 5 infertile and 5 fertile individuals using both amplicon 16S and metagenomics shotgun sequencing methods.

RESULTS AND DISCUSSION: In the infertile group, the bacterial community was primarily represented by three major bacterial genera: Lactobacillus (79.42%), Gardnerella (12.56%) and Prevotella (3.33%), whereas, the fertile group exhibited a more diverse composition with over 8 major bacterial genera, accompanied by significantly reduced abundance of Lactobacillus (48.79%) and Gardnerella (6.98%). At the species level, higher abundances of L. iners, L. gasseri and G. vaginalis were observed in the infertile group. Regarding the microbiome composition, only one fertile and two infertile subjects exhibited the healthiest Community State Types, CST-1, while CST-3 was observed among two infertile and one fertile subject, and CST-4 in three other fertile and one infertile subject. Overall, alpha diversity metrics indicated greater diversity and lower species richness in the control (fertile) group, while the infertile group displayed the opposite trend. However, beta-diversity analysis did not show distinct clustering of samples associated with any specific group; instead, it demonstrated CST-type specific clustering. Shotgun metagenomics further confirmed the dominance of Firmicutes, with a greater abundance of Lactobacillus species in the infertile group. Specifically, L. iners and G. vaginalis were identified as the most dominant and highly abundant in the infertile group. Fungi were only identified in the control group, dominated by Penicillium citrinum (62.5%). Metagenome-assembled genomes (MAGs) corroborated read-based taxonomic profiling, with the taxon L. johnsonii identified exclusively in disease samples. MAG identities shared by both groups include Shamonda orthobunyavirus, L. crispatus, Human endogenous retrovirus K113, L. iners, and G. vaginalis. Interestingly, the healthy microbiomes sequenced in this study contained two clusters, Penicillium and Staphylococcus haemolyticus, not found in the public dataset. In conclusion, this study suggests that lower species diversity with a higher abundance of L. iners, L. gasseri and G. vaginalis, may contribute to female infertility in our study datasets. However, larger sample sizes are necessary to further evaluate such association.},
}

Humans
Female
*Vagina/microbiology
*Metagenomics/methods
*Infertility, Female/microbiology
Adult
*Microbiota/genetics
Bangladesh
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Metagenome
Young Adult
Lactobacillus/isolation & purification/genetics/classification
Dysbiosis/microbiology
Phylogeny

@article {pmid39040390,
year = {2024},
author = {Xu, Q and Han, W and Cai, Y and Yin, Y and Guo, Y and Chen, H and Wang, H},
title = {A case report of the metagenomic next-generation sequencing for timely diagnosis of a traveler with nonspecific febrile Q fever.},
journal = {Heliyon},
volume = {10},
number = {13},
pages = {e33649},
pmid = {39040390},
issn = {2405-8440},
abstract = {Q fever is a worldwide distribution disease caused by Coxiella burnetii（C. burnetii）, an obligate intracellular, Gram-negative acidophilic bacterium belonging to γ-proteobacterium. Most patients present with acute Q-fever accompanied by atypical flu-like symptoms, with only 1%-5% of cases may develop into persistent and focally infected foci, mainly manifest as endocarditis, osteomyelitis and prosthetic arthritis. In this case, the patient experienced an unexplained and uninterrupted fever up to 39.2 °C for a week, accompanied by chills and headaches, as well as abnormal liver function. The laboratory reported negative results for blood culture and respiratory-associated pathogens, however, the metagenomic next-generation sequencing (mNGS) reported that detection of 20 sequence reads of C. burnetii in the patient's peripheral blood. In addition, the patient had traveled to Sri Lanka, Iraq and Saudi Arabia before illness. In clinical, the treatment regimen was adjusted from empirically intravenous moxifloxacin 400 mg a day for 1 week to continuously oral minocyline 100 mg twice daily for 2 weeks. The patient was in good health without any adverse sequelae during outpatient visitation and the phone calls follow-up. In conclusion, the mNGS does provide an early and timely diagnostic basis for rare and difficult to culture pathogens, which contributes to the success of clinical anti-infection.},
}

@article {pmid39039769,
year = {2024},
author = {Schwab, S and Dame, RT},
title = {Identification, characterization and classification of prokaryotic nucleoid-associated proteins.},
journal = {Molecular microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mmi.15298},
pmid = {39039769},
issn = {1365-2958},
support = {OCENW.GROOT.2019.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; VICI 016.160.613/53//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
abstract = {Common throughout life is the need to compact and organize the genome. Possible mechanisms involved in this process include supercoiling, phase separation, charge neutralization, macromolecular crowding, and nucleoid-associated proteins (NAPs). NAPs are special in that they can organize the genome at multiple length scales, and thus are often considered as the architects of the genome. NAPs shape the genome by either bending DNA, wrapping DNA, bridging DNA, or forming nucleoprotein filaments on the DNA. In this mini-review, we discuss recent advancements of unique NAPs with differing architectural properties across the tree of life, including NAPs from bacteria, archaea, and viruses. To help the characterization of NAPs from the ever-increasing number of metagenomes, we recommend a set of cheap and simple in vitro biochemical assays that give unambiguous insights into the architectural properties of NAPs. Finally, we highlight and showcase the usefulness of AlphaFold in the characterization of novel NAPs.},
}

@article {pmid39039586,
year = {2024},
author = {Liang, JL and Feng, SW and Jia, P and Lu, JL and Yi, X and Gao, SM and Wu, ZH and Liao, B and Shu, WS and Li, JT},
title = {Unraveling the habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses across China.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {136},
pmid = {39039586},
issn = {2049-2618},
support = {42177009//National Natural Science Foundation of China/ ; 41622106//National Natural Science Foundation of China/ ; 2023YFC3207300//National Key R&D Program of China/ ; },
mesh = {China ; *Soil Microbiology ; *Metagenome ; *Ecosystem ; *Giant Viruses/genetics/classification ; Soil/chemistry ; Phylogeny ; Genome, Viral/genetics ; Metagenomics ; },
abstract = {BACKGROUND: Soil giant viruses are increasingly believed to have profound effects on ecological functioning by infecting diverse eukaryotes. However, their biogeography and ecology remain poorly understood.

RESULTS: In this study, we analyzed 333 soil metagenomes from 5 habitat types (farmland, forest, grassland, Gobi desert, and mine wasteland) across China and identified 533 distinct giant virus phylotypes affiliated with nine families, thereby greatly expanding the diversity of soil giant viruses. Among the nine families, Pithoviridae were the most diverse. The majority of phylotypes exhibited a heterogeneous distribution among habitat types, with a remarkably high proportion of unique phylotypes in mine wasteland. The abundances of phylotypes were negatively correlated with their environmental ranges. A total of 76 phylotypes recovered in this study were detectable in a published global topsoil metagenome dataset. Among climatic, geographical, edaphic, and biotic characteristics, soil eukaryotes were identified as the most important driver of beta-diversity of giant viral communities across habitat types. Moreover, co-occurrence network analysis revealed some pairings between giant viral phylotypes and eukaryotes (protozoa, fungi, and algae). Analysis of 44 medium- to high-quality giant virus genomes recovered from our metagenomes uncovered not only their highly shared functions but also their novel auxiliary metabolic genes related to carbon, sulfur, and phosphorus cycling.

CONCLUSIONS: These findings extend our knowledge of diversity, habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses. Video Abstract.},
}

China
*Soil Microbiology
*Metagenome
*Ecosystem
*Giant Viruses/genetics/classification
Soil/chemistry
Phylogeny
Genome, Viral/genetics
Metagenomics

@article {pmid39039555,
year = {2024},
author = {Wang, D and Liu, L and Xu, X and Wang, C and Wang, Y and Deng, Y and Zhang, T},
title = {Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {134},
pmid = {39039555},
issn = {2049-2618},
mesh = {*Bacteriophages/genetics/classification/physiology/isolation & purification ; *Sewage/virology/microbiology ; *Wastewater/virology/microbiology ; *Bacteria/virology/genetics/classification ; Biofilms ; Metagenomics ; Water Purification/methods ; Microbiota ; },
abstract = {BACKGROUND: Understanding the interactions and dynamics of microbiotas within biological wastewater treatment systems is essential for ensuring their stability and long-term sustainability. In this study, we developed a systematic framework employing multi-omics and Hi-C sequencing to extensively investigate prokaryotic and phage communities within a hybrid biofilm and activated sludge system.

RESULTS: We uncovered distinct distribution patterns, metabolic capabilities, and activities of functional prokaryotes through the analysis of 454 reconstructed prokaryotic genomes. Additionally, we reconstructed a phage catalog comprising 18,645 viral operational taxonomic units (vOTUs) with high length and contiguity using hybrid assembly, and a distinct distribution of phages was depicted between activated sludge (AS) and biofilm. Importantly, 1340 host-phage pairs were established using Hi-C and conventional in silico methods, unveiling the host-determined phage prevalence. The majority of predicted hosts were found to be involved in various crucial metabolic processes, highlighting the potential vital roles of phages in influencing substance metabolism within this system. Moreover, auxiliary metabolic genes (AMGs) related to various categories (e.g., carbohydrate degradation, sulfur metabolism, transporter) were predicted. Subsequent activity analysis emphasized their potential ability to mediate host metabolism during infection. We also profiled the temporal dynamics of phages and their associated hosts using 13-month time-series metagenomic data, further demonstrating their tight interactions. Notably, we observed lineage-specific infection patterns, such as potentially host abundance- or phage/host ratio-driven phage population changes.

CONCLUSIONS: The insights gained from this research contribute to the growing body of knowledge surrounding interactions and dynamics of host-phage and pave the way for further exploration and potential applications in the field of microbial ecology. Video Abstract.},
}

*Bacteriophages/genetics/classification/physiology/isolation & purification
*Sewage/virology/microbiology
*Wastewater/virology/microbiology
*Bacteria/virology/genetics/classification
Biofilms
Metagenomics
Water Purification/methods
Microbiota

@article {pmid39039498,
year = {2024},
author = {Fan, Q and Tan, Z and Su, W and Li, Q and Jin, D and Du, Y and Zhang, L and Wu, S},
title = {Efficacy, safety and mechanism of Simiaoyongan decoction in the treatment of carotid atherosclerotic plaque: a randomized, double-blind, placebo-controlled clinical trial protocol.},
journal = {BMC complementary medicine and therapies},
volume = {24},
number = {1},
pages = {277},
pmid = {39039498},
issn = {2662-7671},
support = {82174340//General projects of the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Double-Blind Method ; *Plaque, Atherosclerotic/drug therapy ; Carotid Artery Diseases/drug therapy ; Male ; Middle Aged ; Female ; Adult ; Aged ; },
abstract = {INTRODUCTION: Chronic inflammation is the major pathological feature of Atherosclerosis(As). Inflammation may accelerate plaque to develop, which is a key factor resulting in the thinning of the fibrous cap and the vulnerable rupture of plaque. Presently, clinical treatments are still lacking. It is necessary to find a safe and effective treatment for As inflammation. Simiaoyongan Decoction (SMYA) has potential anti-inflammatory and plaque protection effects. This protocol aims to evaluate the efficacy, safety, and mechanism of SMYA for patients with carotid atherosclerotic plaque.

METHODS/DESIGN: The assessment of SMYA clinical trial is designed as a randomized, double-blind, placebo-controlled study. The sample size is 86 cases in total, with 43 participants in the intervention group and the control group respectively. The intervention group takes SMYA, while the control group takes SMYA placebo. The medication lasts for 14 days every 10 weeks, with a total of 50 weeks. We will use carotid artery high resolution magnetic resonance imaging (HR-MRI) to measure plaque. The plaque minimum fiber cap thickness (PMFCT) is adopted as the primary outcome. The secondary outcomes include plaque fiber cap volume, volume percentage of fiber cap, lipid-rich necrotic core (LRNC) volume, volume percentage of LRNC, internal bleeding volume of plaque, internal bleeding volume percentage of plaque, plaque calcification volume, volume percentage of plaque calcification, lumen stenosis rate, average and a maximum of vessel wall thickness, vessel wall volume, total vessel wall load, carotid atherosclerosis score, hs-CRP, IL-1β and IL-6, the level of lipid profiles and blood glucose, blood pressure, and body weight.

DISCUSSION: We anticipate that patients with As plaque will be improved from SMYA by inhibiting inflammation to enhance plaque stability. This study analyzes plaque by using HR-MRI to evaluate the clinical efficacy and safety of SMYA. Moreover, we conduct transcriptome analysis, proteomic analysis, and metagenomic analysis of blood and stool of participants to study the mechanism of SMYA against As plaque. This is the first prospective TCM trial to observe and treat As plaque by inhibiting inflammatory reaction directly. If successful, the finding will be valuable in the treatment of As plaque and drug development, especially in the "statin era".

TRIAL REGISTRATION NUMBER: This trial is registered on Chinese Clinical Trials.gov with number ChiCTR2000039062 on October 15, 2020 (http://www.chictr.org.cn).},
}

Humans
*Drugs, Chinese Herbal/pharmacology/therapeutic use
Double-Blind Method
*Plaque, Atherosclerotic/drug therapy
Carotid Artery Diseases/drug therapy
Male
Middle Aged
Female
Adult
Aged

@article {pmid39039462,
year = {2024},
author = {Yan, L and Ye, B and Yang, M and Shan, Y and Yan, D and Fang, D and Zhang, K and Yu, Y},
title = {Gut microbiota and metabolic changes in children with idiopathic short stature.},
journal = {BMC pediatrics},
volume = {24},
number = {1},
pages = {468},
pmid = {39039462},
issn = {1471-2431},
mesh = {Humans ; *Gastrointestinal Microbiome ; Child ; Male ; Female ; *Feces/microbiology ; Case-Control Studies ; Adolescent ; Body Height ; Growth Disorders/microbiology/metabolism ; Metabolomics/methods ; Metabolome ; },
abstract = {BACKGROUND: Idiopathic short stature (ISS) is characterized by short stature with unknown causes. Recent studies showed different gut microbiota flora and reduced fecal short-chain fatty acids in ISS children. However, the roles of the microbiome and metabolites in the pathogenesis of ISS remains largely unknown.

METHODS: We recruited 51 Chinese subjects, comprising 26 ISS children and 25 normal-height control individuals. Untargeted metabolomics was performed to explore the fecal metabolic profiles between groups. A shotgun metagenomic sequencing approach was used to investigate the microbiome at the strains level. Mediation analyses were done to reveal correlations between the height standard deviation (SD) value, the gut microbiome and metabolites.

RESULTS: We detected marked differences in the composition of fecal metabolites in the ISS group, particularly a significant increase in erucic acid and a decrease in spermidine, adenosine and L-5-Hydroxytryptophan, when compared to those of controls. We further identified specific groups of bacterial strains to be associated with the different metabolic profile. Through mediation analysis, 50 linkages were established. KEGG pathway analysis of microbiota and metabolites indicated nutritional disturbances. 13 selected features were able to accurately distinguish the ISS children from the controls (AUC = 0.933 [95%CI, 79.9-100%]) by receiver operating characteristic (ROC) analysis.

CONCLUSION: Our study suggests that the microbiome and the microbial-derived metabolites play certain roles in children's growth. These findings provide a new research direction for better understanding the mechanism(s) underlying ISS.},
}

Humans
*Gastrointestinal Microbiome
Child
Male
Female
*Feces/microbiology
Case-Control Studies
Adolescent
Body Height
Growth Disorders/microbiology/metabolism
Metabolomics/methods
Metabolome

@article {pmid39039157,
year = {2024},
author = {Hatrongjit, R and Wongsurawat, T and Jenjaroenpun, P and Chopjitt, P and Boueroy, P and Akeda, Y and Okada, K and Iida, T and Hamada, S and Kerdsin, A},
title = {Genomic analysis of carbapenem- and colistin-resistant Klebsiella pneumoniae complex harbouring mcr-8 and mcr-9 from individuals in Thailand.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16836},
pmid = {39039157},
issn = {2045-2322},
mesh = {*Colistin/pharmacology ; *Klebsiella pneumoniae/genetics/drug effects/isolation & purification ; Humans ; *Carbapenems/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Thailand ; *Microbial Sensitivity Tests ; *Bacterial Proteins/genetics ; Klebsiella Infections/microbiology/epidemiology ; Male ; Plasmids/genetics ; Female ; Genomics/methods ; Drug Resistance, Bacterial/genetics ; Middle Aged ; Adult ; Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects/isolation & purification ; Aged ; Genome, Bacterial ; Klebsiella ; },
abstract = {The surge in mobile colistin-resistant genes (mcr) has become an increasing public health concern, especially in carbapenem-resistant Enterobacterales (CRE). Prospective surveillance was conducted to explore the genomic characteristics of clinical CRE isolates harbouring mcr in 2015-2020. In this study, we aimed to examine the genomic characteristics and phonotypes of mcr-8 and mcr-9 harbouring carbapenem-resistant K. pneumoniae complex (CRKpnC). Polymerase chain reaction test and genome analysis identified CRKpnC strain AMR20201034 as K. pneumoniae (CRKP) ST147 and strain AMR20200784 as K. quasipneumoniae (CRKQ) ST476, harbouring mcr-8 and mcr-9, respectively. CRKQ exhibited substitutions in chromosomal-mediated colistin resistance genes (pmrB, pmrC, ramA, and lpxM), while CRKP showed two substitutions in crrB, pmrB, pmrC, lpxM and lapB. Both species showed resistance to colistin, with minimal inhibitory concentrations of 8 µg/ml for mcr-8-carrying CRKP isolate and 32 µg/ml for mcr-9-carrying CRKQ isolate. In addition, CRKP harbouring mcr-8 carried blaNDM, while CRKQ harbouring mcr-9 carried blaIMP, conferring carbapenem resistance. Analysis of plasmid replicon types carrying mcr-8 and mcr-9 showed FIA-FII (96,575 bp) and FIB-HI1B (287,118 bp), respectively. In contrast with the plasmid carrying the carbapenemase genes, the CRKQ carried blaIMP-14 on an IncC plasmid, while the CRKP harboured blaNDM-1 on an FIB plasmid. This finding provides a comprehensive insight into another mcr-carrying CRE from patients in Thailand. The other antimicrobial-resistant genes in the CRKP were blaCTX-M-15, blaSHV-11, blaOXA-1, aac(6')-Ib-cr, aph(3')-VI, ARR-3, qnrS1, oqxA, oqxB, sul1, catB3, fosA, and qacE, while those detected in CRKQ were blaOKP-B-15, qnrA1, oqxA, oqxB, sul1, fosA, and qacE. This observation highlights the importance of strengthening official active surveillance efforts to detect, control, and prevent mcr-harbouring CRE and the need for rational drug use in all sectors.},
}

*Colistin/pharmacology
*Klebsiella pneumoniae/genetics/drug effects/isolation & purification
Humans
*Carbapenems/pharmacology
*Anti-Bacterial Agents/pharmacology
Thailand
*Microbial Sensitivity Tests
*Bacterial Proteins/genetics
Klebsiella Infections/microbiology/epidemiology
Male
Plasmids/genetics
Female
Genomics/methods
Drug Resistance, Bacterial/genetics
Middle Aged
Adult
Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects/isolation & purification
Aged
Genome, Bacterial
Klebsiella

