@article {pmid38647897,
year = {2022},
author = {Mon, ML and Marrero Díaz de Villegas, R and Campos, E and Soria, MA and Talia, PM},
title = {Characterization of a novel GH10 alkali-thermostable xylanase from a termite microbiome.},
journal = {Bioresources and bioprocessing},
volume = {9},
number = {1},
pages = {84},
pmid = {38647897},
issn = {2197-4365},
support = {PI 102//Instituto Nacional de Tecnología Agropecuaria/ ; 106//Instituto Nacional de Tecnología Agropecuaria/ ; 116//Instituto Nacional de Tecnología Agropecuaria/ ; 149//Instituto Nacional de Tecnología Agropecuaria/ ; 159//Instituto Nacional de Tecnología Agropecuaria/ ; (PICT) 2018-#4149//Agencia Nacional de Promoción Científica y Tecnológica/ ; 2020-#3570//Agencia Nacional de Promoción Científica y Tecnológica/ ; PIP-2021-2561//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; },
abstract = {The aim of the present study was to assess the biochemical and molecular structural characteristics of a novel alkali-thermostable GH10 xylanase (Xyl10B) identified in a termite gut microbiome by a shotgun metagenomic approach. This endoxylanase candidate was amplified, cloned, heterologously expressed in Escherichia coli and purified. The recombinant enzyme was active at a broad range of temperatures (37-60 ºC) and pH values (4-10), with optimal activity at 50 ºC and pH 9. Moreover, its activity remained at more than 80% of its maximum at 50 °C for 8 h. In addition, Xyl10B was found to be stable in the presence of salt and several ions and chemical reagents frequently used in the industry. These characteristics make this enzyme an interesting candidate for pulp and paper bleaching industries, since this process requires enzymes without cellulase activity and resistant to high temperatures and alkaline pH (thermo-alkaliphilic enzymes). The products of xylan hydrolysis by Xyl10B (short xylooligosaccharides, xylose and xylobiose) could be suitable for application as prebiotics and in the production of bioethanol.},
}

@article {pmid38647870,
year = {2024},
author = {Yang, F and Li, Q and Yin, X},
title = {Metagenomic analysis of the effects of salinity on microbial community and functional gene diversity in glacial meltwater estuary, Ny-Alesund, Arctic.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {38647870},
issn = {1678-4405},
support = {ZR2020KC036//Natural Science Foundation of Shandong Province/ ; },
abstract = {Due to the inflow of meltwater from the Midre Lovénbreen glacier upstream of Kongsfjorden, the nutrient concentration of Kongsfjorden change from the estuary to the interior of the fjord. Our objective was to explore the changes in bacterial community structure and metabolism-related genes from the estuary to fjord by metagenomic analysis. Our data indicate that glacial meltwater input has altered the physicochemical properties of the fjords, with a significant effect, in particular, on fjords salinity, thus altering the relative abundance of some specific bacterial groups. In addition, we suggest that the salinity of a fjord is an important factor affecting the abundance of genes associated with the nitrogen and sulfur cycles in the fjord. Changes in salinity may affect the relative abundance of microbial populations that carry metabolic genes, thus affecting the relative abundance of genes associated with the nitrogen and sulfur cycles.},
}

@article {pmid38647859,
year = {2024},
author = {Fernandez-Cassi, X and Kohn, T},
title = {Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics.},
journal = {Food and environmental virology},
volume = {},
number = {},
pages = {},
pmid = {38647859},
issn = {1867-0342},
support = {754462//Marie Skłodowska-Curie Grant Agreement/ ; },
abstract = {Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preamplification pipelines (specific to RNA viruses, DNA viruses or both) for viral genome sequencing using spiked-in Phosphate Buffered Saline and sewage samples containing known concentrations of viruses. We found that compared to the pipeline targeting all genome types, the RNA pipeline performed better in detecting RNA viruses in both spiked and unspiked sewage samples, allowing the detection of various mammalian viruses including members from the Reoviridae, Picornaviridae, Astroviridae and Caliciviridae. However, the DNA-specific pipeline did not improve the detection of mammalian DNA viruses. We also measured viral recovery by quantitative reverse transcription polymerase chain reaction and assessed the impact of genetic background (non-viral genetic material) on viral coverage. Our results indicate that viral recoveries were generally lower in sewage (average of 11.0%) and higher in Phosphate Buffered Saline (average of 23.4%) for most viruses. Additionally, spiked-in viruses showed lower genome coverage in sewage, demonstrating the negative effect of genetic background on sequencing. Finally, correlation analysis revealed a relationship between virus concentration and genome normalized reads per million, indicating that viral metagenomic sequencing can be semiquantitative.},
}

@article {pmid38647817,
year = {2023},
author = {Wang, Y and Luo, X and Chu, P and Shi, H and Wang, R and Li, J and Zheng, S},
title = {Cultivation and application of nicotine-degrading bacteria and environmental functioning in tobacco planting soil.},
journal = {Bioresources and bioprocessing},
volume = {10},
number = {1},
pages = {10},
pmid = {38647817},
issn = {2197-4365},
support = {20191307C04//Hubei Tobacco Company/ ; },
abstract = {Nicotine, a toxic and addictive alkaloid from tobacco, is an environmental pollutant. However, nicotine-degrading bacteria (NDB) and their function in tobacco planting soil are not fully understood. First, 52 NDB strains belonging to seven genera were isolated from tobacco soil. The most dominant genera were Flavobacterium (36.5%), Pseudomonas (30.8%), and Arthrobacter (15.4%), and Chitinophaga and Flavobacterium have not been previously reported. Then, two efficient NDB strains, Arthrobacter nitrophenolicus ND6 and Stenotrophomonas geniculata ND16, were screened and inoculated in the compost fertilizer from tobacco waste. The nicotine concentrations were reduced from 1.5 mg/g (DW) to below the safety threshold of 0.5 mg/g. Furthermore, strain ND6 followed the pyridine pathway of nicotine degradation, but the degrading pathway in strain ND16 could not be determined according to genomic analysis and color change. Finally, the abundance of nicotine-degrading genes in tobacco rhizosphere soil was investigated via metagenomic analysis. Five key genes, ndhA, nctB, kdhL, nboR, and dhponh, represent the whole process of nicotine degradation, and their abundance positively correlated with soil nicotine concentrations (p < 0.05). In conclusion, various NDB including unknown species live in tobacco soil and degrade nicotine efficiently. Some key nicotine-degrading genes could be used in monitoring nicotine degradation in the environment. The fermentation of compost from tobacco waste is a promising application of efficient NDB.},
}