@article {pmid38888585,
year = {2024},
author = {Chalita, M and Kim, YO and Park, S and Oh, HS and Cho, JH and Moon, J and Baek, N and Moon, C and Lee, K and Yang, J and Nam, GG and Jung, Y and Na, SI and Bailey, MJ and Chun, J},
title = {EzBioCloud: a genome-driven database and platform for microbiome identification and discovery.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {6},
pages = {},
pmid = {38888585},
issn = {1466-5034},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota ; *Archaea/genetics/classification ; *Genome, Bacterial ; Phylogeny ; Databases, Genetic ; Genome, Archaeal ; Sequence Analysis, DNA ; Computational Biology/methods ; },
abstract = {With the continued evolution of DNA sequencing technologies, the role of genome sequence data has become more integral in the classification and identification of Bacteria and Archaea. Six years after introducing EzBioCloud, an integrated platform representing the taxonomic hierarchy of Bacteria and Archaea through quality-controlled 16S rRNA gene and genome sequences, we present an updated version, that further refines and expands its capabilities. The current update recognizes the growing need for accurate taxonomic information as defining a species increasingly relies on genome sequence comparisons. We also incorporated an advanced strategy for addressing underrepresented or less studied lineages, bolstering the comprehensiveness and accuracy of our database. Our rigorous quality control protocols remain, where whole-genome assemblies from the NCBI Assembly Database undergo stringent screening to remove low-quality sequence data. These are then passed through our enhanced identification bioinformatics pipeline which initiates a 16S rRNA gene similarity search and then calculates the average nucleotide identity (ANI). For genome sequences lacking a 16S rRNA sequence and without a closely related genomic representative for ANI calculation, we apply a different ANI approach using bacterial core genes for improved taxonomic placement (core gene ANI, cgANI). Because of the increase in genome sequences available in NCBI and our newly introduced cgANI method, EzBioCloud now encompasses a total of 109 835 species, of which 21 964 have validly published names. 47 896 are candidate species identified either through 16S rRNA sequence similarity (phylotypes) or through whole genome ANI (genomospecies), and the remaining 39 975 were positioned in the taxonomic tree by cgANI (species clusters). Our EzBioCloud database is accessible at www.ezbiocloud.net/db.},
}

*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
*Microbiota
*Archaea/genetics/classification
*Genome, Bacterial
Phylogeny
Databases, Genetic
Genome, Archaeal
Sequence Analysis, DNA
Computational Biology/methods

@article {pmid39039075,
year = {2024},
author = {Stothart, MR and McLoughlin, PD and Medill, SA and Greuel, RJ and Wilson, AJ and Poissant, J},
title = {Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6012},
pmid = {39039075},
issn = {2041-1723},
support = {2016-06459//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; 2019-04388//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; 25046//Canada Foundation for Innovation (Fondation canadienne pour l'innovation)/ ; D20EQ-05//Morris Animal Foundation (MAF)/ ; D20EQ-05//Morris Animal Foundation (MAF)/ ; D20EQ-05//Morris Animal Foundation (MAF)/ ; },
mesh = {Animals ; Horses/microbiology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Methane/metabolism ; Animals, Wild/microbiology ; Metagenome ; Fatty Acids, Volatile/metabolism ; Metagenomics/methods ; Male ; Female ; Canada ; },
abstract = {Gut microbiomes are widely hypothesised to influence host fitness and have been experimentally shown to affect host health and phenotypes under laboratory conditions. However, the extent to which they do so in free-living animal populations and the proximate mechanisms involved remain open questions. In this study, using long-term, individual-based life history and shallow shotgun metagenomic sequencing data (2394 fecal samples from 794 individuals collected between 2013-2019), we quantify relationships between gut microbiome variation and survival in a feral population of horses under natural food limitation (Sable Island, Canada), and test metagenome-derived predictions using short-chain fatty acid data. We report detailed evidence that variation in the gut microbiome is associated with a host fitness proxy in nature and outline hypotheses of pathogenesis and methanogenesis as key causal mechanisms which may underlie such patterns in feral horses, and perhaps, wild herbivores more generally.},
}

Animals
Horses/microbiology
*Gastrointestinal Microbiome/genetics
*Feces/microbiology
*Methane/metabolism
Animals, Wild/microbiology
Metagenome
Fatty Acids, Volatile/metabolism
Metagenomics/methods
Male
Female
Canada

@article {pmid39038938,
year = {2024},
author = {Chuang, YF and Fan, KC and Su, YY and Wu, MF and Chiu, YL and Liu, YC and Lin, CC},
title = {Precision probiotics supplement strategy in aging population based on gut microbiome composition.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {4},
pages = {},
doi = {10.1093/bib/bbae351},
pmid = {39038938},
issn = {1477-4054},
support = {//Taiwan National Science and Technology Council/ ; MOST 110-2321-B-418//Ministry of Science and Technology/ ; MOHW111-TDU-B-221-114007//Ministry of Health and Welfare/ ; NYCU-FEMH 112DN11//FEMH-NYCU Joint Research Program/ ; },
mesh = {*Probiotics/therapeutic use/administration & dosage ; Humans ; *Gastrointestinal Microbiome ; Aged ; *Aging ; Female ; Male ; *Dietary Supplements ; Aged, 80 and over ; Middle Aged ; Lactobacillus/genetics ; Metagenomics/methods ; Bifidobacterium ; },
abstract = {With the increasing prevalence of age-related chronic diseases burdening healthcare systems, there is a pressing need for innovative management strategies. Our study focuses on the gut microbiota, essential for metabolic, nutritional, and immune functions, which undergoes significant changes with aging. These changes can impair intestinal function, leading to altered microbial diversity and composition that potentially influence health outcomes and disease progression. Using advanced metagenomic sequencing, we explore the potential of personalized probiotic supplements in 297 older adults by analyzing their gut microbiota. We identified distinctive Lactobacillus and Bifidobacterium signatures in the gut microbiota of older adults, revealing probiotic patterns associated with various population characteristics, microbial compositions, cognitive functions, and neuroimaging results. These insights suggest that tailored probiotic supplements, designed to match individual probiotic profile, could offer an innovative method for addressing age-related diseases and functional declines. Our findings enhance the existing evidence base for probiotic use among older adults, highlighting the opportunity to create more targeted and effective probiotic strategies. However, additional research is required to validate our results and further assess the impact of precision probiotics on aging populations. Future studies should employ longitudinal designs and larger cohorts to conclusively demonstrate the benefits of tailored probiotic treatments.},
}

*Probiotics/therapeutic use/administration & dosage
Humans
*Gastrointestinal Microbiome
Aged
*Aging
Female
Male
*Dietary Supplements
Aged, 80 and over
Middle Aged
Lactobacillus/genetics
Metagenomics/methods
Bifidobacterium

@article {pmid39038883,
year = {2024},
author = {Han, PJ and Song, L and Wen, Z and Zhu, HY and Wei, YH and Wang, JW and Bai, M and Luo, LJ and Wang, JW and Chen, SX and You, XL and Han, DY and Bai, FY},
title = {Species-level understanding of the bacterial community in Daqu based on full-length 16S rRNA gene sequences.},
journal = {Food microbiology},
volume = {123},
number = {},
pages = {104566},
doi = {10.1016/j.fm.2024.104566},
pmid = {39038883},
issn = {1095-9998},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Fermentation ; China ; Microbiota ; Phylogeny ; DNA, Bacterial/genetics ; Biodiversity ; Alcoholic Beverages/microbiology/analysis ; Food Microbiology ; Metagenome ; Fermented Foods/microbiology ; },
abstract = {Daqu is used as the fermentation starter of Baijiu and contributes diversified functional microbes for saccharifying grains and converting sugars into ethanol and aroma components in Baijiu products. Daqu is mainly classified into three types, namely low (LTD), medium (MTD) and high (HTD) temperature Daqu, according to the highest temperatures reached in their fermentation processes. In this study, we used the PacBio small-molecule real-time (SMRT) sequencing technology to determine the full-length 16 S rRNA gene sequences from the metagenomes of 296 samples of different types of Daqu collected from ten provinces in China, and revealed the bacterial diversity at the species level in the Daqu samples. We totally identified 310 bacteria species, including 78 highly abundant species (with a relative abundance >0.1% each) which accounted for 91.90% of the reads from all the Daqu samples. We also recognized the differentially enriched bacterial species in different types of Daqu, and in the Daqu samples with the same type but from different provinces. Specifically, Lactobacillales, Enterobacterales and Bacillaceae were significantly enriched in the LTD, MTD and HTD groups, respectively. The potential co-existence and exclusion relationships among the bacteria species involved in all the Daqu samples and in the LTD, MTD and HTD samples from a specific region were also identified. These results provide a better understanding of the bacterial diversity in different types of Daqu at the species level.},
}

*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism
*Fermentation
China
Microbiota
Phylogeny
DNA, Bacterial/genetics
Biodiversity
Alcoholic Beverages/microbiology/analysis
Food Microbiology
Metagenome
Fermented Foods/microbiology

@article {pmid39038849,
year = {2024},
author = {Lee, S and Portlock, T and Le Chatelier, E and Garcia-Guevara, F and Clasen, F and Oñate, FP and Pons, N and Begum, N and Harzandi, A and Proffitt, C and Rosario, D and Vaga, S and Park, J and von Feilitzen, K and Johansson, F and Zhang, C and Edwards, LA and Lombard, V and Gauthier, F and Steves, CJ and Gomez-Cabrero, D and Henrissat, B and Lee, D and Engstrand, L and Shawcross, DL and Proctor, G and Almeida, M and Nielsen, J and Mardinoglu, A and Moyes, DL and Ehrlich, SD and Uhlen, M and Shoaie, S},
title = {Global compositional and functional states of the human gut microbiome in health and disease.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.278637.123},
pmid = {39038849},
issn = {1549-5469},
abstract = {The human gut microbiota is of increasing interest, with metagenomics a key tool for analyzing bacterial diversity and functionality in health and disease. Despite increasing efforts to expand microbial gene catalogs and an increasing number of metagenome-assembled genomes, there have been few pan-metagenomic association studies and in-depth functional analyses across different geographies and diseases. Here, we explored 6014 human gut metagenome samples across 19 countries and 23 diseases by performing compositional, functional cluster, and integrative analyses. Using interpreted machine learning classification models and statistical methods, we identified Fusobacterium nucleatum and Anaerostipes hadrus with the highest frequencies, enriched and depleted, respectively, across different disease cohorts. Distinct functional distributions were observed in the gut microbiomes of both westernized and nonwesternized populations. These compositional and functional analyses are presented in the open-access Human Gut Microbiome Atlas, allowing for the exploration of the richness, disease, and regional signatures of the gut microbiota across different cohorts.},
}

@article {pmid39038424,
year = {2024},
author = {Zhu, YM and Chen, Y and Lu, H and Jin, K and Lin, Y and Ren, H and Xu, K},
title = {Simultaneous efficient removal of tetracycline and mitigation of antibiotic resistance genes enrichment by a modified activated sludge process with static magnetic field.},
journal = {Water research},
volume = {262},
number = {},
pages = {122107},
doi = {10.1016/j.watres.2024.122107},
pmid = {39038424},
issn = {1879-2448},
abstract = {To address the increasing issue of antibiotic wastewater, this study applied a static magnetic field (SMF) to the activated sludge process to increase the efficiency of tetracycline (TC) removal from swine wastewater and to reveal its enhanced mechanisms. The results demonstrated that the SMF-modified activated sludge process could achieve almost complete TC removal at sludge loading rates of 0.3 mg TC/g MLSS/d. Analysis of zeta potential and extracellular polymeric substances composition of the activated sludge revealed that SMF increased electrostatic interactions between TC and activated sludge and made activated sludge has much more binding sites, finally resulting in the increased TC biosorption. Metagenomic analysis showed that SMF promoted the enrichment of ammonia-oxidizing bacteria, TC-degrading bacteria, and aromatic compounds-degrading bacteria; it also enhanced ammonia monooxygenase- and cytochrome P450-mediated TC metabolism while upregulating functional genes associated with oxidase, reductase, and dehydrogenase - all contributing to increased TC biodegradation. Additionally, SMF mitigated the enrichment and spread of antibiotic resistance genes (ARGs) by decreasing the abundance of potential hosts of ARGs and inhibiting the upregulation of genes encoding ABC transporters and putative transposase. Based on these findings, this study demonstrates that magnetic field is an enhancement strategy with great potential to relieve the harmful impacts of the growing antibiotic wastewater problem on human health and the ecosystem.},
}

@article {pmid39038423,
year = {2024},
author = {Li, HQ and Xu, MR and An, XL and Liao, H and Li, LJ and Li, W and Su, JQ},
title = {High-risk ARGs (HRA) Chip: A high-throughput qPCR-based array for assessment of high-risk ARGs from the environment.},
journal = {Water research},
volume = {262},
number = {},
pages = {122106},
doi = {10.1016/j.watres.2024.122106},
pmid = {39038423},
issn = {1879-2448},
abstract = {The global surge in antibiotic resistance genes (ARGs) presents a serious public health challenge. While methods like metagenomic analysis and qPCR arrays have been instrumental in investigating ARG distributions and dynamics, the vast diversity of ARGs often complicates effective monitoring and risk assessment. Here, we developed a High-Risk ARGs (HRA) chip based on high-capacity quantitative PCR array targeting previously identified high-risk ARGs. These ARGs are known to be prevalent in human-related environments, exhibit gene mobility, and are present in ESKAPE pathogens. The HRA chip include 101 primer sets and the 16S rRNA gene as a reference. These primer sets consist of 34 obtained from previous studies, and 67 newly designed primer sets which were validated in silico and experimentally. Absolute quantification of targeted ARGs is accomplished by generating standard curves for all ARGs with serially ten-fold diluted mixed plasmids containing targeted ARG sequences. The amplification efficiencies of all ARGs exceed 99% via plasmid template dilution tests, suggesting high reliability in quantification. The performance of HRA chip is further evaluated by practical applications in environmental samples from wastewater treatment plants (WWTPs) and soils with various land use types and fertilization regimes. The results indicate the dynamics of high-risk ARGs during wastewater treatment process, and reveal the profiles of soil high-risk ARGs which is distinct from those derived via metagenomic approaches. These findings highlight the potentials of HRA Chip in the evaluation of anthropogenic impacts on the environmental resistome with a more focused spectrum of high-risk ARGs. Overall, the HRA Chip emerges as a powerful and efficient high-throughput tool for rapid detection and quantification of high-risk ARGs, facilitating comprehensive profiling of high-risk resistomes in environmental samples which is essential for human health risk assessment of ARGs.},
}

@article {pmid39038418,
year = {2024},
author = {Tsopanakis, V and Anastasiadou, E and Mikkelsen, MD and Meyer, AS and Pavlidis, IV},
title = {Identification and characterization of a novel thermostable PL7 alginate lyase from a submarine volcanic metagenomic library.},
journal = {Enzyme and microbial technology},
volume = {180},
number = {},
pages = {110486},
doi = {10.1016/j.enzmictec.2024.110486},
pmid = {39038418},
issn = {1879-0909},
abstract = {Seaweed biomass is as an abundant and renewable source of complex polysaccharides, including alginate which has a variety of applications. A sustainable method for exploiting alginate towards the production of valuable oligosaccharides is through enzymatic processing, using alginate lyases. Industrial refinement methods demand robust enzymes. Metagenomic libraries from extreme environments are a new source of unique enzymes with great industrial potential. Herein we report the identification of a new thermostable alginate lyase with only 58 % identity to known sequences, identified by mining a metagenomic library obtained from the hydrothermal vents of the volcano Kolumbo in the Aegean Sea (Kolumbo Alginate Lyase, KAlLy). Sequence analysis and biochemical characterization of KAlLy showed that this new alginate lyase is a Polysaccharide Lyase of family 7 (PL7) enzyme with endo- and exo-action on alginate and poly-mannuronic acid, with high activity at 60°C (56 ± 8 U/mg) and high thermostability (half-life time of 30 h at 50°C). The response surface methodology analysis revealed that the reaction optimum conditions with poly-mannuronic acid as substrate are 44°C, pH of 5.5 with 440 mM NaCl. This novel alginate lyase is a valuable addition to the toolbox of alginate modifying enzymes, due to its diverse sequence and its good thermal stability.},
}

@article {pmid39038407,
year = {2024},
author = {Rolbiecki, D and Paukszto, Ł and Krawczyk, K and Korzeniewska, E and Sawicki, J and Harnisz, M},
title = {Genomic and metagenomic analysis reveals shared resistance genes and mobile genetic elements in E. coli and Klebsiella spp. isolated from hospital patients and hospital wastewater at intra- and inter-genus level.},
journal = {International journal of hygiene and environmental health},
volume = {261},
number = {},
pages = {114423},
doi = {10.1016/j.ijheh.2024.114423},
pmid = {39038407},
issn = {1618-131X},
abstract = {Antimicrobial resistance (AMR) is a global problem that gives serious cause for concern. Hospital wastewater (HWW) is an important link between the clinical setting and the natural environment, and an escape route for pathogens that cause hospital infections, including urinary tract infections (UTI). Bacteria of the genera Escherichia and Klebsiella are common etiological factors of UTI, especially in children, and they can cause short-term infections, as well as chronic conditions. ESBL-producing Escherichia and Klebsiella have also emerged as potential indicators for estimating the burden of antimicrobial resistance under environmental conditions and the spread of AMR between clinical settings and the natural environment. In this study, whole-genome sequencing and the nanopore technology were used to analyze the complete genomes of ESBL-producing E.coli and Klebsiella spp. and the HWW metagenome, and to characterize the mechanisms of AMR. The similarities and differences in the encoded mechanisms of AMR in clinical isolates (causing UTI) and environmental strains (isolated from HWW and the HWW metagenome) were analyzed. Special attention was paid to the genetic context and the mobility of antibiotic resistance genes (ARGs) to determine the common sources and potential transmission of these genes. The results of this study suggest that the spread of drug resistance from healthcare facilities via HWW is not limited to the direct transmission of resistant clonal lines that are typically found in the clinical setting, but it also involves the indirect transfer of mobile elements carrying ARGs between bacteria colonizing various environments. Hospital wastewater could offer a supportive environment for plasmid evolution through the insertion of new ARGs, including typical chromosomal regions. These results indicate that interlined environments (hospital patients - HWW) should be closely monitored to evaluate the potential transmission routes of drug resistance in bacteria.},
}

@article {pmid39037720,
year = {2024},
author = {Du, S and Bi, L and Lin, D and Zheng, XQ and Neilson, R and Zhu, D},
title = {Viral Communities Suppress the Earthworm Gut Antibiotic Resistome by Lysing Bacteria on a National Scale.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c03812},
pmid = {39037720},
issn = {1520-5851},
abstract = {Earthworms are critical in regulating soil processes and act as filters for antibiotic resistance genes (ARGs). Yet, the geographic patterns and main drivers of earthworm gut ARGs remain largely unknown. We collected 52 earthworm and soil samples from arable and forest ecosystems along a 3000 km transect across China, analyzing the diversity and abundance of ARGs using shotgun metagenomics. Earthworm guts harbored a lower diversity and abundance of ARGs compared to soil, resulting in a stronger distance-decay rate of ARGs in the gut. Greater deterministic assembly processes of ARGs were found in the gut than in soil. The earthworm gut had a lower frequency of co-occurrence patterns between ARGs and mobile genetic elements (MGEs) in forest than in arable systems. Viral diversity was higher in the gut compared to soil and was negatively correlated with bacterial diversity. Bacteria such as Streptomyces and Pseudomonas were potential hosts of both viruses and ARGs. Viruses had negative effects on the diversity and abundance of ARGs, likely due to the lysis on ARG-bearing bacteria. These findings provide new insights into the variations of ARGs in the earthworm gut and highlight the vital role of viruses in the regulation of ARGs in the soil ecosystem.},
}

@article {pmid39037634,
year = {2024},
author = {Elmagzoub, WA and Idris, SM and Elnaiem, MHE and Mukhtar, ME and Eltayeb, E and Bakhiet, SM and Okuni, JB and Ojok, L and El Sanousi, SM and El Wahed, AA and Gameel, AA and Eltom, KH},
title = {Faecal microbial diversity in a cattle herd infected by Mycobacterium avium subsp. paratuberculosis: a possible effect of production status.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {9},
pages = {276},
pmid = {39037634},
issn = {1573-0972},
support = {Project number 404935781//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; Cattle ; *Mycobacterium avium subsp. paratuberculosis/isolation & purification/genetics ; *Feces/microbiology ; *Paratuberculosis/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Cattle Diseases/microbiology ; *Milk/microbiology ; *DNA, Bacterial/genetics ; Gastrointestinal Microbiome ; Female ; Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; },
abstract = {Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease, or paratuberculosis (PTB) in ruminants, besides having zoonotic potential. It possibly changes the gut microbiome, but no conclusive data are available yet. This study aimed at investigating the influence of MAP on the faecal microbiome of cattle naturally infected with PTB. In a follow up period of 10 months, PTB status was investigated in a herd of dairy cattle with history of clinical cases. Each animal was tested for MAP infection using serum and milk ELISA for MAP anti-bodies and IS900 real-time PCR and recombinase polymerase amplification assays for MAP DNA in the faeces and milk monthly for 4 successive months, then a last one after 6 months. The faecal samples were subjected to 16S rDNA metagenomic analysis using Oxford Nanopore Sequencing Technology. The microbial content was compared between animal groups based on MAP positivity rate and production status. All animals were MAP positive by one or more tests, but two animals were consistently negative for MAP DNA in the faeces. In all animals, the phyla firmicutes and bacteroidetes were highly enriched with a small contribution of proteobacteria, and increased abundance of the families Oscillospiraceae, Planococcaceae, and Streptococcacaceae was noted. Animals with high MAP positivity rate showed comparable faecal microbial content, although MAP faecal positivity had no significant effect (p > 0.05) on the microbiome. Generally, richness and evenness indices decreased with increasing positivity rate. A significantly different microbial content was found between dry cows and heifers (p < 0.05). Particularly, Oscillospiraceae and Rikenellaceae were enriched in heifers, while Planococcaceae and Streptococcaceae were overrepresented in dry cows. Furthermore, abundance of 72 genera was significantly different between these two groups (p < 0.05). Changes in faecal microbiome composition were notably associated with increasing MAP shedding in the faeces. The present findings suggest a combined influence of the production status and MAP on the cattle faecal microbiome. This possibly correlates with the fate of the infection, the concern in disease control, again remains for further investigations.},
}

Animals
Cattle
*Mycobacterium avium subsp. paratuberculosis/isolation & purification/genetics
*Feces/microbiology
*Paratuberculosis/microbiology
*RNA, Ribosomal, 16S/genetics
*Cattle Diseases/microbiology
*Milk/microbiology
*DNA, Bacterial/genetics
Gastrointestinal Microbiome
Female
Bacteria/classification/genetics/isolation & purification
Metagenomics/methods

@article {pmid39037315,
year = {2024},
author = {Marín-Paredes, R and Peña-Ocaña, BA and Martínez-Romero, E and Gutiérrez-Sarmiento, W and Ruíz-Valdiviezo, V and Jasso-Chávez, R and Servín-Garcidueñas, LE},
title = {Metagenome-Assembled Genome of "Candidatus Aramenus sp. CH1" from the Chichon volcano, Mexico.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0052624},
doi = {10.1128/mra.00526-24},
pmid = {39037315},
issn = {2576-098X},
abstract = {The Chichon volcano contains several thermal manifestations including an acidic crater lake. Here we report a metagenome-assembled genome of "Candidatus Aramenus sp. CH1," a Sulfolobales archaeon inhabiting the crater lake from the Chichon volcano. In this study, we generated a novel Aramenus genome sequence from a thermal area in Southern Mexico.},
}

@article {pmid39037310,
year = {2024},
author = {Li, M and Dong, Y and Liu, C and Liu, H and Wang, Z and Ma, J and Wang, X and Zhang, X},
title = {Metagenome-assembled bacterial genomes derived from various aging flue-cured tobacco samples.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0042724},
doi = {10.1128/mra.00427-24},
pmid = {39037310},
issn = {2576-098X},
abstract = {We recovered 16 bacterial metagenome-assembled genomes from 11 flue-cured tobacco samples with different aging stage and various geographic origins. Their sizes range from 2.3 M to 5.4 M, with GC contents of 43.17%-74.45%, completeness of 78.80%-99.25%, and contamination of 0.47%-8.56%.},
}

@article {pmid39036956,
year = {2024},
author = {Popova, AM and Jain, N and Dong, X and Abdollah-Nia, F and Britton, RA and Williamson, JR},
title = {Complete list of canonical post-transcriptional modifications in the Bacillus subtilis ribosome and their link to RbgA driven large subunit assembly.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae626},
pmid = {39036956},
issn = {1362-4962},
support = {R01GM110248/NH/NIH HHS/United States ; //The Scripps Research Institute/ ; },
abstract = {Ribosomal RNA modifications in prokaryotes have been sporadically studied, but there is a lack of a comprehensive picture of modification sites across bacterial phylogeny. Bacillus subtilis is a preeminent model organism for gram-positive bacteria, with a well-annotated and editable genome, convenient for fundamental studies and industrial use. Yet remarkably, there has been no complete characterization of its rRNA modification inventory. By expanding modern MS tools for the discovery of RNA modifications, we found a total of 25 modification sites in 16S and 23S rRNA of B. subtilis, including the chemical identity of the modified nucleosides and their precise sequence location. Furthermore, by perturbing large subunit biogenesis using depletion of an essential factor RbgA and measuring the completion of 23S modifications in the accumulated intermediate, we provide a first look at the order of modification steps during the late stages of assembly in B. subtilis. While our work expands the knowledge of bacterial rRNA modification patterns, adding B. subtilis to the list of fully annotated species after Escherichia coli and Thermus thermophilus, in a broader context, it provides the experimental framework for discovery and functional profiling of rRNA modifications to ultimately elucidate their role in ribosome biogenesis and translation.},
}

@article {pmid39036782,
year = {2024},
author = {Cai, TT and Ma, R},
title = {Matrix Reordering for Noisy Disordered Matrices: Optimality and Computationally Efficient Algorithms.},
journal = {IEEE transactions on information theory},
volume = {70},
number = {1},
pages = {509-531},
pmid = {39036782},
issn = {0018-9448},
abstract = {Motivated by applications in single-cell biology and metagenomics, we investigate the problem of matrix reordering based on a noisy disordered monotone Toeplitz matrix model. We establish the fundamental statistical limit for this problem in a decision-theoretic framework and demonstrate that a constrained least squares estimator achieves the optimal rate. However, due to its computational complexity, we analyze a popular polynomial-time algorithm, spectral seriation, and show that it is suboptimal. To address this, we propose a novel polynomial-time adaptive sorting algorithm with guaranteed performance improvement. Simulations and analyses of two real single-cell RNA sequencing datasets demonstrate the superiority of our algorithm over existing methods.},
}

@article {pmid39035870,
year = {2024},
author = {Rabbachin, L and Nir, I and Waldherr, M and Vassallo, Y and Piñar, G and Graf, A and Kushmaro, A and Sterflinger, K},
title = {Diversity of fungi associated with petroglyph sites in the Negev Desert, Israel, and their potential role in bioweathering.},
journal = {Frontiers in fungal biology},
volume = {5},
number = {},
pages = {1400380},
pmid = {39035870},
issn = {2673-6128},
abstract = {The petroglyphs of the Negev Desert, Israel, are famous and valuable archaeological remains. Previous studies have investigated the microbial communities associated with petroglyphs and their potential role in stone deterioration; nevertheless, the role of fungi remains unclear. In this study, the fungal communities present on the stone and, as a comparison, in the surrounding environment (soil and air) at Negev petroglyph sites were analyzed by means of culture-dependent and -independent (metagenomic) techniques. The metagenomic results showed a high fungal biodiversity in the soil, and both approaches highlighted the prevalence of species producing melanized, large, thick-walled spores (mainly Alternaria spp.). From the air sampling, mostly Cladosporium spp. were retrieved. On the other hand, on the rock, the results seem to indicate a low presence of fungi, but with a rock-specialized mycobiota consisting of extremotolerant microcolonial fungi (MCF) (e.g., Vermiconidia and Coniosporium) and lichens (Flavoplaca). In addition, low proportions of cosmopolitan fungi were detected on the stone, but the comparison of the data clearly indicates that they are transients from the surrounding environment. The ability of the isolated strains to dissolve CaCO3 and therefore be a potential threat to the petroglyphs (limestone substrate) was tested, but only one strain resulted in positive acid production under laboratory conditions. Nevertheless, both lichens and MCF detected in this study are well-known stone deteriogens, which may have a significant impact on the petroglyph's deterioration.},
}

@article {pmid39035737,
year = {2024},
author = {Fan, B and Sun, X and Han, W and Zou, Y and Chen, F and Lan, F and Li, W and Mao, Y},
title = {Immune checkpoint inhibitor increased mortality in lung cancer patients with Pneumocystis jirovecii pneumonia: a comparative retrospective cohort study.},
journal = {Frontiers in oncology},
volume = {14},
number = {},
pages = {1398357},
pmid = {39035737},
issn = {2234-943X},
abstract = {INTRODUCTION: Pneumocystis jirovecii pneumonia (PJP) is a life-threatening infection in immunocompromised individuals. Immune checkpoint inhibitor (ICI) has brought significant survival benefit in lung cancer patients. Although the few studies showed there was high mortality in PJP patients with ICI use, these studies had no comparative control groups.

METHODS: A retrospective study was conducted to compare the mortality in PJP patients with lung cancer between those treated with ICI and a concurrent control group treated without ICI.

RESULTS: A total number of 20 non-human immunodeficiency virus (HIV) patients with confirmed PJP and co-existing lung cancer were included in the current study, and classified into ICI group (n=9) and non-ICI group (n=11).There was a clear trend to a shorter onset of PJP in ICI group than non-ICI group (118.9 ± 60.9 vs 253.0 ± 185.1 days), although without statistical significance (p=0.053). Bronchoscopic alveolar lavage fluid were collected from all patients and used to identify Pneumocystis jirovecii. In both groups, metagenomics next-generation sequencing (mNGS) were the most used diagnostic techniques. Within 28 days after the onset of PJP, mortality was significantly higher in the ICI group than non-ICI group (33.3% vs 0, p=0.042).

CONCLUSION: Lung cancer patients with ICI use had a higher mortality rate after PJP infection than patients without ICI use. Prospective studies with larger sample size and a multi-center design are warranted to further verify the present results.},
}

@article {pmid39035441,
year = {2024},
author = {Guan, Y and Zhao, S and Li, J and Zhang, W and Guo, Z and Luo, Y and Jiang, X and Li, J and Liu, J and Chen, X and Zhao, Z and Zhang, Z},
title = {Insights from metagenomics into gut microbiome associated with acute coronary syndrome therapy.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1369478},
pmid = {39035441},
issn = {1664-302X},
abstract = {Acute coronary syndrome (ACS) is a predominant cause of mortality, and the prompt and precise identification of this condition is crucial to minimize its impact. Recent research indicates that gut microbiota is associated with the onset, progression, and treatment of ACS. To investigate its role, we sequenced the gut microbiota of 38 ACS patients before and after percutaneous coronary intervention and statin therapy at three time points, examining differential species and metabolic pathways. We observed a decrease in the abundance of Parabacteroides, Escherichia, and Blautia in patients after treatment and an increase in the abundance of Gemalla, Klebsiella variicola, Klebsiella pneumoniae, and others. Two pathways related to sugar degradation were more abundant in patients before treatment, possibly correlated with disorders of sugar metabolism and risk factors, such as hyperglycemia, insulin resistance, and insufficient insulin secretion. Additionally, seven pathways related to the biosynthesis of vitamin K2 and its homolog were reduced after treatment, suggesting that ACS patients may gradually recover after therapy. The gut microbiota of patients treated with different statins exhibited notable differences after treatment. Rosuvastatin appeared to promote the growth of anti-inflammatory bacteria while reducing pro-inflammatory bacteria, whereas atorvastatin may have mixed effects on pro-inflammatory and anti-inflammatory bacteria while increasing the abundance of Bacteroides. Our research will provide valuable insights and enhance comprehension of ACS, leading to better patient diagnosis and therapy.},
}

@article {pmid39034696,
year = {2024},
author = {Gaudin, M and Eveillard, D and Chaffron, S},
title = {Ecological associations distribution modelling of marine plankton at a global scale.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1909},
pages = {20230169},
doi = {10.1098/rstb.2023.0169},
pmid = {39034696},
issn = {1471-2970},
support = {//H2020 European Commission project AtlantECO/ ; },
mesh = {*Plankton/physiology ; *Climate Change ; *Models, Biological ; Food Chain ; Ecosystem ; Aquatic Organisms/physiology ; Oceans and Seas ; },
abstract = {Marine plankton communities form intricate networks of interacting organisms at the base of the food chain, and play a central role in regulating ocean biogeochemical cycles and climate. However, predicting plankton community shifts in response to climate change remains challenging. While species distribution models are valuable tools for predicting changes in species biogeography under climate change scenarios, they generally overlook the key role of biotic interactions, which can significantly shape ecological processes and ecosystem responses. Here, we introduce a novel statistical framework, association distribution modelling (ADM), designed to model and predict ecological associations distribution in space and time. Applied on a Tara Oceans genome-resolved metagenomics dataset, the present-day biogeography of ADM-inferred marine plankton associations revealed four major biogeographic biomes organized along a latitudinal gradient. We predicted the evolution of these biome-specific communities in response to a climate change scenario, highlighting differential responses to environmental change. Finally, we explored the functional potential of impacted plankton communities, focusing on carbon fixation, outlining the predicted evolution of its geographical distribution and implications for ecosystem function.This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.},
}

*Plankton/physiology
*Climate Change
*Models, Biological
Food Chain
Ecosystem
Aquatic Organisms/physiology
Oceans and Seas

@article {pmid39034691,
year = {2024},
author = {Nef, C and Pierella Karlusich, JJ and Bowler, C},
title = {From nets to networks: tools for deciphering phytoplankton metabolic interactions within communities and their global significance.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1909},
pages = {20230172},
doi = {10.1098/rstb.2023.0172},
pmid = {39034691},
issn = {1471-2970},
support = {//Université de Recherche Paris Sciences et Lettres/ ; //Horizon 2020 Framework Programme/ ; //Fonds Français pour l'Environnement Mondial/ ; //Simons Foundation/ ; //Agence Nationale de la Recherche/ ; //HORIZON EUROPE European Research Council/ ; },
mesh = {*Phytoplankton/metabolism/physiology ; *Food Chain ; Ecosystem ; },
abstract = {Our oceans are populated with a wide diversity of planktonic organisms that form complex dynamic communities at the base of marine trophic networks. Within such communities are phytoplankton, unicellular photosynthetic taxa that provide an estimated half of global primary production and support biogeochemical cycles, along with other essential ecosystem services. One of the major challenges for microbial ecologists has been to try to make sense of this complexity. While phytoplankton distributions can be well explained by abiotic factors such as temperature and nutrient availability, there is increasing evidence that their ecological roles are tightly linked to their metabolic interactions with other plankton members through complex mechanisms (e.g. competition and symbiosis). Therefore, unravelling phytoplankton metabolic interactions is the key for inferring their dependency on, or antagonism with, other taxa and better integrating them into the context of carbon and nutrient fluxes in marine trophic networks. In this review, we attempt to summarize the current knowledge brought by ecophysiology, organismal imaging, in silico predictions and co-occurrence networks using 'omics data, highlighting successful combinations of approaches that may be helpful for future investigations of phytoplankton metabolic interactions within their complex communities.This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.},
}

*Phytoplankton/metabolism/physiology
*Food Chain
Ecosystem

@article {pmid39034613,
year = {2024},
author = {Krigul, KL and Feeney, RH and Wongkuna, S and Aasmets, O and Holmberg, SM and Andreson, R and Puértolas-Balint, F and Pantiukh, K and Sootak, L and Org, T and Tenson, T and Org, E and Schroeder, BO},
title = {A history of repeated antibiotic usage leads to microbiota-dependent mucus defects.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2377570},
doi = {10.1080/19490976.2024.2377570},
pmid = {39034613},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Anti-Bacterial Agents/pharmacology ; Mice ; *Fecal Microbiota Transplantation ; *Mucus/metabolism/microbiology ; *Bacteria/classification/genetics/drug effects/isolation & purification/metabolism ; Intestinal Mucosa/microbiology/metabolism/drug effects ; Male ; Female ; Feces/microbiology ; Adult ; Middle Aged ; Akkermansia ; Mice, Inbred C57BL ; Colon/microbiology ; Bacteroides fragilis/drug effects ; },
abstract = {Recent evidence indicates that repeated antibiotic usage lowers microbial diversity and ultimately changes the gut microbiota community. However, the physiological effects of repeated - but not recent - antibiotic usage on microbiota-mediated mucosal barrier function are largely unknown. By selecting human individuals from the deeply phenotyped Estonian Microbiome Cohort (EstMB), we here utilized human-to-mouse fecal microbiota transplantation to explore long-term impacts of repeated antibiotic use on intestinal mucus function. While a healthy mucus layer protects the intestinal epithelium against infection and inflammation, using ex vivo mucus function analyses of viable colonic tissue explants, we show that microbiota from humans with a history of repeated antibiotic use causes reduced mucus growth rate and increased mucus penetrability compared to healthy controls in the transplanted mice. Moreover, shotgun metagenomic sequencing identified a significantly altered microbiota composition in the antibiotic-shaped microbial community, with known mucus-utilizing bacteria, including Akkermansia muciniphila and Bacteroides fragilis, dominating in the gut. The altered microbiota composition was further characterized by a distinct metabolite profile, which may be caused by differential mucus degradation capacity. Consequently, our proof-of-concept study suggests that long-term antibiotic use in humans can result in an altered microbial community that has reduced capacity to maintain proper mucus function in the gut.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Animals
*Anti-Bacterial Agents/pharmacology
Mice
*Fecal Microbiota Transplantation
*Mucus/metabolism/microbiology
*Bacteria/classification/genetics/drug effects/isolation & purification/metabolism
Intestinal Mucosa/microbiology/metabolism/drug effects
Male
Female
Feces/microbiology
Adult
Middle Aged
Akkermansia
Mice, Inbred C57BL
Colon/microbiology
Bacteroides fragilis/drug effects

@article {pmid39033825,
year = {2024},
author = {Dong, Z and Han, K and Xie, Q and Lin, C and Shen, X and Hao, Y and Li, J and Xu, H and He, L and Yu, T and Kuang, W},
title = {Core antibiotic resistance genes mediate gut microbiota to intervene in the treatment of major depressive disorder.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jad.2024.07.106},
pmid = {39033825},
issn = {1573-2517},
abstract = {INTRODUCTION: The relationship between depression and gut microbiota remains unclear, but an important role of gut microbiota has been verified. The relationship between gut microbiota and antibiotic resistance genes (ARGs) may be a potential new explanatory pathway.

METHODS: We collected samples from 63 depressed patients and 30 healthy controls for metagenomic sequencing. The two groups' microbiota characteristics, functional characteristics, and ARG differences were analyzed.