@article {pmid38647787,
year = {2023},
author = {Xue, F and Yang, J and Luo, C and Li, D and Shi, G and Song, G and Li, Y},
title = {Metagenomic insight into the biodegradation of biomass and alkaloids in the aging process of cigar.},
journal = {Bioresources and bioprocessing},
volume = {10},
number = {1},
pages = {45},
pmid = {38647787},
issn = {2197-4365},
support = {110202101066(XJ-15)//Major Science and Technology Program of China National Tobacco Corporation/ ; (110202101014(XJ-06)//Major Science and Technology Program of China National Tobacco Corporation/ ; },
abstract = {A significant distinction between cigar production and tobacco lies in the necessary aging process, where intricate microbial growth, metabolic activities, enzymatic catalysis, and chemical reactions interact. Despite its crucial role in determining the final quality of cigars, our comprehension of the underlying chemical and biological mechanisms within this process remains insufficient. Biomass and alkaloids are the primary constituents that influence the flavor of cigars. Consequently, investigating the entire aging process could begin by exploring the involvement of microbes and enzymes in their biodegradation. In this study, handmade cigars were aged under different conditions. Metagenomic sequencing was employed to identify the microbes and enzymes responsible for the degradation of biomass and alkaloids derived from tobacco leaves. The results revealed that various environmental factors, including temperature, humidity, duration time, and turning frequency, yielded varying contents of total sugar and alkaloids in the cigars. Significant correlations were observed between microbial communities and starch, reducing sugars, total sugars, and alkaloids. Key species involved in the breakdown of biomass constituents, such as starch (Bacillus pumilus, Pseudomonas sp. 286, and Aspergillus cristatus), reducing sugars and total sugars (Aspergillus cristatus and Nitrolancea hollandica), were identified. Furthermore, Corynespora cassiicola and Pseudomonas fulva were found to potentially contribute to the degradation of alkaloid compounds, specifically nornicotine and neonicotinoid. Our work contributes to a deeper understanding of the microbial roles in the aging of cigars. Moreover, the selection of specific microbial strains or starter cultures can be employed to control and manipulate the aging process, thereby further refining the flavor development in cigar products.},
}

@article {pmid38647756,
year = {2022},
author = {Zhang, Y and Guan, F and Xu, G and Liu, X and Zhang, Y and Sun, J and Yao, B and Huang, H and Wu, N and Tian, J},
title = {A novel thermophilic chitinase directly mined from the marine metagenome using the deep learning tool Preoptem.},
journal = {Bioresources and bioprocessing},
volume = {9},
number = {1},
pages = {54},
pmid = {38647756},
issn = {2197-4365},
support = {2021YFC2100300//the National Key R&D Program of China/ ; Y2019XK19//the Central Public-interest Scientific Institution Basal Research Fund/ ; 1610392021008//the Central Public-interest Scientific Institution Basal Research Fund/ ; 1610392020001//the Central Public-interest Scientific Institution Basal Research Fund/ ; 19273201D//the Key Research and Development Plan Project of Hebei Province/ ; },
abstract = {Chitin is abundant in nature and its degradation products are highly valuable for numerous applications. Thermophilic chitinases are increasingly appreciated for their capacity to biodegrade chitin at high temperatures and prolonged enzyme stability. Here, using deep learning approaches, we developed a prediction tool, Preoptem, to screen thermophilic proteins. A novel thermophilic chitinase, Chi304, was mined directly from the marine metagenome. Chi304 showed maximum activity at 85 ℃, its Tm reached 89.65 ± 0.22℃, and exhibited excellent thermal stability at 80 and 90 °C. Chi304 had both endo- and exo-chitinase activities, and the (GlcNAc)2 was the main hydrolysis product of chitin-related substrates. The product yields of colloidal chitin degradation reached 97% within 80 min, and 20% over 4 days of reaction with crude chitin powder. This study thus provides a method to mine the novel thermophilic chitinase for efficient chitin biodegradation.},
}

@article {pmid38647577,
year = {2022},
author = {Wang, D and Unsal, T and Kumseranee, S and Punpruk, S and Saleh, MA and Alotaibi, MD and Xu, D and Gu, T},
title = {Mitigation of carbon steel biocorrosion using a green biocide enhanced by a nature-mimicking anti-biofilm peptide in a flow loop.},
journal = {Bioresources and bioprocessing},
volume = {9},
number = {1},
pages = {67},
pmid = {38647577},
issn = {2197-4365},
abstract = {Biocorrosion, also called microbiologically influenced corrosion (MIC), is a common operational threat to many industrial processes. It threatens carbon steel, stainless steel and many other metals. In the bioprocessing industry, reactor vessels in biomass processing and bioleaching are prone to MIC. MIC is caused by biofilms. The formation and morphology of biofilms can be impacted by fluid flow. Fluid velocity affects biocide distribution and MIC. Thus, assessing the efficacy of a biocide for the mitigation of MIC under flow condition is desired before a field trial. In this work, a benchtop closed flow loop bioreactor design was used to investigate the biocide mitigation of MIC of C1018 carbon steel at 25 °C for 7 days using enriched artificial seawater. An oilfield biofilm consortium was analyzed using metagenomics. The biofilm consortium was grown anaerobically in the flow loop which had a holding vessel for the culture medium and a chamber to hold C1018 carbon steel coupons. Peptide A (codename) was a chemically synthesized cyclic 14-mer (cys-ser-val-pro-tyr-asp-tyr-asn-trp-tyr-ser-asn-trp-cys) with its core 12-mer sequence originated from a biofilm dispersing protein secreted by a sea anemone which possesses a biofilm-free exterior. It was used as a biocide enhancer. The combination of 50 ppm (w/w) THPS (tetrakis hydroxymethyl phosphonium sulfate) biocide + 100 nM (180 ppb by mass) Peptide A resulted in extra 1-log reduction in the sulfate reducing bacteria (SRB) sessile cell count and the acid producing bacteria (APB) sessile cell count compared to 50 ppm THPS alone treatment. Furthermore, with the enhancement of 100 nM Peptide A, extra 44% reduction in weight loss and 36% abatement in corrosion pit depth were achieved compared to 50 ppm THPS alone treatment.},
}

@article {pmid38647315,
year = {2024},
author = {Chen, L-p and Zhang, L-f and Liu, S and Hua, H and Zhang, L and Liu, B-c and Wang, R-r},
title = {Ling-Gui-Zhu-Gan decoction ameliorates nonalcoholic fatty liver disease via modulating the gut microbiota.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0197923},
doi = {10.1128/spectrum.01979-23},
pmid = {38647315},
issn = {2165-0497},
abstract = {UNLABELLED: Numerous studies have supported that nonalcoholic fatty liver disease (NAFLD) is highly associated with gut microbiota dysbiosis. Ling-Gui-Zhu-Gan decoction (LG) has been clinically used to treat NAFLD, but the underlying mechanism remains unknown. This study investigated the therapeutic effect and mechanisms of LG in mice with NAFLD induced by a high-fat diet (HD). An HD-induced NAFLD mice model was established to evaluate the efficacy of LG followed by biochemical and histopathological analysis. Metagenomics, metabolomics, and transcriptomics were used to explore the structure and metabolism of the gut microbiota. LG significantly improved hepatic function and decreased lipid droplet accumulation in HD-induced NAFLD mice. LG reversed the structure of the gut microbiota that is damaged by HD and improved intestinal barrier function. Meanwhile, the LG group showed a lower total blood bile acids (BAs) concentration, a shifted BAs composition, and a higher fecal short-chain fatty acids (SCFAs) concentration. Furthermore, LG could regulate the hepatic expression of genes associated with the primary BAs biosynthesis pathway and peroxisome proliferator-activated receptor (PPAR) signaling pathway. Our study suggested that LG could ameliorate NAFLD by altering the structure and metabolism of gut microbiota, while BAs and SCFAs are considered possible mediating substances.

IMPORTANCE: Until now, there has still been no study on the gut microbiota and metabolomics of Ling-Gui-Zhu-Gan decoction (LG) in nonalcoholic fatty liver disease (NAFLD) mouse models. Our study is the first to report on the reshaping of the structure and metabolism of the gut microbiota by LG, as well as explore the potential mechanism underlying the improvement of NAFLD. Specifically, our study demonstrates the potential of gut microbial-derived short-chain fatty acids (SCFAs) and blood bile acids (BAs) as mediators of LG therapy for NAFLD in animal models. Based on the results of transcriptomics, we further verified that LG attenuates NAFLD by restoring the metabolic disorder of BAs via the up-regulation of Fgf15/FXR in the ileum and down-regulation of CYP7A1/FXR in the liver. LG also reduces lipogenesis in NAFLD mice by mediating the peroxisome proliferator-activated receptor (PPAR) signaling pathway, which then contributes to reducing hepatic inflammation and improving intestinal barrier function to treat NAFLD.},
}

@article {pmid38647296,
year = {2024},
author = {Barno, AR and Green, K and Rohwer, F and Silveira, CB},
title = {Snow viruses and their implications on red snow algal blooms.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0008324},
doi = {10.1128/msystems.00083-24},
pmid = {38647296},
issn = {2379-5077},
abstract = {Algal blooms can give snowmelt a red color, reducing snow albedo and creating a runaway effect that accelerates snow melting. The occurrence of red snow is predicted to grow in polar and subpolar regions with increasing global temperatures. We hypothesize that these algal blooms affect virus-bacteria interactions in snow, with potential effects on snowmelt dynamics. A genomic analysis of double-stranded DNA virus communities in red and white snow from the Whistler region of British Columbia, Canada, identified 792 putative viruses infecting bacteria. The most abundant putative snow viruses displayed low genomic similarity with known viruses. We recovered the complete circular genomes of nine putative viruses, two of which were classified as temperate. Putative snow viruses encoded genes involved in energy metabolisms, such as NAD[+] synthesis and salvage pathways. In model phages, these genes facilitate increased viral particle production and lysis rates. The frequency of temperate phages was positively correlated with microbial abundance in the snow samples. These results suggest the increased frequency of temperate virus-bacteria interactions as microbial densities increase during snowmelt. We propose that this virus-bacteria dynamic may facilitate the red snow algae growth stimulated by bacteria.IMPORTANCEMicrobial communities in red snow algal blooms contribute to intensifying snowmelt rates. The role of viruses in snow during this environmental shift, however, has yet to be elucidated. Here, we characterize novel viruses extracted from snow viral metagenomes and define the functional capacities of snow viruses in both white and red snow. These results are contextualized using the composition and functions observed in the bacterial communities from the same snow samples. Together, these data demonstrate the energy metabolism performed by viruses and bacteria in a snow algal bloom, as well as expand the overall knowledge of viral genomes in extreme environments.},
}

@article {pmid38646847,
year = {2024},
author = {Fontana, F and Longhi, G and Carli, E and Alessandri, G and Mancabelli, L and Lugli, GA and Tarracchini, C and Viappiani, A and Anzalone, R and Turroni, F and Milani, C and Ventura, M},
title = {Revealing the genetic traits of the foodborne microbial genus hafnia: Implications for the human gut microbiome.},
journal = {Environmental microbiology},
volume = {26},
number = {4},
pages = {e16626},
doi = {10.1111/1462-2920.16626},
pmid = {38646847},
issn = {1462-2920},
support = {//Cariparma/ ; //GenProbio Srl/ ; CUP D93C22000890001//Concession Decree No.1550 of 11 October 2022, Italian Ministry of University and Research/ ; PE00000003//Mission 4 Component 2 Investment 1.3 - Call for tender No. 341 of 15 March 2022, Italian Ministry of University and Research funded by the European Union-NextGenerationEU/ ; //the National Recovery and Resilience Plan (NRRP)/ ; //ON Foods - Research and innovation network on food and nutrition Sustainability, Safety and Security -Working ON Foods/ ; },
abstract = {The bacterial genus Hafnia has recently attracted attention due to its complex metabolic features and host-interaction capabilities, which are associated with health benefits, primarily weight loss. However, significant gaps remain in our understanding of the genomic characteristics of this emerging microbial group. In this study, we utilized all available high-quality genomes of Hafnia alvei and Hafnia paralvei to uncover the broad distribution of Hafnia in human and honeybee guts, as well as in dairy products, by analysing 1068 metagenomic datasets. We then investigated the genetic traits related to Hafnia's production of vitamins and short-chain fatty acids (SCFAs) through a comparative genomics analysis that included all dominant bacterial species in the three environments under study. Our findings underscore the extensive metabolic capabilities of Hafnia, particularly in the production of vitamins such as thiamine (B1), nicotinate (B3), pyridoxine (B6), biotin (B7), folate (B9), cobalamin (B12), and menaquinone (K2). Additionally, Hafnia demonstrated a conserved genetic makeup associated with SCFA production, including acetate, propanoate, and butanoate. These metabolic traits were further confirmed using RNAseq analyses of a newly isolated H. paralvei strain T10. Overall, our study illuminates the ecological distribution and genetic attributes of this bacterial genus, which is of increasing scientific and industrial relevance.},
}