RESULTS: We obtained 30 differential KEGG orthologs (KOs) and their producers in 5 genera and 7 species by HUMAnN3. We found 6 KOs from Weissella_cibaria and Lactobacillus_plantaru are potentially coring functional mechanism of gut microbiota. Different metabolites including sphingolipids, pyrans, prenol lipids, and isoflavonoids also showed significance between MDD and HC. We detected 48 significantly different ARGs: 5 ARGs up-regulated and 43 ARGs down-regulated in MDD compared to HC. Based on Cox model results, Three ARGs significantly affected drug efficacy (ARG29, ARG105, and ARG111). Eggerthella, Weissella, and Lactobacillus were correlated with different core ARGs, which indicated different mechanisms in affecting MDD.

LIMITATIONS: The present study needs to be replicated in different ethnic groups. At the same time, a larger Chinese cohort study and detailed experimental verification are also the key to further discussion.

CONCLUSION: Our findings suggest that ARGs play a role in the interplay between major depressive disorder and gut microbiota. The role of ARGs should be taken into account when understanding the relationship between depression and gut microbiota.},
}

@article {pmid39033688,
year = {2024},
author = {Berryman, MA and Ilonen, J and Triplett, EW and Ludvigsson, J},
title = {Functional metagenomic analysis reveals potential inflammatory triggers associated with genetic risk for autoimmune disease.},
journal = {Journal of autoimmunity},
volume = {148},
number = {},
pages = {103290},
doi = {10.1016/j.jaut.2024.103290},
pmid = {39033688},
issn = {1095-9157},
abstract = {To assess functional differences between the microbiomes of individuals with autoimmune risk-associated human leukocyte antigen (HLA) genetics and autoimmune protection-associated HLA, we performed a metagenomic analysis of stool samples from 72 infants in the All Babies in Southeast Sweden general-population cohort and assessed haplotype-peptide binding affinities. Infants with risk-associated HLA DR3-DQ2.5 and DR4-DQ8 had a higher abundance of known pathogen-associated molecular patterns and virulence related genes than infants with protection-associated HLA DR15-DQ6.2. However, there was limited overlap in the type of inflammatory trigger between risk groups. Supported by a high Firmicutes/Bacteroides ratio and differentially abundant flagellated species, genes related to the synthesis of flagella were prominent in those with HLA DR3-DQ2.5. However, this haplotype had a significantly lower likelihood of binding affinity to flagellin peptides. O-antigen biosynthesis genes were significantly correlated with the risk genotypes and absent from protective genotype association, supported by the differential abundance of gram-negative bacteria seen in the risk-associated groups. Genes related to vitamin B biosynthesis stood out in higher abundance in infants with HLA DR3-DQ2.5/DR4-DQ8 heterozygosity compared to those with autoimmune-protective genetics. Prevotella species and genus were significantly abundant in all infant groups with high risk for autoimmune disease. The potential inflammatory triggers associated with genetic risk for autoimmunity have significant implications. These results suggest that certain HLA haplotypes may be creating the opportunity for dysbiosis and subsequent inflammation early in life by clearing beneficial microbes or not clearing proinflammatory microbes. This HLA gatekeeping may prevent genetically at-risk individuals from benefiting from probiotic therapies by restricting the colonization of those beneficial bacteria.},
}

@article {pmid39033587,
year = {2024},
author = {Pavon, JAR and da Silva Neves, NA and Pinho, JB and de Souza, VJ and Patroca da Silva, S and Ribeiro Cruz, AC and de Almeida Medeiros, DB and Teixeira Nunes, MR and Slhessarenko, RD},
title = {Disclosing the virome of Aedes, Anopheles and Culex female mosquitoes, Alto Pantanal of Mato Grosso, Brazil, 2019.},
journal = {Virology},
volume = {598},
number = {},
pages = {110182},
doi = {10.1016/j.virol.2024.110182},
pmid = {39033587},
issn = {1096-0341},
abstract = {Using Illumina NextSeq sequencing and bioinformatics, we identified and characterized thirty-three viral sequences of unsegmented and multipartite viral families in Aedes spp., Culex sp. and Anopheles darlingi female mosquito pools from Porto São Luiz and Pirizal, Alto Pantanal. Seventeen sequences belong to unsegmented viral families, twelve represent putative novel insect-specific viruses (ISVs) within families Chuviridae (3/33; partial genomes) and coding-complete sequences of Xinmoviridae (1/33), Rhabdoviridae (2/33) and Metaviridae (6/33); and five coding-complete sequences of already-known ISVs. Notably, two putative novel rhabdoviruses, Corixo rhabdovirus 1 and 2, were phylogenetically related to Coxipo dielmovirus, but separated from other Alpharhabdovirinae genera, sharing Anopheles spp. as host. Regarding multipartite families, sixteen segments of different putative novel viruses were identified (13 coding-complete segments) within Durnavirales (4/33), Elliovirales (1/33), Hareavirales (3/33) and Reovirales (8/33) orders. Overall, this study describes twenty-eight (28/33) putative novel ISVs and five (5/33) already described viruses using metagenomics approach.},
}

@article {pmid39033282,
year = {2024},
author = {Tsola, SL and Prevodnik, AA and Sinclair, LF and Sanders, IA and Economou, CK and Eyice, Ö},
title = {Methanomethylovorans are the dominant dimethylsulfide-degrading methanogens in gravel and sandy river sediment microcosms.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {51},
pmid = {39033282},
issn = {2524-6372},
support = {10.46936/10.25585/60001216//Joint Genome Institute/ ; },
abstract = {BACKGROUND: Rivers and streams are important components of the global carbon cycle and methane budget. However, our understanding of the microbial diversity and the metabolic pathways underpinning methylotrophic methane production in river sediments is limited. Dimethylsulfide is an important methylated compound, found in freshwater sediments. Yet, the magnitude of DMS-dependent methanogenesis nor the methanogens carrying out this process in river sediments have been explored before. This study addressed this knowledge gap in DMS-dependent methanogenesis in gravel and sandy river sediments.

RESULTS: Significant methane production via DMS degradation was found in all sediment  microcosms. Sandy, less permeable river sediments had higher methane yields (83 and 92%) than gravel, permeable sediments (40 and 48%). There was no significant difference between the methanogen diversity in DMS-amended gravel and sandy sediment microcosms, which Methanomethylovorans dominated. Metagenomics data analysis also showed the dominance of Methanomethylovorans and Methanosarcina. DMS-specific methyltransferase genes (mts) were found in very low relative abundances whilst the methanol-, trimethylamine- and dimethylamine-specific methyltransferase genes (mtaA, mttB and mtbB) had the highest relative abundances, suggesting their involvement in DMS-dependent methanogenesis.

CONCLUSIONS: This is the first study demonstrating a significant potential for DMS-dependent methanogenesis in river sediments with contrasting geologies. Methanomethylovorans were the dominant methylotrophic methanogen in all river sediment microcosms. Methyltransferases specific to methylotrophic substrates other than DMS are likely key enzymes in DMS-dependent methanogenesis, highlighting their versatility and importance in the methane cycle in freshwater sediments, which would warrant further study.},
}

@article {pmid39033279,
year = {2024},
author = {Trinh, P and Teichman, S and Roberts, MC and Rabinowitz, PM and Willis, AD},
title = {A cross-sectional comparison of gut metagenomes between dairy workers and community controls.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {708},
doi = {10.1186/s12864-024-10562-1},
pmid = {39033279},
issn = {1471-2164},
support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; T32 ES015459/ES/NIEHS NIH HHS/United States ; R21 AI168679/AI/NIAID NIH HHS/United States ; R21 AI168679/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; *Metagenome ; Female ; Dairying ; Metagenomics/methods ; Adult ; Animals ; Middle Aged ; Bacteria/genetics/classification ; Farmers ; Male ; Drug Resistance, Bacterial/genetics ; },
abstract = {BACKGROUND: As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens before a spillover event. In light of this, we aimed to characterize the microbiomes and resistomes of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases.

RESULTS: Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of 10 dairy farm workers and 6 community controls' gut metagenomes, contextualizing these samples with additional publicly available gut metagenomes. We found no significant differences in the prevalence of resistance genes, virulence factors, or taxonomic composition between the two groups. The lack of statistical significance may be attributed, in part, to the limited sample size of our study or the potential similarities in exposures between the dairy workers and community controls. We did, however, observe patterns warranting further investigation including greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes as well as lower average gene diversity (even after accounting for differential sequencing depth) in dairy workers' metagenomes. We also found evidence of commensal organism association with tetracycline resistance genes in both groups (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii).

CONCLUSIONS: This study highlights the utility of shotgun metagenomics in examining the microbiomes and resistomes of livestock workers, focusing on a cohort of dairy workers in the United States. While our study revealed no statistically significant differences between groups in taxonomy, diversity and gene presence, we observed patterns in antibiotic resistance gene abundance and prevalence that align with findings from previous studies of livestock workers in China and Europe. Our results lay the groundwork for future research involving larger cohorts of dairy and non-dairy workers to better understand the impact of occupational exposure to livestock farming on the microbiomes and resistomes of workers.},
}

Humans
*Gastrointestinal Microbiome/genetics
Cross-Sectional Studies
*Metagenome
Female
Dairying
Metagenomics/methods
Adult
Animals
Middle Aged
Bacteria/genetics/classification
Farmers
Male
Drug Resistance, Bacterial/genetics

@article {pmid39033154,
year = {2024},
author = {Wu, H and Wu, X and Wu, T and Miao, X and Zheng, S and Huang, G and Cheng, X},
title = {Detection Ewingella americana from a patient with Andersson lesion in ankylosing spondylitis by metagenomic next-generation sequencing test: a case report.},
journal = {BMC musculoskeletal disorders},
volume = {25},
number = {1},
pages = {568},
pmid = {39033154},
issn = {1471-2474},
support = {82060403//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Spondylitis, Ankylosing/diagnosis/complications/microbiology ; Male ; *High-Throughput Nucleotide Sequencing ; Adult ; Metagenomics ; Thoracic Vertebrae/diagnostic imaging/microbiology/pathology/surgery ; },
abstract = {BACKGROUND: Andersen's lesion (AL) is a rare complication of ankylosing spondylitis (AS), characterized by nonneoplastic bone destruction, typically manifested as bone destruction and sclerosis in the vertebral body and/or intervertebral disc area. At present, there is no consensus on the pathology and etiology of AL. Repeated trauma, inflammation in essence and part of the natural history of Ankylosing spondylitis itself are the most widely recognized theories of the etiology of AL. However, positive bacteria cultured in bone biopsy of Andersen's lesion (AL) in Ankylosing spondylitis patients are extremely rare. Herein, we report a rare case of detecting Ewingella americana from a patient with Andersson lesion in ankylosing spondylitis by Metagenomic Next-Generation Sequencing (mNGS) Test.

CASE PRESENTATION: This case involved a 39-year-old male with a history of AS for 11 years, who developed AL (T11/12) in the thoracic vertebrae. After sufficient preoperative preparation, we successfully performed one-stage posterior approach corrective surgery and collected bone biopsies samples for examination. Cultured bacteria were not found, and pathological histology indicated infiltration of inflammatory cells. However, it is worth noting that we discovered a gram-negative bacterium, the Ewingella americana, through mNGS testing. Further histopathological examination suggests chronic inflammatory cell infiltration. After one-stage posterior approach corrective surgery, the patient's condition significantly improved. At the 6-month follow-up, the pain significantly decreased, and the patient returned to normal life.

CONCLUSION: We detected Ewinia americana in the bone biopsies of Andersson lesion (AL) in ankylosing spondylitis patient by mNGS.},
}

Humans
*Spondylitis, Ankylosing/diagnosis/complications/microbiology
Male
*High-Throughput Nucleotide Sequencing
Adult
Metagenomics
Thoracic Vertebrae/diagnostic imaging/microbiology/pathology/surgery

@article {pmid39033123,
year = {2024},
author = {Mercado-Evans, V and Zulk, JJ and Hameed, ZA and Patras, KA},
title = {Gestational diabetes as a risk factor for GBS maternal rectovaginal colonization: a systematic review and meta-analysis.},
journal = {BMC pregnancy and childbirth},
volume = {24},
number = {1},
pages = {488},
pmid = {39033123},
issn = {1471-2393},
support = {AI167547//National Institute of Allergy and Infectious Diseases/ ; AI173448//National Institute of Allergy and Infectious Diseases/ ; DK136201/DK/NIDDK NIH HHS/United States ; DK128053/DK/NIDDK NIH HHS/United States ; GM136554/GM/NIGMS NIH HHS/United States ; NGP10103//Burroughs Wellcome Fund/ ; },
mesh = {Humans ; *Diabetes, Gestational/epidemiology ; Female ; Pregnancy ; Risk Factors ; *Streptococcal Infections/epidemiology ; *Streptococcus agalactiae ; *Vagina/microbiology ; *Pregnancy Complications, Infectious/epidemiology/microbiology ; *Rectum/microbiology ; },
abstract = {BACKGROUND: Maternal rectovaginal colonization by group B Streptococcus (GBS) increases the risk of perinatal GBS disease that can lead to death or long-term neurological impairment. Factors that increase the risk of rectovaginal GBS carriage are incompletely understood resulting in missed opportunities for detecting GBS in risk-based clinical approaches. There is a lacking consensus on whether gestational diabetes mellitus (GDM) is a risk factor for rectovaginal GBS. This systematic review and meta-analysis aims to address current conflicting findings and determine whether GDM should be clinically considered as a risk factor for maternal GBS colonization.

METHODS: Peer-reviewed studies that provided GDM prevalence and documented GBS vaginal and/or rectal colonization in women with and without GDM were included in this analysis. From study inception to October 30, 2023, we identified 6,275 relevant studies from EMBASE and PUBMED of which 19 were eligible for inclusion. Eligible studies were analyzed and thoroughly assessed for risk of bias with a modified Newcastle-Ottawa Scale that interrogated representativeness and comparability of cohorts, quality of reporting for GDM and GBS status, and potential bias from other metabolic diseases. Results were synthesized using STATA 18 and analyzed using random-effects meta-analyses.

RESULTS: Studies encompassed 266,706 women from 10 different countries, with study periods spanning from 1981 to 2020. Meta-analysis revealed that gestational diabetes is associated with a 16% increased risk of rectovaginal GBS carriage (OR 1.16, CI 1.07-1.26, P = 0.003). We also performed subgroup analyses to assess independent effects of pregestational vs. gestational diabetes on risk of maternal GBS carriage. Pregestational diabetes (Type 1 or Type 2 diabetes mellitus) was also associated with an increased risk of 76% (pooled OR 1.76, CI 1.27-2.45, P = 0.0008).

CONCLUSIONS: This study achieved a consensus among previously discrepant observations and demonstrated that gestational diabetes and pregestational diabetes are significant risk factors for maternal rectovaginal carriage of GBS. Recognition of GDM as a risk factor during clinical decisions about GBS screening and intrapartum antibiotic prophylaxis may decrease the global burden of GBS on maternal-perinatal health.},
}

Humans
*Diabetes, Gestational/epidemiology
Female
Pregnancy
Risk Factors
*Streptococcal Infections/epidemiology
*Streptococcus agalactiae
*Vagina/microbiology
*Pregnancy Complications, Infectious/epidemiology/microbiology
*Rectum/microbiology

@article {pmid39032544,
year = {2024},
author = {Ioannou, M and Borkent, J and Andreu-Sánchez, S and Wu, J and Fu, J and Sommer, IEC and Haarman, BCM},
title = {Reproducible gut microbial signatures in bipolar and schizophrenia spectrum disorders: A metagenome-wide study.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2024.07.009},
pmid = {39032544},
issn = {1090-2139},
abstract = {BACKGROUND: Numerous studies report gut microbiome variations in bipolar disorder (BD) and schizophrenia spectrum disorders (SSD) compared to healthy individuals, though, there is limited consensus on which specific bacteria are associated with these disorders.

METHODS: In this study, we performed a comprehensive metagenomic shotgun sequencing analysis in 103 Dutch patients with BD/SSD and 128 healthy controls matched for age, sex, body mass index and income, while accounting for diet quality, transit time and technical confounders. To assess the replicability of the findings, we used two validation cohorts (total n = 203), including participants from a distinct population with a different metagenomic isolation protocol.

RESULTS: The gut microbiome of the patients had a significantly different β-diversity, but not α-diversity nor neuroactive potential compared to healthy controls. Initially, twenty-six bacterial taxa were identified as differentially abundant in patients. Among these, the previously reported genera Lachnoclostridium and Eggerthella were replicated in the validation cohorts. Employing the CoDaCoRe learning algorithm, we identified two bacterial balances specific to BD/SSD, which demonstrated an area under the receiver operating characteristic curve (AUC) of 0.77 in the test dataset. These balances were replicated in the validation cohorts and showed a positive correlation with the severity of psychiatric symptoms and antipsychotic use. Last, we showed a positive association between the relative abundance of Klebsiella and Klebsiella pneumoniae with antipsychotic use and between the Anaeromassilibacillus and lithium use.

CONCLUSIONS: Our findings suggest that microbial balances could be a reproducible method for identifying BD/SSD-specific microbial signatures, with potential diagnostic and prognostic applications. Notably, Lachnoclostridium and Eggerthella emerge as frequently occurring bacteria in BD/SSD. Last, our study reaffirms the previously established link between Klebsiella and antipsychotic medication use and identifies a novel association between Anaeromassilibacillus and lithium use.},
}

@article {pmid39032335,
year = {2024},
author = {Fan, Y and Zhou, Z and Liu, F and Qian, L and Yu, X and Huang, F and Hu, R and Su, H and Gu, H and Yan, Q and He, Z and Wang, C},
title = {The vertical partitioning between denitrification and dissimilatory nitrate reduction to ammonium of coastal mangrove sediment microbiomes.},
journal = {Water research},
volume = {262},
number = {},
pages = {122113},
doi = {10.1016/j.watres.2024.122113},
pmid = {39032335},
issn = {1879-2448},
abstract = {Mangrove aquatic ecosystems receive substantial nitrogen (N) inputs from both land and sea, playing critical roles in modulating coastal N fluxes. The microbially-mediated competition between denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in mangrove sediments significantly impacts the N fate and transformation processes. Despite their recognized role in N loss or retention in surface sediments, how these two processes vary with sediment depths and their influential factors remain elusive. Here, we employed a comprehensive approach combining [15]N isotope tracer, quantitative PCR (qPCR) and metagenomics to verify the vertical dynamics of denitrification and DNRA across five 100-cm mangrove sediment cores. Our results revealed a clear vertical partitioning, with denitrification dominated in 0-30 cm sediments, while DNRA played a greater role with increasing depths. Quantification of denitrification and DNRA functional genes further explained this phenomenon. Taxonomic analysis identified Pseudomonadota as the primary denitrification group, while Planctomycetota and Pseudomonadota exhibited high proportion in DNRA group. Furthermore, genome-resolved metagenomics revealed multiple salt-tolerance strategies and aromatic compound utilization potential in denitrification assemblages. This allowed denitrification to dominate in oxygen-fluctuating and higher-salinity surface sediments. However, the elevated C/N in anaerobic deep sediments favored DNRA, tending to generate biologically available NH4[+]. Together, our results uncover the depth-related variations in the microbially-mediated competition between denitrification and DNRA, regulating N dynamics in mangrove ecosystems.},
}