@article {pmid38646629,
year = {2024},
author = {Nivetha, N and Shukla, PS and Nori, SS and Kumar, S and Suryanarayan, S},
title = {A red seaweed Kappaphycus alvarezii-based biostimulant (AgroGain[®]) improves the growth of Zea mays and impacts agricultural sustainability by beneficially priming rhizosphere soil microbial community.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1330237},
pmid = {38646629},
issn = {1664-302X},
abstract = {The overuse of chemical-based agricultural inputs has led to the degradation of soil with associated adverse effects on soil attributes and microbial population. This scenario leads to poor soil health and is reportedly on the rise globally. Additionally, chemical fertilizers pose serious risks to the ecosystem and human health. In this study, foliar sprays of biostimulant (AgroGain/LBS6) prepared from the cultivated, tropical red seaweed Kappaphycus alvarezii increased the phenotypic growth of Zea mays in terms of greater leaf area, total plant height, and shoot fresh and dry weights. In addition, LBS6 improved the accumulation of chlorophyll a and b, total carotenoids, total soluble sugars, amino acids, flavonoids, and phenolics in the treated plants. LBS6 applications also improved the total bacterial and fungal count in rhizospheric soil. The V3-V4 region of 16S rRNA gene from the soil metagenome was analyzed to study the abundance of bacterial communities which were increased in the rhizosphere of LBS6-treated plants. Treatments were found to enrich beneficial soil bacteria, i.e., Proteobacteria, especially the classes Alphaproteobacteria, Cyanobacteria, Firmicutes, Actinobacteriota, Verrucomicrobiota, Chloroflexi, and Acidobacteriota and several other phyla related to plant growth promotion. A metagenomic study of those soil samples from LBS6-sprayed plants was correlated with functional potential of soil microbiota. Enrichment of metabolisms such as nitrogen, sulfur, phosphorous, plant defense, amino acid, co-factors, and vitamins was observed in soils grown with LBS6-sprayed plants. These results were further confirmed by a significant increase in the activity of soil enzymes such as urease, acid phosphatase, FDAse, dehydrogenase, catalase, and biological index of fertility in the rhizosphere of LBS6-treated corn plant. These findings conclude that the foliar application of LBS6 on Z. mays improves and recruits beneficial microbes and alters soil ecology in a sustainable manner.},
}

@article {pmid38645890,
year = {2024},
author = {Zhou, J and Xu, H and Du, W and Peng, L},
title = {The First Case Report of Inactive Nontuberculous Mycobacterial Pulmonary Disease (NTM-PD) in a Pneumoconiosis Patient Caused by Mycobacterium europaeum in China.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {1515-1521},
pmid = {38645890},
issn = {1178-6973},
abstract = {We reported a 51-year-old male electric welder with stage I pneumoconiosis, who had no significant cough, sputum, fever, chest pain, or other discomfort. However, regular physical examination at our hospital revealed bilateral pulmonary nodules with cavity formation. Blood routine, liver or kidney function, and infection-related biomarkers, including interleukin-6 (IL-6), high-sensitivity C-reactive protein (hs-CRP), and procalcitonin (PCT), were normal. Sputum and alveolar lavage fluid (BALF) acid-fast bacilli (AFB) smears, BALF Mycobacterium tuberculosis (TB) PCR, and T-SPOT.TB were negative. The nucleic acid sequence of Mycobacterium europaeum was detected by BALF metagenomic next-generation sequencing (mNGS), which was confirmed by the subsequent positive culture for NTM. Considering stable conditions, no significant discomfort, and no significant changes in the lung lesion, the patient was diagnosed with inactive nontuberculous mycobacterial pulmonary disease (NTM-PD).},
}

@article {pmid38645888,
year = {2024},
author = {Song, RJ and Zhang, GL},
title = {A Rare Case Report of Disseminated Nocardia Farcinica Granulomatous Hepatitis and Clinical Management Experience.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {1523-1528},
pmid = {38645888},
issn = {1178-6973},
abstract = {BACKGROUND: Nocardiosis is primarily an opportunistic infection affecting immunocompromised individuals, with a predilection for the lungs, brain, or skin in those with compromised immune function. Granulomatous hepatitis caused by Nocardia is a rare clinical manifestation. This study aims to provide a systematic overview of the clinical features of Nocardiosis caused by Nocardia farcinica, enhancing our understanding of this disease.

METHODS: We report a case of a 75-year-old male with no underlying diseases presenting with a history of "recurrent fever for more than 4 months", along with fatigue, poor appetite, and pleural and abdominal effusion. Despite treatment at multiple hospitals, the patient showed little improvement. Chest CT revealed chronic inflammation, small nodules, bilateral pleural effusion, and pleural thickening. Abdominal CT indicated multiple low-density lesions in the liver, multiple small calcifications, and abdominal effusion.

RESULTS: Liver biopsy suggested inflammatory changes, with focal granuloma formation. Metagenomic next-generation sequencing (mNGS) of liver tissue indicated Nocardia farcinica, leading to the final diagnosis of disseminated Nocardia farcinica granulomatous hepatitis.