@article {pmid39032333,
year = {2024},
author = {Li, Z and Qiu, S and Xu, S and Lu, X and Wang, Y and Ge, S},
title = {Nano zero valent iron stimulated acetaldehyde oxidation, electron transfer, and RBO pathway for enhanced medium-chain carboxylic acids production.},
journal = {Water research},
volume = {262},
number = {},
pages = {122103},
doi = {10.1016/j.watres.2024.122103},
pmid = {39032333},
issn = {1879-2448},
abstract = {Nano zero-valent iron (NZVI) has been shown to effectively enhance the chain elongation (CE) process, addressing the issue of limited yield of medium-chain carboxylic acids (MCCA) from organic wastewater. However, the specific impact of NZVI on the metabolism of CE bacteria (CEB) is not well understood. In this study, it was aimed to investigate the mechanism by which an optimal concentration of NZVI influences CE metabolism, particularly in relation to ethanol oxidation, electron transfer, and MCCA synthesis. This was achieved through single-factor influence experiments and metagenomic analysis. The results showed that the addition of 1 g/gVSS NZVI achieved the highest MCCA yield (n-caproic acid + n-octanoic acid) at 2.02 g COD/L, which was 4.9 times higher than the control. This improvement in MCCA production induced by NZVI was attributed to several factors. Firstly, NZVI facilitated the oxidation of acetaldehyde, leading to its reduced accumulation in the system (from 18.4 % to 5.8 %), due to the optimized chemical environment created by NZVI corrosion, including near-neutral pH and a more reductive oxidation-reduction potential (ORP). Additionally, the inherent conductivity property of NZVI and the additional Fe ions released during corrosion improved the electron transfer efficiency between CEB. Lastly, both the composition of microbial communities and the abundance of unique enzyme genes confirmed the selective stimulation of NZVI on the reverse β-oxidation (RBO) pathway. These findings provide valuable insights into the role of NZVI in CEB metabolism and its potential application for enhancing MCCA production in CE bioreactors.},
}

@article {pmid39032176,
year = {2024},
author = {Zhang, T and Sun, Y and Parikh, SJ and Colinet, G and Garland, G and Huo, L and Zhang, N and Shan, H and Zeng, X and Su, S},
title = {Water-fertilizer regulation drives microorganisms to promote iron, nitrogen and manganese cycling: A solution for arsenic and cadmium pollution in paddy soils.},
journal = {Journal of hazardous materials},
volume = {477},
number = {},
pages = {135244},
doi = {10.1016/j.jhazmat.2024.135244},
pmid = {39032176},
issn = {1873-3336},
abstract = {The co-contamination of arsenic (As) and cadmium (Cd) in rice fields presents a global imperative for resolution. However, understanding the complex microbially driven geochemical processes and network connectivity crucial for As and Cd bioavailability under the frequent redox transitions in rice fields remains limited. Here, we conducted a series of microcosm experiments, using flooding and drainage, alongside fertilization treatments to emulate different redox environment in paddy soils. Soil As significantly reduced in drained conditions following applications of biochar or calcium-magnesium-phosphate (CMP) fertilizers by 26.3 % and 31.2 %, respectively, with concurrent decreases in Cd levels. Utilizing geochemical models, we identified the primary redox cycles dynamically altering during flooding (Fe and S cycles) and drainage (Fe, Mn, and N cycles). PLS-SEM elucidated 76 % and 61 % of the variation in Cd and As through Mn and N cycles. Functional genes implicated in multi-element cycles were analyzed, revealing a significantly higher abundance of assimilatory N reduction genes (nasA, nirA/B, narB) in drained soil, whereas an increase in ammonia-oxidizing genes (amoA/B) and a decrease in nitrate reduction to ammonium genes were observed after CMP fertilizer application. Biochar application led to significant enrichment of the substrate-binding protein of the Mn transport gene (mntC). Moreover, Fe transport genes were enriched after biochar or CMP application compared to drained soils. Among 40 high-quality metagenome-assembled genomes (MAGs), microbial predictors associated with low Cd and As contents across different treatments were examined. Bradyrhizobacea harbored abundant Mn and Fe[III] transport genes, while Nitrososphaeraceae carried nitrification-related genes. Two MAGs affiliated with Caulobacteraceae, carrying diverse Fe transport genes, were enriched in biochar-applied soils. Therefore, applying CMP fertilizer or biochar in aerobic rice fields can synergistically reduce the bioavailability of Cd and As by specifically enhancing the circulation of essential elements.},
}

@article {pmid39031269,
year = {2024},
author = {Hong, JJ and Zhang, RT and Ma, CL and Hu, QY},
title = {Pulmonary microbial spectrum in late-stage SARS-CoV-2 infection: a case series.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39031269},
issn = {1435-4373},
support = {2020S0180104//2020 Wenling City Social Development Science and Technology Project/ ; 2021KY1229//2021 Zhejiang Province Health and Wellness Science and Technology Plan Project/ ; },
abstract = {Coronavirus disease 2019 (COVID-19), a kind of respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), primarily spreads through the respiratory tract from human to human. Its extensive and rapid spread has led to a global pandemic, causing great harm to human health and economic development all over the world. Current known evidence indicates that SARS-CoV-2 has evolved accumulating multiple mutations, with altered infectivity and viral replication capacity. A better understanding of the complications of COVID-19 and its relationship with underlying diseases is crucial for the prevention and treatment of SARS-CoV-2. This case series reviewed case data of our 4 recent patients with severe or critical COVID-19, including treatment plan, status of pulmonary infection and their microbiology workup with metagenomic next-generation sequencing with bronchoalveolar lavage fluid. This report shed light on the significance of rapid and accurate clinical diagnosis and treatment on COVID-19.},
}

@article {pmid39031093,
year = {2024},
author = {Dong, Q and Su, H and Sun, Y and Zhao, Y and Zhou, D and Wang, X and Jiang, C and Liu, X and Zhong, C and Zhang, H and Kang, S and Zhao, X and Yu, H},
title = {Metagenomic insights into nitrogen cycling functional gene responses to nitrogen fixation and transfer in maize-peanut intercropping.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15034},
pmid = {39031093},
issn = {1365-3040},
support = {//China Agricultural Research System/ ; //Liaoning Province science and technology plan project/ ; },
abstract = {The fixation and transfer of biological nitrogen from peanuts to maize in maize-peanut intercropping systems play a pivotal role in maintaining the soil nutrient balance. However, the mechanisms through which root interactions regulate biological nitrogen fixation and transfer remain unclear. This study employed a [15]N isotope labelling method to quantify nitrogen fixation and transfer from peanuts to maize, concurrently elucidating key microorganisms and genera in the nitrogen cycle through metagenomic sequencing. The results revealed that biological nitrogen fixation in peanut was 50 mg and transfer to maize was 230 mg when the roots interacted. Moreover, root interactions significantly increased nitrogen content and the activities of protease, dehydrogenase (DHO) and nitrate reductase in the rhizosphere soil. Metagenomic analyses and structural equation modelling indicated that nrfC and nirA genes played important roles in regulating nitrogen fixation and transfer. Bradyrhizobium was affected by soil nitrogen content and DHO, indirectly influencing the efficiency of nitrogen fixation and transfer. Overall, our study identified key bacterial genera and genes associated with nitrogen fixation and transfer, thus advancing our understanding of interspecific interactions and highlighting the pivotal role of soil microorganisms and functional genes in maintaining soil ecosystem stability from a molecular ecological perspective.},
}

@article {pmid39030898,
year = {2024},
author = {Stevens, C and Norris, S and Arbeeva, L and Carter, S and Enomoto, M and Nelson, AE and Lascelles, BDX},
title = {Gut microbiome and osteoarthritis: insights from the naturally occurring canine model of OA.},
journal = {Arthritis & rheumatology (Hoboken, N.J.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/art.42956},
pmid = {39030898},
issn = {2326-5205},
abstract = {OBJECTIVES: The purpose was to enhance the current knowledge of the relationship between the gut microbiome and osteoarthritis (OA) and associated pain using pet dogs as a clinically relevant translational model.

METHODS: Fecal samples were collected from 93 owned pet dogs. Dogs were designated either clinically healthy or OA-pain using validated methods. Metagenomic profiling was performed through shotgun sequencing using the Illumina Novaseq platform. MetaPhlAn2 and HUMAnN2 were used to evaluate bacterial taxonomic and pathway relative abundance. Comparisons between healthy and OA-pain groups were performed individually for each taxa using non-parametric tests following Benjamini and Hochberg adjustment for multiple comparisons. Permutation analysis of variance was performed using Bray-Curtis distance matrices. All downstream analyses were completed in R.

RESULTS: No significant differences between healthy and OA-pain dogs were observed for alpha and beta-diversity. We found 13 taxa with nominally significant (p<0.05) associations with OA case status, but none of the associations remained significant after adjustment for multiple comparisons. No differences in alpha, beta diversities or Firmicutes/Bacteroidetes ratio (FBR) were found regarding pain severity, mobility/ activity level, age, or body composition score.

CONCLUSIONS: Similar to recent studies in humans, the present study did not demonstrate a significant difference in the fecal microbial communities between dogs with OA pain and healthy control dogs. Future research in this naturally occurring model should expand on these data and relate the gut microbiome to gut permeability and circulating pro- and anti-inflammatory molecules to better understand the influence of the gut microbiome on OA and OA-pain.},
}

@article {pmid39030686,
year = {2024},
author = {Wallace, BA and Varona, NS and Hesketh-Best, PJ and Stiffler, AK and Silveira, CB},
title = {Globally distributed bacteriophage genomes reveal mechanisms of tripartite phage-bacteria-coral interactions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae132},
pmid = {39030686},
issn = {1751-7370},
abstract = {Reef-building corals depend on an intricate community of microorganisms for functioning and resilience. The infection of coral-associated bacteria by bacteriophages can modify bacteria-host interactions, yet very little is known about phage functions in the holobiont. This gap stems from methodological limitations that have prevented the recovery of high-quality viral genomes and bacterial host assignment from coral samples. Here, we introduce a size fractionation approach that increased bacterial and viral recovery in coral metagenomes by 9-fold and 2-fold, respectively, and enabled the assembly and binning of bacterial and viral genomes at relatively low sequencing coverage. We combined these viral genomes with those derived from 677 publicly available metagenomes, viromes, and bacterial isolates from stony corals to build a global coral virus database of over 20 000 viral genomic sequences spanning four viral realms. The tailed bacteriophage families Kyanoviridae and Autographiviridae were the most abundant, replacing groups formerly referred to as Myoviridae and Podoviridae, respectively. Prophage and CRISPR spacer linkages between these viruses and 626 bacterial metagenome-assembled genomes and bacterial isolates showed that most viruses infected Alphaproteobacteria, the most abundant class, and less abundant taxa like Halanaerobiia and Bacteroidia. A host-phage-gene network identified keystone viruses with the genomic capacity to modulate bacterial metabolic pathways and direct molecular interactions with eukaryotic cells. This study reveals the genomic basis of nested symbioses between bacteriophage, bacteria, and the coral host and its endosymbiotic algae.},
}

@article {pmid39030654,
year = {2024},
author = {Drake, MJ and Daniel, SG and Baker, LD and Indugu, N and Bittinger, K and Dickens, C and Zackular, JP and Pitta, D and Redding, LE},
title = {Effects of dietary zinc on the gut microbiome and resistome of the gestating cow and neonatal calf.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {39},
pmid = {39030654},
issn = {2524-4671},
support = {R35GM138369//National Institutes of General Medical Sciences, National Institutes of Health/ ; 5K23AI163351/NH/NIH HHS/United States ; },
abstract = {Zinc is an essential trace element required in the diet of all species. While the effects of zinc have been studied in growing calves, little is known about the effect of zinc on the microbiota of the gestating cow or her neonatal calf. Understanding factors that shape the gut health of neonatal animals and evaluating the effect of dietary supplements in adult gestating animals is important in promoting animal health and informing feeding practices. The aims of this study were to determine the effect of dietary zinc on the microbiota and resistome of the gestating cow and calf. Gestating cows received standard (40 ppm) or high (205 ppm) dietary zinc levels from dry off to calving. Fecal samples were collected from cows upon enrollment and at calving and from neonatal calves. Fecal samples underwent 16S rRNA sequencing and a subset also underwent shotgun metagenomic sequencing. The effect of zinc supplementation on the diversity and composition of the cow and calf microbiome and resistome was assessed. Alpha and beta diversity and composition of the microbiota were significantly altered over time but not by treatment in the cows, with alpha diversity decreasing and 14 genera found at significantly higher relative abundances at calving compared to enrollment. Levels of 27 antimicrobial resistance genes significantly increased over time. Only a small number of taxa were differentially expressed at calving in treatment and control groups, including Faecalibacterium, Bacteroides, Turicibacter, and Bifidobacterium pseudolongum. No effect of the dam's treatment group was observed on the diversity or composition of the neonatal calf microbiota. The calf resistome, which was relatively rich and diverse compared to the cow, was also unaffected by the dam's treatment group. The impact of high levels of dietary zinc thus appeared to be minimal, with no observed changes in alpha or beta diversity, and few changes in the relative abundance of a small number of taxa and antimicrobial resistance genes.},
}

@article {pmid39030648,
year = {2024},
author = {Moretti, LG and Crusciol, CAC and Leite, MFA and Momesso, L and Bossolani, JW and Costa, OYA and Hungria, M and Kuramae, EE},
title = {Diverse bacterial consortia: key drivers of rhizosoil fertility modulating microbiome functions, plant physiology, nutrition, and soybean grain yield.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {50},
pmid = {39030648},
issn = {2524-6372},
support = {2016/23699-8; 2018/14892-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 151120/2020-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {Soybean cultivation in tropical regions relies on symbioses with nitrogen-fixing Bradyrhizobium and plant growth-promoting bacteria (PGPBs), reducing environmental impacts of N fertilizers and pesticides. We evaluate the effects of soybean inoculation with different bacterial consortia combined with PGPBs or microbial secondary metabolites (MSMs) on rhizosoil chemistry, plant physiology, plant nutrition, grain yield, and rhizosphere microbial functions under field conditions over three growing seasons with four treatments: standard inoculation of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens consortium (SI); SI plus foliar spraying with Bacillus subtilis (SI + Bs); SI plus foliar spraying with Azospirillum brasilense (SI + Az); and SI plus seed application of MSMs enriched in lipo-chitooligosaccharides extracted from B. diazoefficiens and Rhizobium tropici (SI + MSM). Rhizosphere microbial composition, diversity, and function was assessed by metagenomics. The relationships between rhizosoil chemistry, plant nutrition, grain yield, and the abundance of microbial taxa and functions were determined by generalized joint attribute modeling. The bacterial consortia had the most significant impact on rhizosphere soil fertility, which in turn affected the bacterial community, plant physiology, nutrient availability, and production. Cluster analysis identified microbial groups and functions correlated with shifts in rhizosoil chemistry and plant nutrition. Bacterial consortia positively modulated specific genera and functional pathways involved in biosynthesis of plant secondary metabolites, amino acids, lipopolysaccharides, photosynthesis, bacterial secretion systems, and sulfur metabolism. The effects of the bacterial consortia on the soybean holobiont, particularly the rhizomicrobiome and rhizosoil fertility, highlight the importance of selecting appropriate consortia for desired outcomes. These findings have implications for microbial-based agricultural practices that enhance crop productivity, quality, and sustainability.},
}

@article {pmid39030632,
year = {2024},
author = {Krinos, AI and Bowers, RM and Rohwer, RR and McMahon, KD and Woyke, T and Schulz, F},
title = {Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {133},
pmid = {39030632},
issn = {2049-2618},
support = {SC0020347//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; 2011002//National Science Foundation/ ; WIS01516//U.S. Department of Agriculture/ ; DEB-9632853//U.S. National Science Foundation/ ; },
mesh = {*Lakes/microbiology/parasitology ; *Metagenomics ; Animals ; *Bacteria/genetics/classification/isolation & purification ; Eukaryota/genetics/classification ; Phytoplankton/genetics/classification ; Food Chain ; Metagenome ; Zooplankton/genetics/classification ; },
abstract = {BACKGROUND: Protists, single-celled eukaryotic organisms, are critical to food web ecology, contributing to primary productivity and connecting small bacteria and archaea to higher trophic levels. Lake Mendota is a large, eutrophic natural lake that is a Long-Term Ecological Research site and among the world's best-studied freshwater systems. Metagenomic samples have been collected and shotgun sequenced from Lake Mendota for the last 20 years. Here, we analyze this comprehensive time series to infer changes to the structure and function of the protistan community and to hypothesize about their interactions with bacteria.

RESULTS: Based on small subunit rRNA genes extracted from the metagenomes and metagenome-assembled genomes of microeukaryotes, we identify shifts in the eukaryotic phytoplankton community over time, which we predict to be a consequence of reduced zooplankton grazing pressures after the invasion of a invasive predator (the spiny water flea) to the lake. The metagenomic data also reveal the presence of the spiny water flea and the zebra mussel, a second invasive species to Lake Mendota, prior to their visual identification during routine monitoring. Furthermore, we use species co-occurrence and co-abundance analysis to connect the protistan community with bacterial taxa. Correlation analysis suggests that protists and bacteria may interact or respond similarly to environmental conditions. Cryptophytes declined in the second decade of the timeseries, while many alveolate groups (e.g., ciliates and dinoflagellates) and diatoms increased in abundance, changes that have implications for food web efficiency in Lake Mendota.

CONCLUSIONS: We demonstrate that metagenomic sequence-based community analysis can complement existing efforts to monitor protists in Lake Mendota based on microscopy-based count surveys. We observed patterns of seasonal abundance in microeukaryotes in Lake Mendota that corroborated expectations from other systems, including high abundance of cryptophytes in winter and diatoms in fall and spring, but with much higher resolution than previous surveys. Our study identified long-term changes in the abundance of eukaryotic microbes and provided context for the known establishment of an invasive species that catalyzes a trophic cascade involving protists. Our findings are important for decoding potential long-term consequences of human interventions, including invasive species introduction. Video Abstract.},
}

*Lakes/microbiology/parasitology
*Metagenomics
Animals
*Bacteria/genetics/classification/isolation & purification
Eukaryota/genetics/classification
Phytoplankton/genetics/classification
Food Chain
Metagenome
Zooplankton/genetics/classification

@article {pmid39030599,
year = {2024},
author = {Xu, SY and Feng, XR and Zhao, W and Bi, YL and Diao, QY and Tu, Y},
title = {Rumen and hindgut microbiome regulate average daily gain of preweaning Holstein heifer calves in different ways.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {131},
pmid = {39030599},
issn = {2049-2618},
mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Weaning ; Bacteria/classification/isolation & purification/metabolism/genetics ; Female ; Fermentation ; Metagenomics/methods ; Metabolomics ; Fatty Acids, Volatile/metabolism/analysis ; Weight Gain ; Butyrates/metabolism ; },
abstract = {BACKGROUND: The average daily gain (ADG) of preweaning calves significantly influences their adult productivity and reproductive performance. Gastrointestinal microbes are known to exert an impact on host phenotypes, including ADG. The aim of this study was to investigate the mechanisms by which gastrointestinal microbiome regulate ADG in preweaning calves and to further validate them by isolating ADG-associated rumen microbes in vitro.