CONCLUSION: Nocardia infection is a rare disease primarily observed in immunocompromised patients but can also occur in those with normal immune function. The clinical and radiological features lack specificity; however, the utilization of mNGS technology enables rapid identification of the pathogenic microorganism. Nocardia farcinica is generally susceptible to sulfonamide drugs and amikacin, offering viable treatment options.},
}

@article {pmid38645300,
year = {2024},
author = {Daher, M and Iordanov, R and Al Mohajer, M and Sohail, MR and Staggers, KA and Hamdi, AM},
title = {Clinical utility of metagenomic next-generation sequencing in fever of undetermined origin.},
journal = {Therapeutic advances in infectious disease},
volume = {11},
number = {},
pages = {20499361241244969},
pmid = {38645300},
issn = {2049-9361},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a novel diagnostic tool increasingly used in the field of infectious diseases. Little guidance is available regarding its appropriate use in different patient populations and clinical syndromes. We aimed to review the clinical utility of mNGS in patients with a specific clinical syndrome and identify factors that may increase its utility.

METHODS: We retrospectively reviewed charts of 72 non-immunocompromised adults hospitalized with the clinical syndrome of 'fever of undetermined origin' and underwent mNGS testing. Standardized criteria from a previously published study were used to determine the clinical impact of mNGS testing. We applied logistic regression to identify factors associated with a positive clinical impact.

RESULTS: Of the 72 patients identified, 62.5% were males with a median age of 56. All patients had a fever at the time of evaluation. At least one organism was identified in 65.3% of cases; most commonly were Epstein-Barr virus (13.9%), cytomegalovirus (12.5%), and Rickettsia typhi (11.1%). Of those determined to have an infectious etiology of their febrile syndrome, 89.5% (n = 34/38) had a positive mNGS. Consistency between the organism(s) on mNGS and the clinically determined infectious etiology was 82.4%. mNGS had a positive clinical impact in 40.3% of cases, a negative impact in 2.8%, and no impact in 56.9% of cases. Besides age, we did not identify other factors associated with a higher likelihood of positive clinical impact.

CONCLUSION: In our review, mNGS had a positive clinical impact in a large proportion of adults with fever of undetermined origin, with minimal negative impact. However, mNGS results should be interpreted carefully given the high rate of detection of pathogens of unclear clinical significance. Randomized clinical trials are needed to assess the clinical utility of this novel diagnostic tool.},
}

@article {pmid38645218,
year = {2024},
author = {Moodley, S and Kroon, E and Naidoo, CC and Nyawo, GR and Wu, BG and Naidoo, S and Chiyaka, TL and Tshivhula, H and Singh, S and Li, Y and Warren, RM and Hoal, EG and Schurr, E and Clemente, J and Segal, LN and Möller, M and Theron, G},
title = {Latent tuberculosis infection is associated with an enrichment of short chain fatty acid producing bacteria in the stool of women living with HIV.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4182285/v1},
pmid = {38645218},
abstract = {Background: Latent tuberculosis infection (LTBI) is common in people living with HIV (PLHIV) in high TB burden settings. Active TB is associated with specific stool taxa; however, little is known about the stool microbiota and LTBI, including in PLHIV. Method : Within a parent study that recruited adult females with HIV from Cape Town, South Africa into predefined age categories (18-25, 35-60 years), we characterised the stool microbiota of those with [interferon- γ release assay (IGRA)- and tuberculin skin test (TST)-positive] or without (IGRA- and TST-negative) LTBI (n=25 per group). 16S rRNA DNA sequences were analysed using QIIME2, Dirichlet Multinomial Mixtures, DESeq2 and PICRUSt2. Results: No α- or β-diversity differences occurred by LTBI status; however, LTBI-positives were Faecalibacterium-, Blautia-, Gemmiger-, Bacteroides- enriched and Moryella-, Atopobium-, Corynebacterium-, Streptococcus -depleted. Inferred metagenome data showed LTBI-negative-enriched pathways included several involved in methylglyoxal degradation, L-arginine, putrescine, 4-aminobutanoate degradation and L-arginine and ornithine degradation. Stool from LTBI-positives demonstrated differential taxa abundance based on a quantitative response to antigen stimulation (Acidaminococcus- enrichment and Megamonas -, Alistipes -, and Paraprevotella -depletion associated with higher IGRA or TST responses, respectively). In LTBI-positives, older people had different β-diversities than younger people whereas, in LTBI-negatives, no differences occurred across age groups. Conclusion: Amongst female PLHIV, those with LTBI had, vs. those without LTBI, Faecalibacterium , Blautia , Gemmiger, Bacteriodes -enriched, which are producers of short chain fatty acids. Taxonomic differences amongst people with LTBI occurred according to quantitative response to antigen stimulation and age. These data enhance our understanding of the microbiome's potential role in LTBI.},
}

@article {pmid38645206,
year = {2024},
author = {Lu, D and Kalantar, KL and Chu, VT and Glascock, AL and Guerrero, ES and Bernick, N and Butcher, X and Ewing, K and Fahsbender, E and Holmes, O and Hoops, E and Jones, AE and Lim, R and McCanny, S and Reynoso, L and Rosario, K and Tang, J and Valenzuela, O and Mourani, PM and Pickering, AJ and Raphenya, AR and Alcock, BP and McArthur, AG and Langelier, CR},
title = {Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.12.589250},
pmid = {38645206},
abstract = {Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the Chan Zuckerberg ID (CZ ID) AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data. It leverages the Comprehensive Antibiotic Resistance Database and associated Resistance Gene Identifier software, and works synergistically with the CZ ID short-read mNGS module to enable broad detection of both microbes and AMR genes. We highlight diverse applications of the AMR module through analysis of both publicly available and newly generated mNGS and WGS data from four clinical cohort studies and an environmental surveillance project. Through genomic investigations of bacterial sepsis and pneumonia cases, hospital outbreaks, and wastewater surveillance data, we gain a deeper understanding of infectious agents and their resistomes, highlighting the value of integrating microbial identification and AMR profiling for both research and public health. We leverage additional functionalities of the CZ ID mNGS platform to couple resistome profiling with the assessment of phylogenetic relationships between nosocomial pathogens, and further demonstrate the potential to capture the longitudinal dynamics of pathogen and AMR genes in hospital acquired bacterial infections. In sum, the new AMR module advances the capabilities of the open-access CZ ID microbial bioinformatics platform by integrating pathogen detection and AMR profiling from mNGS and WGS data. Its development represents a critical step toward democratizing pathogen genomic analysis and supporting collaborative efforts to combat the growing threat of AMR.},
}

@article {pmid38645157,
year = {2024},
author = {Goh, CE and Bohn, B and Genkinger, JM and Molinsky, R and Roy, S and Paster, BJ and Chen, CY and Yuzefpolskaya, M and Colombo, PC and Rosenbaum, M and Knight, R and Desvarieux, M and Papapanou, PN and Jacobs, DR and Demmer, RT},
title = {Dietary nitrate intake and net nitrite-generating capacity of the oral microbiome interact to enhance cardiometabolic health: Results from the Oral Infections Glucose Intolerance and Insulin Resistance Study (ORIGINS).},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.10.24305636},
pmid = {38645157},
abstract = {BACKGROUND: We investigated the association between dietary nitrate intake and early clinical cardiometabolic risk biomarkers, and explored whether the oral microbiome modifies the association between dietary nitrate intake and cardiometabolic biomarkers.

METHODS: Cross-sectional data from 668 (mean [SD] age 31 [9] years, 73% women) participants was analyzed. Dietary nitrate intakes and alternative healthy eating index (AHEI) scores were calculated from food frequency questionnaire responses and a validated US food database. Subgingival 16S rRNA microbial genes (Illumina, MiSeq) were sequenced, and PICRUSt2 estimated metagenomic content. The Microbiome Induced Nitric oxide Enrichment Score (MINES) was calculated as a microbial gene abundance ratio representing enhanced net capacity for NO generation. Cardiometabolic risk biomarkers included systolic and diastolic blood pressure, HbA1c, glucose, insulin, and insulin resistance (HOMA-IR), and were regressed on nitrate intake tertiles in adjusted multivariable linear models.

RESULTS: Mean nitrate intake was 190[171] mg/day. Higher nitrate intake was associated with lower insulin, and HOMA-IR but particularly among participants with low abundance of oral nitrite enriching bacteria. For example, among participants with a low MINES, mean insulin[95%CI] levels in high vs. low dietary nitrate consumers were 5.8[5.3,6.5] vs. 6.8[6.2,7.5] (p=0.004) while respective insulin levels were 6.0[5.4,6.6] vs. 5.9[5.3,6.5] (p=0.76) among partcipants with high MINES (interaction p=0.02).

CONCLUSION: Higher dietary nitrate intake was only associated with lower insulin and insulin resistance among individuals with reduced capacity for oral microbe-induced nitrite enrichment. These findings have implications for future precision medicine-oriented approaches that might consider assessing the oral microbiome prior to enrollment into dietary interventions or making dietary recommendations.

CLINICAL PERSPECTIVE: What is new?: In this population-based study we identified an interaction between dietary nitrate intake and oral nitrite enriching bacteria on cardiometabolic outcomes. Higher dietary nitrate intake was associated with lower insulin and insulin resistance only among participants with low abundance of oral nitrite enriching bacteria. This study suggests that cardiometabolic benefits of nitrate consumption might depend on the host microbiome's capacity to metabolize nitrates.What are the clinical implications?: Among people with low microbiome capacity for nitrate metabolism, higher levels of nitrate might be necessary to realize cardiometabolic benefits.Lack of microbiome assessments in prior studies could partially explain inconsistent findings from previous nitrate supplementation trials and observational studies.Future precision-medicine oriented trials studying the effects of dietary nitrate recommendations on cardiometabolic health, should consider assessing the oral microbiome.},
}

@article {pmid38645133,
year = {2024},
author = {Zelasko, S and Swaney, MH and Sandstrom, S and Davenport, TC and Seroogy, CM and Gern, JE and Kalan, LR and Currie, CR},
title = {Upper respiratory microbial communities of healthy populations are shaped by niche and age.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.14.589416},
pmid = {38645133},
abstract = {BACKGROUND: Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and functioning across healthy 24-month-old infant (n=229) and adult (n=100) populations.

RESULTS: We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity.

CONCLUSIONS: In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functioning, with important implications for host health across the lifespan.},
}

@article {pmid38644786,
year = {2024},
author = {Xu, Z and Gao, X and Li, G and Nghiem, LD and Luo, W and Zhang, F},
title = {Microbial Sources and Sinks of Nitrous Oxide during Organic Waste Composting.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.3c10341},
pmid = {38644786},
issn = {1520-5851},
abstract = {Composting is widely used for organic waste management and is also a major source of nitrous oxide (N2O) emission. New insight into microbial sources and sinks is essential for process regulation to reduce N2O emission from composting. This study used genome-resolved metagenomics to decipher the genomic structures and physiological behaviors of individual bacteria for N2O sources and sinks during composting. Results showed that several nosZ-lacking denitrifiers in feedstocks drove N2O emission at the beginning of the composting. Such emission became negligible at the thermophilic stage, as high temperatures inhibited all denitrifiers for N2O production except for those containing nirK. The nosZ-lacking denitrifiers were notably enriched to increase N2O production at the cooling stage. Nevertheless, organic biodegradation limited energy availability for chemotaxis and flagellar assembly to restrain nirKS-containing denitrifiers for nitrate reduction toward N2O sources but insignificantly interrupt norBC- and nosZ-containing bacteria (particularly nosZ-containing nondenitrifiers) for N2O sinks by capturing N2O and nitric oxide (NO) for energy production, thereby reducing N2O emission at the mature stage. Furthermore, nosZII-type bacteria included all nosZ-containing nondenitrifiers and dominated N2O sinks. Thus, targeted strategies can be developed to restrict the physiological behaviors of nirKS-containing denitrifiers and expand the taxonomic distribution of nosZ for effective N2O mitigation in composting.},
}

@article {pmid38644605,
year = {2024},
author = {Castejon-Ramirez, S and Glasgow, HL and Ferrolino, JA and Hayden, RT and Maron, G and Hijano, DR},
title = {Plasma Metagenomic Sequencing in Immunocompromised Children: a Call for Caution in the Interpretation of Results.},
journal = {Journal of the Pediatric Infectious Diseases Society},
volume = {},
number = {},
pages = {},
doi = {10.1093/jpids/piae038},
pmid = {38644605},
issn = {2048-7207},
}

@article {pmid38644496,
year = {2024},
author = {Gaston, JM and Alm, EJ and Zhang, AN},
title = {Fast and accurate variant identification tool for sequencing-based studies.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {90},
pmid = {38644496},
issn = {1741-7007},
support = {6934500//Massachusetts Institute of Technology/ ; },
abstract = {BACKGROUND: Accurate identification of genetic variants, such as point mutations and insertions/deletions (indels), is crucial for various genetic studies into epidemic tracking, population genetics, and disease diagnosis. Genetic studies into microbiomes often require processing numerous sequencing datasets, necessitating variant identifiers with high speed, accuracy, and robustness.