RESULTS: Sixteen Holstein heifer calves were selected from a cohort with 106 calves and divided into higher ADG (HADG; n = 8) and lower ADG (LADG; n = 8) groups. On the day of weaning, samples of rumen contents, hindgut contents, and plasma were collected for rumen metagenomics, rumen metabolomics, hindgut metagenomics, hindgut metabolomics, and plasma metabolomics analyses. Subsequently, rumen contents of preweaning Holstein heifer calves from the same dairy farm were collected to isolate ADG-associated rumen microbes. The results showed that the rumen microbes, including Pyramidobacter sp. C12-8, Pyramidobacter sp. CG50-2, Pyramidobacter porci, unclassified_g_Pyramidobacter, Pyramidobacter piscolens, and Acidaminococcus fermentans, were enriched in the rumen of HADG calves (LDA > 2, P < 0.05). Enrichment of these microbes in HADG calves' rumen promoted carbohydrate degradation and volatile fatty acid production, increasing proportion of butyrate in the rumen and ultimately contributing to higher preweaning ADG in calves (P < 0.05). The presence of active carbohydrate degradation in the rumen was further suggested by the negative correlation of the rumen microbes P. piscolens, P. sp. C12-8 and unclassified_g_Pyramidobacter with the rumen metabolites D-fructose (R <  - 0.50, P < 0.05). Widespread positive correlations were observed between rumen microbes (such as P. piscolens, P. porci, and A. fermentans) and beneficial plasma metabolites (such as 1-pyrroline-5-carboxylic acid and 4-fluoro-L-phenylalanine), which were subsequently positively associated with the growth rate of HADG calves (R > 0.50, P < 0.05). We succeeded in isolating a strain of A. fermentans from the rumen contents of preweaning calves and named it Acidaminococcus fermentans P41. The in vitro cultivation revealed its capability to produce butyrate. In vitro fermentation experiments demonstrated that the addition of A. fermentans P41 significantly increased the proportion of butyrate in the rumen fluid (P < 0.05). These results further validated our findings. The relative abundance of Bifidobacterium pseudolongum in the hindgut of HADG calves was negatively correlated with hindgut 4-hydroxyglucobrassicin levels, which were positively correlated with plasma 4-hydroxyglucobrassicin levels, and plasma 4-hydroxyglucobrassicin levels were positively correlated with ADG (P < 0.05).

CONCLUSIONS: This study's findings unveil that rumen and hindgut microbes play distinctive roles in regulating the preweaning ADG of Holstein heifer calves. Additionally, the successful isolation of A. fermentans P41 not only validated our findings but also provided a valuable strain resource for modulating rumen microbes in preweaning calves. Video Abstract.},
}

Animals
Cattle
*Rumen/microbiology/metabolism
*Gastrointestinal Microbiome
*Weaning
Bacteria/classification/isolation & purification/metabolism/genetics
Female
Fermentation
Metagenomics/methods
Metabolomics
Fatty Acids, Volatile/metabolism/analysis
Weight Gain
Butyrates/metabolism

@article {pmid39029947,
year = {2024},
author = {Azizpour, A and Balaji, A and Treangen, TJ and Segarra, S},
title = {Graph-based self-supervised learning for repeat detection in metagenomic assembly.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279136.124},
pmid = {39029947},
issn = {1549-5469},
abstract = {Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene duplication, and gene loss/gain complicate accurate genome assembly from metagenomic communities. Detecting repeats is a crucial first step in overcoming these challenges. To address this issue, we propose GraSSRep, a novel approach that leverages the assembly graph's structure through graph neural networks (GNNs) within a self-supervised learning framework to classify DNA sequences into repetitive and non-repetitive categories. Specifically, we frame this problem as a node classification task within a metagenomic assembly graph. In a self-supervised fashion, we rely on a high-precision (but low-recall) heuristic to generate pseudo-labels for a small proportion of the nodes. We then use those pseudo-labels to train a GNN embedding and a random forest classifier to propagate the labels to the remaining nodes. In this way, GraSSRep combines sequencing features with predefined and learned graph features to achieve state-of-the-art performance in repeat detection. We evaluate our method using simulated and synthetic metagenomic datasets. The results on the simulated data highlight our GraSSRep's robustness to repeat attributes, demonstrating its effectiveness in handling the complexity of repeated sequences. Additionally, our experiments with synthetic metagenomic datasets reveal that incorporating the graph structure and the GNN enhances our detection performance. Finally, in comparative analyses, GraSSRep outperforms existing repeat detection tools with respect to precision and recall.},
}

@article {pmid39029911,
year = {2024},
author = {Tyagi, S and Katara, P},
title = {Metatranscriptomics: A Tool for Clinical Metagenomics.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/omi.2024.0130},
pmid = {39029911},
issn = {1557-8100},
abstract = {In the field of bioinformatics, amplicon sequencing of 16S rRNA genes has long been used to investigate community membership and taxonomic abundance in microbiome studies. As we can observe, shotgun metagenomics has become the dominant method in this field. This is largely owing to advancements in sequencing technology, which now allow for random sequencing of the entire genetic content of a microbiome. Furthermore, this method allows profiling both genes and the microbiome's membership. Although these methods have provided extensive insights into various microbiomes, they solely assess the existence of organisms or genes, without determining their active role within the microbiome. Microbiome scholarship now includes metatranscriptomics to decipher how a community of microorganisms responds to changing environmental conditions over a period of time. Metagenomic studies identify the microbes that make up a community but metatranscriptomics explores the diversity of active genes within that community, understanding their expression profile and observing how these genes respond to changes in environmental conditions. This expert review article offers a critical examination of the computational metatranscriptomics tools for studying the transcriptomes of microbial communities. First, we unpack the reasons behind the need for community transcriptomics. Second, we explore the prospects and challenges of metatranscriptomic workflows, starting with isolation and sequencing of the RNA community, then moving on to bioinformatics approaches for quantifying RNA features, and statistical techniques for detecting differential expression in a community. Finally, we discuss strengths and shortcomings in relation to other microbiome analysis approaches, pipelines, use cases and limitations, and contextualize metatranscriptomics as a tool for clinical metagenomics.},
}

@article {pmid39029824,
year = {2024},
author = {Wani, AK and Chopra, C and Ansari, MA and Dar, MA and Américo-Pinheiro, JHP and Singh, R},
title = {Characterization of thermostable carboxypeptidase from high-altitude hot spring metagenome.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {133974},
doi = {10.1016/j.ijbiomac.2024.133974},
pmid = {39029824},
issn = {1879-0003},
abstract = {This study explored the metagenome of the Pir Panjal Hot Spring (PPHS) to identify thermostable hydrolases. The carboxypeptidase (CarP) gene was successfully amplified and cloned into Escherichia coli DH5-α cells, followed by expression in E. coli BL21-DE3 cells. The CarP enzyme was comprehensively characterized in vitro. Sequencing analysis revealed an open reading frame encoding a functional protein of 504 amino acids, with a molecular weight of 58.65 kDa and an isoelectric point of 4.81. The CarP protein was purified using Ni-His affinity chromatography, and the experimental molecular weight matched in silico predictions. The enzyme exhibited significant thermostability and alkaliphilic properties, with optimal activity at 70 °C and pH 10.0. Additionally, the presence of Zn[+2] ions at concentrations of 5 and 10 mmol/L enhanced protease activity by 1.4 and 1.5-fold, respectively. This study reports the discovery of a novel, multifunctional, and thermostable CarP from hot-spring metagenomes. The enzyme's stability against high temperatures, metal ions, surfactants, and inhibitors, along with its specific substrate interactions, highlights its potential for various biotechnological applications.},
}

@article {pmid39029427,
year = {2024},
author = {Iacovacci, J and Serafini, MS and Avuzzi, B and Badenchini, F and Cicchetti, A and Devecchi, A and Dispinzieri, M and Doldi, V and Giandini, T and Gioscio, E and Mancinelli, E and Noris Chiorda, B and Orlandi, E and Palorini, F and Possenti, L and Reis Ferreira, M and Villa, S and Zaffaroni, N and De Cecco, L and Valdagni, R and Rancati, T},
title = {Intestinal microbiota composition is predictive of radiotherapy-induced acute gastrointestinal toxicity in prostate cancer patients.},
journal = {EBioMedicine},
volume = {106},
number = {},
pages = {105246},
doi = {10.1016/j.ebiom.2024.105246},
pmid = {39029427},
issn = {2352-3964},
abstract = {BACKGROUND: The search for factors beyond the radiotherapy dose that could identify patients more at risk of developing radio-induced toxicity is essential to establish personalised treatment protocols for improving the quality-of-life of survivors. To investigate the role of the intestinal microbiota in the development of radiotherapy-induced gastrointestinal toxicity, the MicroLearner observational cohort study characterised the intestinal microbiota of 136 (discovery) and 79 (validation) consecutive prostate cancer patients at baseline radiotherapy.

METHODS: Gastrointestinal toxicity was assessed weekly during RT using CTCAE. An average grade >1.3 over time points was used to identify patients suffering from persistent acute toxicity (endpoint). The microbiota of patients was quantified from the baseline faecal samples using 16S rRNA gene sequencing technology and the Ion Reporter metagenomic pipeline. Statistical techniques and computational and machine learning tools were used to extract, functionally characterise, and predict core features of the bacterial communities of patients who developed acute gastrointestinal toxicity.

FINDINGS: Analysis of the core bacterial composition in the discovery cohort revealed a cluster of patients significantly enriched for toxicity, displaying a toxicity rate of 60%. Based on selected high-risk microbiota compositional features, we developed a clinical decision tree that could effectively predict the risk of toxicity based on the relative abundance of genera Faecalibacterium, Bacteroides, Parabacteroides, Alistipes, Prevotella and Phascolarctobacterium both in internal and external validation cohorts.

INTERPRETATION: We provide evidence showing that intestinal bacteria profiling from baseline faecal samples can be effectively used in the clinic to improve the pre-radiotherapy assessment of gastrointestinal toxicity risk in prostate cancer patients.

FUNDING: Italian Ministry of Health (Promotion of Institutional Research INT-year 2016, 5 × 1000, Ricerca Corrente funds). Fondazione Regionale per la Ricerca Biomedica (ID 2721017). AIRC (IG 21479).},
}

@article {pmid39029415,
year = {2024},
author = {Kim, S and Kim, N and Park, WB and Kang, CK and Park, JH and Lee, ST and Jung, KH and Park, KI and Lee, SK and Moon, J and Chu, K},
title = {Real-time application of ITS and D1-D3 nanopore amplicon metagenomic sequencing in fungal infections: Enhancing fungal infection diagnostics.},
journal = {International journal of medical microbiology : IJMM},
volume = {316},
number = {},
pages = {151630},
doi = {10.1016/j.ijmm.2024.151630},
pmid = {39029415},
issn = {1618-0607},
abstract = {While fungal infections cause considerable morbidity and mortality, the performance of the current diagnostic tests for fungal infection is low. Even though fungal metagenomics or targeted next-generation sequencing have been investigated for various clinical samples, the real-time clinical utility of these methods still needs to be elucidated. In this study, we used internal transcribed spacer (ITS) and D1-D3 ribosomal DNA nanopore amplicon metagenomic sequencing to assess its utility in patients with fungal infections. Eighty-four samples from seventy-three patients were included and categorized into 'Fungal infection,' 'Fungal colonization,' and 'Fungal contamination' groups based on the judgement of infectious disease specialists. In the 'Fungal infection' group, forty-seven initial samples were obtained from forty-seven patients. Three fungal cases detected not by the sequencing but by conventional fungal assays were excluded from the analysis. In the remaining cases, the conventional fungal assay-negative/sequencing-positive group (n=11) and conventional fungal assay-positive/sequencing-positive group (n=33) were compared. Non-Candida and non-Aspergillus fungi infections were more frequent in the conventional-negative/sequencing-positive group (p-value = 0.031). We demonstrated the presence of rare human pathogens, such as Trichosporon asahii and Phycomyces blakesleeanus. In the 'Fungal infection' group and 'Fungal colonization' group, sequencing was faster than culturing (mean difference = 4.92 days, p-value < 0.001/ mean difference = 4.67, p-value <0.001). Compared to the conventional diagnostic methods including culture, nanopore amplicon sequencing showed a shorter turnaround time and a higher detection rate for uncommon fungal pathogens.},
}

@article {pmid39029331,
year = {2024},
author = {Stratton, CE and Reisinger, LS and Behringer, DC and Gray, SN and Larson, ER and Bojko, J},
title = {North American crayfish harbour diverse members of the Nudiviridae.},
journal = {Virology},
volume = {598},
number = {},
pages = {110183},
doi = {10.1016/j.virol.2024.110183},
pmid = {39029331},
issn = {1096-0341},
abstract = {Three novel crayfish-infecting nudiviruses from crayfish in North America represent the first genomic confirmation of nudiviruses in crayfish: Faxonius propinquus nudivirus (FpNV), Faxonius rusticus nudivirus (FrNV), and Faxonius virilis nudivirus (FvNV). Histopathology and electron microscopy revealed nuclear infections, including nuclear hypertrophy in hepatopancreatic epithelial cells and the presence of membrane-bound bacilliform virions. Metagenomic sequencing resulted in complete circular genome assembly, and phylogenetic analyses (based on nudivirus core genes) placed these viruses within the unofficial Epsilonnudivirus genus. One of the nudiviruses was detected in the antennal gland of its host, and another is correlated with invasive crayfish decline in one infected lake ecosystem - suggesting a potential route for viral transmission through water, and possible population level impact. This study highlights the importance of genomic and ecological data in elucidating the diversity and evolutionary relationships of the Nudiviridae, while expanding their known diversity and range of host species.},
}

@article {pmid39029015,
year = {2024},
author = {Xue, K and Zhang, A and Liu, S and Chen, D},
title = {Multiple brain abscesses caused by Nocardia farcinica infection after hand injury: A case report and literature review.},
journal = {Medicine},
volume = {103},
number = {29},
pages = {e39019},
doi = {10.1097/MD.0000000000039019},
pmid = {39029015},
issn = {1536-5964},
mesh = {Humans ; Female ; *Nocardia Infections/diagnosis/drug therapy ; *Brain Abscess/microbiology/etiology/diagnosis ; *Nocardia/isolation & purification ; Aged ; *Anti-Bacterial Agents/therapeutic use ; *Hand Injuries/complications ; Magnetic Resonance Imaging ; High-Throughput Nucleotide Sequencing ; },
abstract = {RATIONALE: Nocardia infection is commonly regarded as an opportunistic pulmonary pathogen affecting debilitated or immunocompromised individuals. Brain abscesses caused by Nocardia farcinica are rare and pose a diagnostic challenge. Traditional diagnostic techniques for identifying Nocardia species, such as blood culture, microscopy, and pathology, have shown inadequate performance. In the reported case, we applied metagenomic next-generation sequencing (mNGS) to diagnose a case of brain abscess due to N. farcinica.

PATIENT CONCERNS: A 66-year-old female developed a brain abscess after sustaining a hand injury. The patient exhibited a gradual change in personality and experienced tremors in her right upper limb for a duration of 1 month.

DIAGNOSES: The pathogen responsible for the multiple brain abscesses was identified in the cerebrospinal fluid as N. farcinica through mNGS.

INTERVENTIONS: Antibiotic treatment included trimethoprim-sulfamethoxazole, linezolid, amikacin, meropenem, and moxifloxacin.

OUTCOMES: The patient's symptoms and signs improved significantly after administration of antibiotics to which the pathogen is known to be sensitive. After 5 months of follow-up, magnetic resonance imaging of the head showed that the abscess was basically cured. The patient lived a normal life with no adverse drug reactions.

LESSONS: Nocardia brain infection is characterized by an insidious onset and lacks distinctive clinical and imaging features. mNGS was advantageous for the timely identification and management of Nocardia-associated brain abscess in the present case and obviated the need for invasive brain surgery. Expeditious and precise diagnosis coupled with prompt antibiotic therapy can significantly reduce the mortality rate associated with this condition.},
}

Humans
Female
*Nocardia Infections/diagnosis/drug therapy
*Brain Abscess/microbiology/etiology/diagnosis
*Nocardia/isolation & purification
Aged
*Anti-Bacterial Agents/therapeutic use
*Hand Injuries/complications
Magnetic Resonance Imaging
High-Throughput Nucleotide Sequencing

@article {pmid39028665,
year = {2024},
author = {Zhou, X and Yang, M and Chen, F and Wang, L and Han, P and Jiang, Z and Shen, S and Rao, G and Yang, F},
title = {Prediction of antimicrobial resistance in Klebsiella pneumoniae using genomic and metagenomic next-generation sequencing data.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1093/jac/dkae248},
pmid = {39028665},
issn = {1460-2091},
support = {3030231003//Shanghai Antimicrobial Surveillance Network/ ; WI207259//China Antimicrobial Surveillance Network/ ; },
abstract = {OBJECTIVES: Klebsiella pneumoniae is a significant pathogen with increasing resistance and high mortality rates. Conventional antibiotic susceptibility testing methods are time-consuming. Next-generation sequencing has shown promise for predicting antimicrobial resistance (AMR). This study aims to develop prediction models using whole-genome sequencing data and assess their feasibility with metagenomic next-generation sequencing data from clinical samples.

METHODS: On the basis of 4170 K. pneumoniae genomes, the main genetic characteristics associated with AMR were identified using a LASSO regression model. Consequently, the prediction model was established, validated and optimized using clinical isolate read simulation sequences. To evaluate the efficacy of the model, clinical specimens were collected.

RESULTS: Four predictive models for amikacin, ciprofloxacin, levofloxacin and piperacillin/tazobactam, initially had positive predictive values (PPVs) of 90%, 85%, 84% and 94%, respectively, when they were originally constructed. When applied to clinical specimens, their PPVs increased to 96%, 96%, 95% and 100%, respectively. Meanwhile, there were negative predictive values (NPVs) of 100% for ciprofloxacin and levofloxacin, and 'not applicable' (NA) for amikacin and piperacillin/tazobactam. Our method achieved antibacterial phenotype classification accuracy rates of 96.08% for amikacin, 96.15% for ciprofloxacin, 95.31% for levofloxacin and 100% for piperacillin/tazobactam. The sequence-based prediction antibiotic susceptibility testing (AST) reported results in an average time of 19.5 h, compared with the 67.9 h needed for culture-based AST, resulting in a significant reduction of 48.4 h.

CONCLUSIONS: These preliminary results demonstrated that the performance of prediction model for a clinically significant antimicrobial-species pair was comparable to that of phenotypic methods, thereby encouraging the expansion of sequence-based susceptibility prediction and its clinical validation and application.},
}

@article {pmid39028528,
year = {2024},
author = {Han, Y and Zhang, Y and Yang, Z and Zhang, Q and He, X and Song, Y and Tian, L and Wu, H},
title = {Improving Aerobic Digestion of Food Waste by Adding a Personalized Microbial Inoculum.},
journal = {Current microbiology},
volume = {81},
number = {9},
pages = {277},
pmid = {39028528},
issn = {1432-0991},
support = {236Z3301G//Natural Science Foundation of Hebei Province/ ; B2020203005//Natural Science Foundation of Hebei Province/ ; 2021LGQN027//Cultivation Project for Basic Research and Innovation of YanShan University/ ; 236Z3604G//National Science Founbdation of Hebei Province/ ; 2023GJJG396//Hebei Education Department/ ; ZD2022088//China Hebei Education Department/ ; ZC2023041//China Hebei Education Department/ ; 2021LGQN018//Cultivation Project for Basic Research and Innovation of YanShan University/ ; },
mesh = {Aerobiosis ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Microbial Consortia ; Garbage ; China ; Refuse Disposal/methods ; Hydrolysis ; Metagenomics ; Food Loss and Waste ; },
abstract = {In the context of China's garbage classification policy, on-site aerobic food waste (FW) digestion is crucial for reducing transportation and disposal costs. The efficiency of this process is largely determined by the microbial community structure and its functions. Therefore, this study aimed to analyze the impact of a personalized microbial consortium (MCM) on the efficiency of aerobic FW digestion and to reveal the underlying mechanisms. An MCM, sourced from naturally degrading FW, was selected to enrich degrading bacteria with relatively high hydrolyzing ability. The functionality of the MCM was evaluated by tracing the successions of microbial communities, and comparing the differences in the forms of organic compounds, metabolic functions, and hydrolase activities. X-ray photoelectron spectroscopy demonstrated that the MCM metabolized faster, and produced more acidic metabolites. Metagenomic analysis indicated that FW inoculated with the personalized MCM increased abundance of Bacillaceae producing hydrolysis enzymes and promoted glycolysis metabolic pathways, enhancing energy generation for metabolism, compared to the commercial effective bacterial agent. This paper provides both theoretical and practical evidence for the improvement of biochemical processor of FW with the personalized MCM, which has promising application prospects and economic value.},
}

Aerobiosis
*Bacteria/classification/metabolism/genetics/isolation & purification
Microbial Consortia
Garbage
China
Refuse Disposal/methods
Hydrolysis
Metagenomics
Food Loss and Waste

@article {pmid39027502,
year = {2024},
author = {Li, Z and Guo, Z and Wu, W and Tan, L and Long, Q and Xia, H and Hu, M},
title = {The effects of sequencing strategies on Metagenomic pathogen detection using bronchoalveolar lavage fluid samples.},
journal = {Heliyon},
volume = {10},
number = {13},
pages = {e33429},
pmid = {39027502},
issn = {2405-8440},
abstract = {OBJECTIVES: Metagenomic next-generation sequencing (mNGS) is a powerful tool for pathogen detection. The accuracy depends on both wet lab and dry lab procedures. The objective of our study was to assess the influence of read length and dataset size on pathogen detection.