RESULTS: We present QuickVariants, a bioinformatics tool that effectively summarizes variant information from read alignments and identifies variants. When tested on diverse bacterial sequencing data, QuickVariants demonstrates a ninefold higher median speed than bcftools, a widely used variant identifier, with higher accuracy in identifying both point mutations and indels. This accuracy extends to variant identification in virus samples, including SARS-CoV-2, particularly with significantly fewer false negative indels than bcftools. The high accuracy of QuickVariants is further demonstrated by its detection of a greater number of Omicron-specific indels (5 versus 0) and point mutations (61 versus 48-54) than bcftools in sewage metagenomes predominated by Omicron variants. Much of the reduced accuracy of bcftools was attributable to its misinterpretation of indels, often producing false negative indels and false positive point mutations at the same locations.

CONCLUSIONS: We introduce QuickVariants, a fast, accurate, and robust bioinformatics tool designed for identifying genetic variants for microbial studies. QuickVariants is available at https://github.com/caozhichongchong/QuickVariants .},
}

@article {pmid38644048,
year = {2024},
author = {Wielkopolan, B and Szabelska-Beręsewicz, A and Gawor, J and Obrępalska-Stęplowska, A},
title = {Cereal leaf beetle-associated bacteria enhance the survival of their host upon insecticide treatments and respond differently to insecticides with different modes of action.},
journal = {Environmental microbiology reports},
volume = {16},
number = {2},
pages = {e13247},
doi = {10.1111/1758-2229.13247},
pmid = {38644048},
issn = {1758-2229},
support = {UMO-2020/37/N/NZ9/02577//Polish National Science Centre/ ; },
abstract = {The cereal leaf beetle (CLB, Oulema melanopus) is one of the major cereal pests. The effect of insecticides belonging to different chemical classes, with different mechanisms of action and the active substances' concentrations on the CLB bacterial microbiome, was investigated. Targeted metagenomic analysis of the V3-V4 regions of the 16S ribosomal gene was used to determine the composition of the CLB bacterial microbiome. Each of the insecticides caused a decrease in the abundance of bacteria of the genus Pantoea, and an increase in the abundance of bacteria of the genus Stenotrophomonas, Acinetobacter, compared to untreated insects. After cypermethrin application, a decrease in the relative abundance of bacteria of the genus Pseudomonas was noted. The dominant bacterial genera in cypermethrin-treated larvae were Lactococcus, Pantoea, while in insects exposed to chlorpyrifos or flonicamid it was Pseudomonas. Insecticide-treated larvae were characterized, on average, by higher biodiversity and richness of bacterial genera, compared to untreated insects. The depletion of CLB-associated bacteria resulted in a decrease in larval survival, especially after cypermethrin and chlorpyrifos treatments. The use of a metagenome-based functional prediction approach revealed a higher predicted function of bacterial acetyl-CoA C-acetyltransferase in flonicamid and chlorpyrifos-treated larvae and tRNA dimethyltransferase in cypermethrin-treated insects than in untreated insects.},
}

@article {pmid38643884,
year = {2024},
author = {Liu, W and Xie, WY and Liu, HJ and Chen, C and Chen, SY and Jiang, GF and Zhao, FJ},
title = {Assessing intracellular and extracellular distribution of antibiotic resistance genes in the commercial organic fertilizers.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172558},
doi = {10.1016/j.scitotenv.2024.172558},
pmid = {38643884},
issn = {1879-1026},
abstract = {Compost-based organic fertilizers often contain high levels of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). Previous studies focused on quantification of total ARGs and MGEs. For a more accurate risk assessment of the dissemination risk of antibiotic resistance, it is necessary to quantify the intracellular and extracellular distribution of ARGs and MGEs. In the present study, extracellular ARGs and MGEs (eARGs and eMGEs) and intracellular ARGs and MGEs (iARGs and iMGEs) were separately analyzed in 51 commercial composts derived from different raw materials by quantitative polymerase chain reaction (qPCR) and metagenomic sequencing. Results showed that eARGs and eMGEs accounted for 11-56 % and 4-45 % of the total absolute abundance of ARGs and MGEs, respectively. Comparable diversity, host composition and association with MGEs were observed between eARGs and iARGs. Contents of high-risk ARGs were similar between eARGs and iARGs, with high-risk ARGs in the two forms accounting for 6.7 % and 8.2 % of the total abundances, respectively. Twenty-four percent of the overall ARGs were present in plasmids, while 56.7 % of potentially mobile ARGs were found to be associated with plasmids. Variation partitioning analysis, null model and neutral community model indicated that the compositions of both eARGs and iARGs were largely driven by deterministic mechanisms. These results provide important insights into the cellular distribution of ARGs in manure composts that should be paid with specific attention in risk assessment and management.},
}