METHODS: In this study, 43 clinical BALF samples, which tested positive via clinical mNGS and were consistent with the diagnosis, were subjected to re-sequencing on the Illumina NovaSeq 6000 platform. The raw re-sequencing data, consisting of 100 million (M) paired-end 150 bp (PE150) reads, were divided into simulated datasets with eight different data sizes (5 M, 10 M, 15 M, 20 M, 30 M, 50 M, 75 M, 100 M) and five different read lengths (single-end 50 bp (SE50), SE75, SE100, PE100, and PE150). Both Kraken2 and IDseq bioinformatics pipelines were employed to analyze the previously diagnosed pathogens in the simulated data. Detection of pathogens was based on read counts ranging from 1 to 10 and RPM values ranging from 0.2 to 2.

RESULTS: Our results revealed that increasing dataset sizes and read lengths can enhance the performance of mNGS in pathogen detection. However, a larger data sizes for mNGS require higher economic costs and longer turnaround time for data analysis. Our findings indicate 20 M reads being sufficient for SE75 mode to achieve high recall rates. Additionally, high nucleic acid loads in samples can lead to increased stability in pathogen detection efficiency, reducing the impact of sequencing strategies. The choice of bioinformatics pipelines had a significant impact on recall rates achieved in pathogen detection.

CONCLUSIONS: Increasing dataset sizes and read lengths can enhance the performance of mNGS in pathogen detection but increase the economic and time costs of sequencing and data analysis. Currently, the 20 M reads in SE75 mode may be the best sequencing option.},
}

@article {pmid39027434,
year = {2024},
author = {Ralli, T and Ahmad, S and Saifi, Z and Alhalmi, A and Aeri, V and Aqil, M and Kohli, K},
title = {Exploring the therapeutic potential of silymarin-based herbal remedy (prebiotic) and probiotic blend in a mouse model of NAFLD: Insights into gut microbiota modulation and liver health.},
journal = {Heliyon},
volume = {10},
number = {12},
pages = {e33505},
pmid = {39027434},
issn = {2405-8440},
abstract = {Non-alcoholic fatty liver disease (NAFLD) is a significant consequence of metabolic dysfunction, often associated with changes in the intestinal microbiota. Prebiotics and probiotics have shown promise in NAFLD management. This study evaluated a silymarin-based herbal remedy with piperine and fulvic acid, alongside a probiotic blend of Bifidobacterium adolescentis, Bifidobacterium bifidum, Lactobacillus casei, and Lactobacillus rhamnosus. Using a NAFLD mouse model induced by a high-fat and high-fructose diet, we assessed biochemical parameters, liver function, glucose levels, and conducted histological analysis. Stool samples underwent 16S rRNA metagenomic analysis to explore changes in microbiota composition. Mice on the high-fat diet exhibited elevated lipids, liver enzymes, and glucose, with reduced high-density lipoprotein levels (with p value < 0.001). Treatment, particularly with F3 (silymarin-piperine-fulvic acid herbal remedy and probiotic blend), significantly reduced hepatic fat accumulation and improved gut microbiota composition. This study highlights the potential of silymarin-based therapy combined with probiotics in attenuating NAFLD progression.},
}

@article {pmid39027100,
year = {2024},
author = {Mohapatra, A and Trivedi, S and Kolte, AP and Tejpal, CS and Elavarasan, K and Vaswani, S and Malik, PK and Ravishankar, CN and Bhatta, R},
title = {Effect of Padina gymnospora biowaste inclusion on in vitro methane production, feed fermentation, and microbial diversity.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1431131},
doi = {10.3389/fmicb.2024.1431131},
pmid = {39027100},
issn = {1664-302X},
abstract = {In vitro studies were undertaken aiming to study the methane (CH4) mitigation potential of biowaste (BW) of Padina gymnospora at the graded inclusion of 0% (C), 2% (A2), 5% (A5), and 10% (A10) of the diet composed of straw and concentrate in 40:60 ratio. The chemical composition analysis revealed that the BW contained higher crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), and ether extract (EE) than the PF (fresh seaweed, P. gymnospora). The concentration of cinnamic acid, sinapic acid, kaempferol, fisetin p-coumaric acid, ellagic acid, and luteolin in BW was 1.5-6-folds less than the PF. Inclusion of BW decreased (P < 0.0001) CH4 production by 34%, 38%, and 45% in A2, A5, and A10 treatments, respectively. A decrease (P < 0.0001) of 7.5%-8% in dry matter (DM) and organic matter (OM) digestibility was also recorded with the BW supplementation. The BW inclusion also decreased the numbers of total (P = 0.007), Entodinomorphs (P = 0.011), and Holotrichs (P = 0.004) protozoa. Metagenome data revealed the dominance of Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria, and Fibrobacter microbial phyla. At the phylum level, Euryarchaeota dominated the archaeal community, whereas Methanobrevibacter was most abundant at the genus level. It can be concluded that the inclusion of BW in straw and concentrate based diet by affecting rumen fermentation, protozoal numbers, and compositional shift in the archaeal community significantly decreased CH4 production. Utilization of biowaste of P. gymnospora as a CH4 mitigating agent will ensure its efficient utilization rather than dumping, which shall cause environmental pollution and health hazards.},
}

@article {pmid39027090,
year = {2024},
author = {Vasileva, S and Yap, CX and Whitehouse, AJO and Gratten, J and Eyles, D},
title = {Absence of association between maternal adverse events and long-term gut microbiome outcomes in the Australian autism biobank.},
journal = {Brain, behavior, & immunity - health},
volume = {39},
number = {},
pages = {100814},
doi = {10.1016/j.bbih.2024.100814},
pmid = {39027090},
issn = {2666-3546},
abstract = {INTRODUCTION: Maternal immune activation (MIA) and prenatal maternal stress (MatS) are well-studied risk factors for psychiatric conditions such as autism and schizophrenia. Animal studies have proposed the gut microbiome as a mechanism underlying this association and have found that risk factor-related gut microbiome alterations persist in the adult offspring. In this cross-sectional study, we assessed whether maternal immune activation and prenatal maternal stress were associated with long-term gut microbiome alterations in children using shotgun metagenomics.

METHODS: This cross-sectional study included children diagnosed with autism (N = 92), siblings without a diagnosis (N = 42), and unrelated children (N = 40) without a diagnosis who were recruited into the Australian Autism Biobank and provided a faecal sample. MIA exposure was inferred from self-reported data and included asthma/allergies, complications during pregnancy triggering an immune response, auto-immune conditions, and acute inflammation. Maternal stress included any of up to 9 stressful life events during pregnancy, such as divorce, job loss, and money problems. Data were analysed for a total of 174 children, of whom 63 (36%) were born to mothers with MIA and 84 (48%) were born to mothers who experienced maternal stress during pregnancy (where 33 [19%] experienced both). Gut microbiome data was assessed using shotgun metagenomic sequencing of the children's faecal samples.

RESULTS: In our cohort, MIA, but not MatS, was associated with ASD. Variance component analysis revealed no associations between any of the gut microbiome datasets and neither MIA nor MatS. After adjusting for age, sex, diet and autism diagnosis, there was no significant difference between groups for bacterial richness, α-diversity or β-diversity. We found no significant differences in species abundance in the main analyses. However, when stratifying the cohort by age, we found that Faecalibacterium prausnitzii E was significantly decreased in MIA children aged 11-17.

DISCUSSION: Consistent with previous findings, we found that children who were born to mothers with MIA were more likely to be diagnosed with autism. Unlike within animal studies, we found negligible microbiome differences associated with MIA and maternal stress. Given the current interest in the microbiome-gut-brain axis, researchers should exercise caution in translating microbiome findings from animal models to human contexts and the clinical setting.},
}

@article {pmid39026795,
year = {2024},
author = {Uppal, S and Waterworth, SC and Nick, A and Vogel, H and Flórez, LV and Kaltenpoth, M and Kwan, JC},
title = {Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.01.23.576914},
pmid = {39026795},
issn = {2692-8205},
abstract = {Microbial symbionts associate with multicellular organisms on a continuum from facultative associations to mutual codependency. In some of the oldest intracellular symbioses there is exclusive vertical symbiont transmission, and co-diversification of symbiotic partners over millions of years. Such symbionts often undergo genome reduction due to low effective population sizes, frequent population bottlenecks, and reduced purifying selection. Here, we describe multiple independent acquisition events of closely related defensive symbionts followed by genome erosion in a group of Lagriinae beetles. Previous work in Lagria villosa revealed the dominant genome-eroded symbiont of the genus Burkholderia produces the antifungal compound lagriamide and protects the beetle's eggs and larvae from antagonistic fungi. Here, we use metagenomics to assemble 11 additional genomes of lagriamide-producing symbionts from seven different host species within Lagriinae from five countries, to unravel the evolutionary history of this symbiotic relationship. In each host species, we detected one dominant genome-eroded Burkholderia symbiont encoding the lagriamide biosynthetic gene cluster (BGC). Surprisingly, however, we did not find evidence for host-symbiont co-diversification, or for a monophyly of the lagriamide-producing symbionts. Instead, our analyses support at least four independent acquisition events of lagriamide-encoding symbionts and subsequent genome erosion in each of these lineages. By contrast, a clade of plant-associated relatives retained large genomes but secondarily lost the lagriamide BGC. In conclusion, our results reveal a dynamic evolutionary history with multiple independent symbiont acquisitions characterized by high degree of specificity. They highlight the importance of the specialized metabolite lagriamide for the establishment and maintenance of this defensive symbiosis.},
}

@article {pmid39026785,
year = {2024},
author = {Şapcı, AOB and Mirarab, S},
title = {Memory-bound k -mer selection for large and evolutionary diverse reference libraries.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.02.12.580015},
pmid = {39026785},
issn = {2692-8205},
abstract = {Using k -mers to find sequence matches is increasingly used in many bioinformatic applications, including metagenomic sequence classification. The accuracy of these down-stream applications relies on the density of the reference databases, which, luckily, are rapidly growing. While the increased density provides hope for dramatic improvements in accuracy, scalability is a concern. Reference k -mers are kept in the memory during the query time, and saving all k -mers of these ever-expanding databases is fast becoming impractical. Several strategies for subsampling have been proposed, including minimizers and finding taxon-specific k -mers. However, we contend that these strategies are inadequate, especially when reference sets are taxonomically imbalanced, as are most microbial libraries. In this paper, we explore approaches for selecting a fixed-size subset of k -mers present in an ultra-large dataset to include in a library such that the classification of reads suffers the least. Our experiments demonstrate the limitations of existing approaches, especially for novel and poorly sampled groups. We propose a library construction algorithm called KRANK (K-mer RANKer) that combines several components, including a hierarchical selection strategy with adaptive size restrictions and an equitable coverage strategy. We implement KRANK in highly optimized code and combine it with the locality-sensitive-hashing classifier CONSULT-II to build a taxonomic classification and profiling method. On several benchmarks, KRANK k -mer selection dramatically reduces memory consumption with minimal loss in classification accuracy. We show in extensive analyses based on CAMI benchmarks that KRANK outperforms k -mer-based alternatives in terms of taxonomic profiling and comes close to the best marker-based methods in terms of accuracy.},
}

@article {pmid39026780,
year = {2024},
author = {Bashor, L and Rawlinson, JE and Kozakiewicz, CP and Behzadi, E and Miller, C and Kim, J and Conry, M and Nehring, M and Carver, S and Abdo, Z and VandeWoude, S},
title = {Impacts of Antiretroviral Therapy on the Oral Microbiome and Periodontal Health of Feline Immunodeficiency Virus Positive Cats.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.07.10.602918},
pmid = {39026780},
issn = {2692-8205},
abstract = {UNLABELLED: Feline immunodeficiency virus (FIV) is the domestic cat analogue of HIV infection in humans. Both viruses induce oral disease in untreated individuals, with clinical signs that include gingivitis and periodontal lesions. Oral disease manifestations in HIV patients are abated by highly effective combination antiretroviral therapy (cART), though certain oral manifestations persist despite therapy. Microorganisms associated with oral cavity opportunistic infections in patients with HIV cause similar pathologies in cats. To further develop this model, we evaluated characteristics of feline oral health and oral microbiome during experimental FIV infection over an 8-month period following cART. Using 16S metagenomics sequencing, we evaluated gingival bacterial communities at four timepoints in uninfected and FIV-infected cats treated with cART or placebo. Comprehensive oral examinations were also conducted by a veterinary dental specialist over the experimental period. Gingival inflammation was higher in FIV-infected cats treated with placebo compared to cART-treated cats and controls at study endpoint. Oral microbiome alpha diversity increased in all groups, while beta diversity differed among treatment groups, documenting a significant effect of cART therapy on microbiome community composition. This finding has not previously been reported and indicates cART ameliorates immunodeficiency virus-associated oral disease via preservation of oral mucosal microbiota. Further, this study illustrates the value of the FIV animal model for investigations of mechanistic associations and therapeutic interventions for HIV oral manifestations.

IMPORTANCE: Feline Immunodeficiency Virus (FIV) is the viral analogue to HIV in humans, and both infections are associated with oral disease. Our study explored how antiretroviral treatment affects the oral health and microbiome of domestic cats infected with FIV. Cats treated with antiretroviral therapy had less gum inflammation and a different community of oral bacteria compared to untreated FIV-positive cats. This suggests that antiretroviral therapy not only helps in controlling FIV infection but also benefits feline oral health. These findings advance our understanding of antiretroviral treatment for lentiviral-associated oral disease and highlight FIV as a valuable experimental model for the similar condition in humans.},
}

@article {pmid39026261,
year = {2024},
author = {Lee, M and Kaul, A and Ward, JM and Zhu, Q and Richards, M and Wang, Z and González, A and Parks, CG and Beane Freeman, LE and Umbach, DM and Motsinger-Reif, AA and Knight, R and London, SJ},
title = {House dust metagenome and pulmonary function in a US farming population.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {129},
pmid = {39026261},
issn = {2049-2618},
support = {Z01-ES049030 and Z01-ES102385//National Institutes of Health, the National Institute of Environmental Health Sciences/ ; Z01-ES049030 and Z01-ES102385//National Institutes of Health, the National Institute of Environmental Health Sciences/ ; Z01-ES049030 and Z01-ES102385//National Institutes of Health, the National Institute of Environmental Health Sciences/ ; Z01-CP010119B/CA/NCI NIH HHS/United States ; },
mesh = {*Dust/analysis ; Humans ; *Metagenome ; Female ; Male ; United States ; *Microbiota/genetics ; Middle Aged ; Lung/microbiology ; Adult ; Bacteria/classification/genetics/isolation & purification ; Forced Expiratory Volume ; Agriculture ; Respiratory Function Tests ; Vital Capacity ; Metagenomics/methods ; },
abstract = {BACKGROUND: Chronic exposure to microorganisms inside homes can impact respiratory health. Few studies have used advanced sequencing methods to examine adult respiratory outcomes, especially continuous measures. We aimed to identify metagenomic profiles in house dust related to the quantitative traits of pulmonary function and airway inflammation in adults. Microbial communities, 1264 species (389 genera), in vacuumed bedroom dust from 779 homes in a US cohort were characterized by whole metagenome shotgun sequencing. We examined two overall microbial diversity measures: richness (the number of individual microbial species) and Shannon index (reflecting both richness and relative abundance). To identify specific differentially abundant genera, we applied the Lasso estimator with high-dimensional inference methods, a novel framework for analyzing microbiome data in relation to continuous traits after accounting for all taxa examined together.

RESULTS: Pulmonary function measures (forced expiratory volume in one second (FEV1), forced vital capacity (FVC), and FEV1/FVC ratio) were not associated with overall dust microbial diversity. However, many individual microbial genera were differentially abundant (p-value < 0.05 controlling for all other microbial taxa examined) in relation to FEV1, FVC, or FEV1/FVC. Similarly, fractional exhaled nitric oxide (FeNO), a marker of airway inflammation, was unrelated to overall microbial diversity but associated with differential abundance for many individual genera. Several genera, including Limosilactobacillus, were associated with a pulmonary function measure and FeNO, while others, including Moraxella to FEV1/FVC and Stenotrophomonas to FeNO, were associated with a single trait.

CONCLUSIONS: Using state-of-the-art metagenomic sequencing, we identified specific microorganisms in indoor dust related to pulmonary function and airway inflammation. Some were previously associated with respiratory conditions; others were novel, suggesting specific environmental microbial components contribute to various respiratory outcomes. The methods used are applicable to studying microbiome in relation to other continuous outcomes. Video Abstract.},
}

*Dust/analysis
Humans
*Metagenome
Female
Male
United States
*Microbiota/genetics
Middle Aged
Lung/microbiology
Adult
Bacteria/classification/genetics/isolation & purification
Forced Expiratory Volume
Agriculture
Respiratory Function Tests
Vital Capacity
Metagenomics/methods

@article {pmid39026166,
year = {2024},
author = {Jing, Z and Zheng, W and Jianwen, S and Hong, S and Xiaojian, Y and Qiang, W and Yunfeng, Y and Xinyue, W and Shuwen, H and Feimin, Z},
title = {Gut microbes on the risk of advanced adenomas.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {264},
pmid = {39026166},
issn = {1471-2180},
support = {No.2023KY1178//Zhejiang Medical and Health Technology Project/ ; No.2023KY1178//Zhejiang Medical and Health Technology Project/ ; No.2023HT078//China University Industry University Research Innovation Fund/ ; No.2023HT078//China University Industry University Research Innovation Fund/ ; No. 2023GY18//PublicWelfare Technology Application Research Program of Huzhou/ ; No. 2023GY18//PublicWelfare Technology Application Research Program of Huzhou/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Adenoma/microbiology/virology ; *Feces/microbiology/virology ; *Colorectal Neoplasms/microbiology/virology ; Male ; Middle Aged ; Female ; Viruses/isolation & purification/classification/genetics/pathogenicity ; High-Throughput Nucleotide Sequencing ; Aged ; Machine Learning ; },
abstract = {BACKGROUND: More than 90% of colorectal cancer (CRC) arises from advanced adenomas (AA) and gut microbes are closely associated with the initiation and progression of both AA and CRC.

OBJECTIVE: To analyze the characteristic microbes in AA.

METHODS: Fecal samples were collected from 92 AA and 184 negative control (NC). Illumina HiSeq X sequencing platform was used for high-throughput sequencing of microbial populations. The sequencing results were annotated and compared with NCBI RefSeq database to find the microbial characteristics of AA. R-vegan package was used to analyze α diversity and β diversity. α diversity included box diagram, and β diversity included Principal Component Analysis (PCA), principal co-ordinates analysis (PCoA), and non-metric multidimensional scaling (NMDS). The AA risk prediction models were constructed based on six kinds of machine learning algorithms. In addition, unsupervised clustering methods were used to classify bacteria and viruses. Finally, the characteristics of bacteria and viruses in different subtypes were analyzed.

RESULTS: The abundance of Prevotella sp900557255, Alistipes putredinis, and Megamonas funiformis were higher in AA, while the abundance of Lilyvirus, Felixounavirus, and Drulisvirus were also higher in AA. The Catboost based model for predicting the risk of AA has the highest accuracy (bacteria test set: 87.27%; virus test set: 83.33%). In addition, 4 subtypes (B1V1, B1V2, B2V1, and B2V2) were distinguished based on the abundance of gut bacteria and enteroviruses (EVs). Escherichia coli D, Prevotella sp900557255, CAG-180 sp000432435, Phocaeicola plebeiuA, Teseptimavirus, Svunavirus, Felixounavirus, and Jiaodavirus are the characteristic bacteria and viruses of 4 subtypes. The results of Catboost model indicated that the accuracy of prediction improved after incorporating subtypes. The accuracy of discovery sets was 100%, 96.34%, 100%, and 98.46% in 4 subtypes, respectively.

CONCLUSION: Prevotella sp900557255 and Felixounavirus have high value in early warning of AA. As promising non-invasive biomarkers, gut microbes can become potential diagnostic targets for AA, and the accuracy of predicting AA can be improved by typing.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/classification/isolation & purification
*Adenoma/microbiology/virology
*Feces/microbiology/virology
*Colorectal Neoplasms/microbiology/virology
Male
Middle Aged
Female
Viruses/isolation & purification/classification/genetics/pathogenicity
High-Throughput Nucleotide Sequencing
Aged
Machine Learning

@article {pmid39025875,
year = {2024},
author = {Liu, Z and Chen, H and Chen, D and Wu, X and Xu, H and Chen, P and Wang, R and Chen, Y},
title = {Metagenomic next-generation sequencing for the diagnosis of invasive pulmonary aspergillosis in type 2 diabetes mellitus patients.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16618},
pmid = {39025875},
issn = {2045-2322},
support = {2023A1515011252//the Guangdong Natural Science Foundation/ ; 82302599//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Diabetes Mellitus, Type 2/complications ; Male ; Female ; *Invasive Pulmonary Aspergillosis/diagnosis/microbiology ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Aged ; Galactose/analogs & derivatives ; Mannans/blood/analysis ; Sensitivity and Specificity ; Bronchoalveolar Lavage Fluid/microbiology ; },
abstract = {Invasive pulmonary aspergillosis (IPA) in patients with diabetes mellitus has high incidence, especially in Type 2 diabetes mellitus (T2DM). The aim of this study was to evaluate the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) for IPA in patients with T2DM. A total of 66 patients with T2DM were included, including 21 IPA and 45 non-IPA patients, from January 2022 to December 2022. The demographic characteristics, comorbidities, laboratory test results, antibiotic treatment response, and 30-day mortality rate of patients were analyzed. The diagnostic accuracy of mNGS and conventional methods was compared, including sensitivity, specificity, positive predictive value and negative predictive value. The sensitivity and specificity of mNGS were 66.7% and 100.0%, respectively, which were significantly higher than those of fluorescence staining (42.1% and 100%), serum 1,3-β-D-glucan detection (38.1% and 90.9%), serum galactomannan detection (14.3% and 94.9%) and BALF galactomannan detection (47.3% and 70.7%). Although the sensitivity of BALF culture (75.0%) was higher than that of mNGS (66.7%), the turnover time of mNGS was significantly shorter than that of traditional culture (1.6 days vs. 5.0 days). The sensitivity of mNGS combined with BALF culture reached 100.0%. In addition, mNGS has a stronger ability to detect co-pathogens with IPA. 47.6% of T2DM patients with IPA were adjusted the initial antimicrobial therapy according to the mNGS results. This is the first study to focus on the diagnostic performance of mNGS in IPA infection in T2DM patients. MNGS can be used as a supplement to conventional methods for the diagnosis of IPA in patients with T2DM.},
}

Humans
*Diabetes Mellitus, Type 2/complications
Male
Female
*Invasive Pulmonary Aspergillosis/diagnosis/microbiology
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Aged
Galactose/analogs & derivatives
Mannans/blood/analysis
Sensitivity and Specificity
Bronchoalveolar Lavage Fluid/microbiology

@article {pmid39025014,
year = {2024},
author = {Liu, Y and Wu, J and Wu, R and Li, J and Zhang, Q and Sheng, G},
title = {Nitrogen-doped activated carbon-based steel slag composite material as an accelerant for enhancing the resilience of flexible biogas production process against shock loads: Performance, mechanism and modified ADM1 modeling.},
journal = {Journal of environmental management},
volume = {366},
number = {},
pages = {121874},
doi = {10.1016/j.jenvman.2024.121874},
pmid = {39025014},
issn = {1095-8630},
abstract = {Anaerobic digestion for flexible biogas production can lead to digestion inhibition under high shock loads. While steel slag addition has shown promise in enhancing system buffering, its limitations necessitate innovation. This study synthesized the nitrogen-doped activated carbon composite from steel slag to mitigate intermediate product accumulation during flexible biogas production. Material characterization preceded experiments introducing the composite into anaerobic digestion systems, evaluating its impact on methane production efficiency under hydraulic and concentration sudden shocks. Mechanistic insights were derived from microbial community and metagenomic analyses, facilitating the construction of the modified Anaerobic Digestion Model No. 1 (ADM1) to quantitatively assess the material's effects. Results indicate superior resistance to concentration shocks with substantial increment of methane production rate up to 33.45% compared with control group, which is mediated by direct interspecies electron transfer, though diminishing with increasing shock intensity. This study contributes theoretical foundations for stable flexible biogas production and offers an effective predictive tool for conductor material reinforcement processes.},
}

@article {pmid39024936,
year = {2024},
author = {Tao, Y and Du, R and Mao, H},
title = {Tropheryma whipplei pneumonia revealed by Metagenomic next-generation sequencing: Report of two cases.},
journal = {Diagnostic microbiology and infectious disease},
volume = {110},
number = {1},
pages = {116427},
doi = {10.1016/j.diagmicrobio.2024.116427},
pmid = {39024936},
issn = {1879-0070},
abstract = {Tropheryma whipplei is the causative agent of Whipple's disease, which is a rare multiorgan systemic disease. We report two cases of Tropheryma whipplei infection, all routine tests were negative and it was finally detected by mNGS. This may help clinicians increase awareness of the diagnosis and treatment of acute severe pneumonia and interstitial pneumonia caused by Tropheryma whipplei.},
}

@article {pmid39005434,
year = {2024},
author = {Kosch, TA and Torres-Sánchez, M and Liedtke, HC and Summers, K and Yun, MH and Crawford, AJ and Maddock, ST and Ahammed, MS and Araújo, VLN and Bertola, LV and Bucciarelli, G and Carné, A and Carneiro, CM and Chan, KO and Chen, Y and Crottini, A and da Silva, JM and Denton, RD and Dittrich, C and Themudo, GE and Farquharson, KA and Forsdick, NJ and Gilbert, E and Jing, C and Katzenback, BA and Kotharambath, R and Levis, NA and Márquez, R and Mazepa, G and Mulder, KP and Müller, H and O'Connell, MJ and Orozco-terWengel, P and Palomar, G and Petzold, A and Pfennig, DW and Pfennig, KS and Reichert, MS and Robert, J and Scherz, MD and Siu-Ting, K and Snead, AA and Stöck, M and Stuckert, AMM and Stynoski, JL and Tarvin, RD and Valero, KCW and , },
title = {The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39005434},
issn = {2692-8205},
abstract = {Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomics resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomics resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, antipredator strategies, and resilience and adaptive responses. They also serve as critical models for understanding widespread genomic characteristics, including evolutionary genome expansions and contractions given they have the largest range in genome sizes of any animal taxon and multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The advent of long-read sequencing technologies, along with computational techniques that enhance scaffolding capabilities and streamline computational workload is now enabling the ability to overcome some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC) in early 2023. This burgeoning community already has more than 282 members from 41 countries (6 in Africa, 131 in the Americas, 27 in Asia, 29 in Australasia, and 89 in Europe). The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and outline how the AGC can enable amphibian genomics research to "leap" to the next level.},
}

@article {pmid39024931,
year = {2024},
author = {Xu, L and Wang, L and Song, Y and Tong, L},
title = {Metagenomic next-generation sequencing assistance in identifying Mycobacterium iranicum pulmonary infection: A case report.},
journal = {Diagnostic microbiology and infectious disease},
volume = {110},
number = {1},
pages = {116445},
doi = {10.1016/j.diagmicrobio.2024.116445},
pmid = {39024931},
issn = {1879-0070},
abstract = {Nontuberculous mycobacteria (NTM) are important opportunistic pathogens in humans, mostly affecting the lungs, and potentially causing progressive disease in individuals with underlying diseases. The prevalence of NTM infections is increasing worldwide. However, Mycobacterium iranicum (M. iranicum) infections are less common. Here we report a 65-year-old female who developed pneumonia caused by Mycobacterium iranicum, which was detected in bronchoalveolar lavage fluid (BALF) through metagenomic next-generation sequencing (mNGS). The patient was treated with moxifloxacin, doxycycline, and sulfamethoxazole/trimethoprim. Symptoms were relieved and lung abnormalities were shown to be partially absorbed on the follow-up chest computed tomography (CT) scans. As we know, this is the first case of Mycobacterium iranicum pulmonary infection identified by mNGS in BALF.},
}

@article {pmid39024692,
year = {2024},
author = {Chen, L and Bao, Y and Wang, D and Tian, Y and Zeng, T and Gu, T and Xu, W and Lu, L},
title = {Integrated omics analysis reveals the differentiation of intestinal microbiota and metabolites between Pekin ducks and Shaoxing ducks.},
journal = {Poultry science},
volume = {103},
number = {9},
pages = {103976},
doi = {10.1016/j.psj.2024.103976},
pmid = {39024692},
issn = {1525-3171},
abstract = {Pekin ducks and Shaoxing ducks are 2 Chinese local duck breeds, both domesticated from mallard, but after domestication and long-term artificial selection, the body weight of Pekin ducks is significantly higher than that of Shaoxing ducks. It is no debate that genetic factors are the main factors responsible for this difference, but whether intestinal microbiota contribute to this difference is yet unknown. Thus, we performed comparative intestinal metagenomics and metabolomics analysis between Pekin ducks and Shaoxing ducks. We found obvious differentiation of intestinal metagenome and metabolome between the 2 breeds. Four cecal microbial genera, including Fusobacterium, Methanobrevibacter, Butyricicoccus, and Anaerotignum showed higher abundance in Pekin ducks. Among them, Methanobrevibacter and Butyricicoccus may positively correlate with fat deposition and body weight. A total of 310 metabolites showed difference between the 2 breeds. Functions of these differential metabolites were mainly enriched in amino acid metabolism, including energy metabolism-related histidine metabolism. Integrated omics analysis showed that microbial changes were closely related to altered metabolites. Especially, Butyricicoccus showing higher abundance in Pekin ducks was significantly negatively correlated with D-glucosamine-6-phosphate, which has been reported to prevent body weight gains. These findings may contribute to further understand the difference in body weight between Pekin ducks and Shaoxing ducks.},
}

@article {pmid39024671,
year = {2024},
author = {Yang, Y and Li, H and Wang, D and Shi, D and Yang, Z and Zhou, S and Yang, D and Chen, T and Li, J and Chen, J and Jin, M},
title = {Metagenomics of high-altitude groundwater reveal different health risks associated with antibiotic-resistant pathogens and bacterial resistome in the latitudinal gradient.},
journal = {Water research},
volume = {262},
number = {},
pages = {122032},
doi = {10.1016/j.watres.2024.122032},
pmid = {39024671},
issn = {1879-2448},
abstract = {Groundwater on the Tibetan Plateau is a critical water resource to people in Asia. However, its prevalence of antibiotic-resistant pathogens (ARPs), bacterial resistome and their driving factors remain unknown. Using metagenomics analysis, a hotspot of antibiotic-resistance genes (ARGs) and last-resort ARGs (LARGs) with a total of 639 subtypes was identified in the groundwater. Importantly, 164 metagenome-assembled genomes (MAGs) which possessed both ARGs and virulence factors (VFs) were assigned as potential ARPs, with the most abundant species being Acinetobacter johnsonii and Acinetobacter pittii. A total of 157 potential ARPs, involving Escherichia coli, were predicted as "natural" ARGs supercarriers. Thirty-six ARPs dominated by the genus Acinetobacter and Pseudomonas were found to harbour LARGs. Co-localizations of the ARG-mobile genetic elements (MGEs) showed that MGEs were significantly associated with ARGs in the ARPs, which suggests ARPs play a prominent role in ARG dissemination. Notably, latitudinal gradient is a driving factor in the occurrence of ARGs and ARPs. The average abundances of ARGs and ARP decreased as the latitude increased, with the highest abundance occurring in the region between 28.6[◦]N and 29.5[◦]N. MetaCompare further revealed health risks associated with the resistome decreased as the latitudes increased. These findings indicated different health risks associated with ARPs and bacterial resistome in latitudinal gradient groundwater. They raise the concerns of mitigating ARPs risk in groundwater on the Tibetan Plateau.},
}

@article {pmid39024228,
year = {2024},
author = {Ravelo, AD and Ferm, P and Guo, Y and Omontese, BO and Morley, PS and Chen, C and Noyes, NR and Caixeta, LS},
title = {Using a multi-omics approach to explore potential associations with rumen content and serum of cows with different milk production levels based on genomic predicted transmitting ability for milk and phenotypic milk production.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0305674},
doi = {10.1371/journal.pone.0305674},
pmid = {39024228},
issn = {1932-6203},
mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; Female ; *Milk/metabolism/microbiology ; *Lactation ; Phenotype ; Metabolome ; Microbiota ; Genomics/methods ; Metagenome ; Metabolomics/methods ; Multiomics ; },
abstract = {This study aims to compare rumen microbiome and metabolites between second lactation dairy cows in the 75th percentile (n = 12; 57.2 ± 5.08 kg/d) of production according to genomic predicted transmitting ability for milk (GPTAM) and their counterparts in the 25th percentile (n = 12; 47.2 ± 8.61 kg/d). It was hypothesized that the metagenome and metabolome would differ between production levels. Cows were matched by days in milk (DIM), sire, occurrence of disease, and days open in previous lactation. For an additional comparison, the cows were also divided by phenotype into high (n = 6; 61.3 ± 2.8 kg/d), medium (n = 10; 55 ± 1.2 kg/d), and low (n = 8; 41.9 ± 5.6 kg/d) based on their milk production. Samples were collected 65 ± 14 DIM. Rumen content was collected using an oro-gastric tube and serum samples were collected from the coccygeal vessels. High-resolution liquid chromatography-mass spectrometry (LC-MS) was used for rumen and serum metabolite profiling. Shotgun metagenomics was used for rumen microbiome profiling. Microbiome sample richness and diversity were used to determine alpha and Bray-Curtis dissimilarity index was used to estimate beta diversity. Differences in metabolites were determined using t-tests or ANOVA. Pearson correlations were used to consider associations between serum metabolites and milk production. There was no evidence of a difference in rumen metabolites or microbial communities by GPTAM or phenotype. Cows in the phenotypic low group had greater serum acetate to propionate ratio and acetate proportion compared to the cows in the phenotypic medium group. Likewise, serum propionate proportion was greater in the medium compared to the low phenotypic group. Serum acetate, butyrate, and propionate concentrations had a weak positive correlation with milk production. When investigating associations between rumen environment and milk production, future studies must consider the impact of the ruminal epithelium absorption and post-absorption processes in relation to milk production.},
}

Animals
Cattle
*Rumen/microbiology/metabolism
Female
*Milk/metabolism/microbiology
*Lactation
Phenotype
Metabolome
Microbiota
Genomics/methods
Metagenome
Metabolomics/methods
Multiomics

@article {pmid39023746,
year = {2024},
author = {Li, Y and Zhang, M and Li, L and Gao, W and Huang, F and Lai, G and Jia, L and Liu, R},
title = {Nutrient removal efficacy and microbial dynamics in constructed wetlands using Fe(III)-mineral substrates for low carbon-nitrogen ratio sewage treatment.},
journal = {Bioprocess and biosystems engineering},
volume = {},
number = {},
pages = {},
pmid = {39023746},
issn = {1615-7605},
support = {2023B1212060048//Science and Technology Planning Project of Guangdong Province, China/ ; 42372055//National Natural Science Foundation of China/ ; 202103AC100001//Special Project for Social Development of Yunnan Province, China/ ; },
abstract = {This study evaluated the roles of two common sources of Fe(III)-minerals-volcanic rock (VR) and synthetic banded iron formations from waste iron tailings (BIF-W)-in vertical flow-constructed wetlands (VFCWs). The evaluation was conducted in the absence of critical environmental factors, including Fe(II), Fe(III), and soil organic matter (SOM), using metagenomic analysis and integrated correlation networks to predict nitrogen removal pathways. Our findings revealed that Fe(III)-minerals enhanced metabolic activities and cellular processes related to carbohydrate decomposition, thereby increasing the average COD removal rates by 10.7% for VR and 5.90% for BIF-W. Notably, VR improved nitrogen removal by 1.70% and 5.40% compared to BIF-W and the control, respectively. Fe(III)-mineral amendment in bioreactors also improved the retention of denitrification and nitrification bacteria (phylum Proteobacteria) and anammox bacteria (phylum Planctomycetes), with increases of 3.60% and 3.20% using VR compared to BIF-W. Metagenomic functional prediction indicated that the nitrogen removal mechanisms in VFCWs with low C/N ratios involve simultaneous partial nitrification, ANAMMOX, and denitrification (SNAD). Network-based analyses and correlation pathways further suggest that the advantages of Fe(III)-minerals are manifested in the enhancement of denitrification microorganisms. Microbial communities may be activated by the functional dissolution of Fe(III)-minerals, which improves the stability of SOM or the conversion of Fe(III)/Fe(II). This study provides new insights into the functional roles of Fe(III)-minerals in VFCWs at the microbial community level, and provides a foundation for developing Fe-based SNAD enhancement technologies.},
}

@article {pmid39023219,
year = {2024},
author = {López-Beltrán, A and Botelho, J and Iranzo, J},
title = {Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae134},
pmid = {39023219},
issn = {1751-7370},
abstract = {Arms races between mobile genetic elements and prokaryotic hosts are major drivers of ecological and evolutionary change in microbial communities. Prokaryotic defense systems such as CRISPR-Cas have the potential to regulate microbiome composition by modifying the interactions among bacteria, plasmids, and phages. Here, we used longitudinal metagenomic data from 130 healthy and diseased individuals to study how the interplay of genetic parasites and CRISPR-Cas immunity reflects on the dynamics and composition of the human gut microbiome. Based on the coordinated study of 80 000 CRISPR-Cas loci and their targets, we show that CRISPR-Cas immunity effectively modulates bacteriophage abundances in the gut. Acquisition of CRISPR-Cas immunity typically leads to a decrease in the abundance of lytic phages but does not necessarily cause their complete disappearance. Much smaller effects are observed for lysogenic phages and plasmids. Conversely, phage-CRISPR interactions shape bacterial microdiversity by producing weak selective sweeps that benefit immune host lineages. We also show that distal (and chronologically older) regions of CRISPR arrays are enriched in spacers that are potentially functional and target crass-like phages and local prophages. This suggests that exposure to reactivated prophages and other endemic viruses is a major selective pressure in the gut microbiome that drives the maintenance of long-lasting immune memory.},
}