@article {pmid38643745,
year = {2024},
author = {Mang, Q and Gao, J and Li, Q and Sun, Y and Xu, G and Xu, P},
title = {Integrative analysis of metagenome and metabolome provides new insights into intestinal health protection in Coilia nasus larvae via probiotic intervention.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {50},
number = {},
pages = {101230},
doi = {10.1016/j.cbd.2024.101230},
pmid = {38643745},
issn = {1878-0407},
abstract = {With the development of large-scale intensive feeding, growth performance and animal welfare have attracted more and more attention. Exogenous probiotics can promote the growth performance of fish through improving intestinal microbiota; however, it remains unclear whether intestinal microbiota influence physiological biomarkers. Therefore, we performed metagenomic and metabolomic analysis to investigate the effects of a 90-day Lactiplantibacillus plantarum supplementation to a basal diet (1.0 × 10[8] CFU/g) on the growth performance, intestinal microbiota and their metabolites, and physiological biomarkers in Coilia nasus larvae. The results showed that the probiotic supplementation could significantly increase weight and body length. Moreover, it could also enhance digestive enzymes and tight junctions, and inhibit oxidative stress and inflammation. The metagenomic analysis showed that L. plantarum supplementation could significantly decrease the relative abundance of Proteobacteria and increase the relative abundance of Firmicutes. Additionally, pathogenic bacteria (Aeromonadaceae, Aeromonas, and Enterobacterales) were inhibited and beneficial bacteria (Bacillales) were promoted. The metabolome analysis showed that acetic acid and propanoic acid were significantly elevated, and were associated with Kitasatospora, Seonamhaeicola, and Thauera. A correlation analysis demonstrated that the digestive enzymes, tight junction, oxidative stress, and inflammation effects were significantly associated with the increased acetic acid and propanoic acid levels. These results indicated that L. plantarum supplementation could improve intestinal microbial community structure and function, which could raise acetic acid and propanoic acid levels to protect intestinal health and improve growth performance in C. nasus larvae.},
}

@article {pmid38643583,
year = {2024},
author = {Xu, R and Zhang, Y and Li, Y and Song, J and Liang, Y and Chen, F and Wei, X and Li, C and Liu, W and Rensing, C and Wang, Y and Chen, Y},
title = {Linking bacterial life strategies with the distribution pattern of antibiotic resistance genes in soil aggregates after straw addition.},
journal = {Journal of hazardous materials},
volume = {471},
number = {},
pages = {134355},
doi = {10.1016/j.jhazmat.2024.134355},
pmid = {38643583},
issn = {1873-3336},
abstract = {Straw addition markedly affects the soil aggregates and microbial community structure. However, its influence on the profile of antibiotic resistance genes (ARGs), which are likely associated with changes in bacterial life strategies, remains unclear. To clarify this issue, a soil microcosm experiment was incubated under aerobic (WS) or anaerobic (AnWS) conditions after straw addition, and metagenomic sequencing was used to characterise ARGs and bacterial communities in soil aggregates. The results showed that straw addition shifted the bacterial life strategies from K- to r-strategists in all aggregates, and the aerobic and anaerobic conditions stimulated the growth of aerobic and anaerobic r-strategist bacteria, respectively. The WS decreased the relative abundances of dominant ARGs such as QnrS5, whereas the AnWS increased their abundance. After straw addition, the macroaggregates consistently exhibited a higher number of significantly altered bacteria and ARGs than the silt+clay fractions. Network analysis revealed that the WS increased the number of aerobic r-strategist bacterial nodes and fostered more interactions between r-and K-strategist bacteria, thus promoting ARGs prevalence, whereas AnWS exhibited an opposite trend. These findings provide a new perspective for understanding the fate of ARGs and their controlling factors in soil ecosystems after straw addition. ENVIRONMENTAL IMPLICATIONS: Straw soil amendment has been recommended to mitigate soil fertility degradation, improve soil structure, and ultimately increase crop yields. However, our findings highlight the importance of the elevated prevalence of ARGs associated with r-strategist bacteria in macroaggregates following the addition of organic matter, particularly fresh substrates. In addition, when assessing the environmental risk posed by ARGs in soil that receives crop straw, it is essential to account for the soil moisture content. This is because the species of r-strategist bacteria that thrive under aerobic and anaerobic conditions play a dominant role in the dissemination and accumulation of ARG.},
}

@article {pmid38643524,
year = {2024},
author = {Mishra, S and Zhang, X and Yang, X},
title = {Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition.},
journal = {Microbiological research},
volume = {284},
number = {},
pages = {127726},
doi = {10.1016/j.micres.2024.127726},
pmid = {38643524},
issn = {1618-0623},
abstract = {Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.},
}

@article {pmid38643472,
year = {2024},
author = {Kerekes, IK and Nagy, Á and Ősz, Á and Zalka, P},
title = {[Examination possibilities of microbial nucleic acid samples derived from the environment].},
journal = {Orvosi hetilap},
volume = {165},
number = {16},
pages = {613-619},
doi = {10.1556/650.2024.33025},
pmid = {38643472},
issn = {1788-6120},
}

@article {pmid38643272,
year = {2024},
author = {Hauptfeld, E and Pappas, N and van Iwaarden, S and Snoek, BL and Aldas-Vargas, A and Dutilh, BE and von Meijenfeldt, FAB},
title = {Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3373},
pmid = {38643272},
issn = {2041-1723},
abstract = {Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks. Thus, RAT integrative profiling provides an accurate and comprehensive view of the microbiome from shotgun metagenomics data. The package of Contig Annotation Tool (CAT), Bin Annotation Tool (BAT), and RAT is available at https://github.com/MGXlab/CAT_pack (from CAT pack v6.0). The CAT pack now also supports Genome Taxonomy Database (GTDB) annotations.},
}

@article {pmid38643166,
year = {2024},
author = {Luo, K and Peters, BA and Moon, JY and Xue, X and Wang, Z and Usyk, M and Hanna, DB and Landay, AL and Schneider, MF and Gustafson, D and Weber, KM and French, A and Sharma, A and Anastos, K and Wang, T and Brown, T and Clish, CB and Kaplan, RC and Knight, R and Burk, RD and Qi, Q},
title = {Metabolic and inflammatory perturbation of diabetes associated gut dysbiosis in people living with and without HIV infection.},
journal = {Genome medicine},
volume = {16},
number = {1},
pages = {59},
pmid = {38643166},
issn = {1756-994X},
support = {R01HL140976/HL/NHLBI NIH HHS/United States ; R01DK119268/DK/NIDDK NIH HHS/United States ; },
abstract = {BACKGROUND: Gut dysbiosis has been linked with both HIV infection and diabetes, but its interplay with metabolic and inflammatory responses in diabetes, particularly in the context of HIV infection, remains unclear.

METHODS: We first conducted a cross-sectional association analysis to characterize the gut microbial, circulating metabolite, and immune/inflammatory protein features associated with diabetes in up to 493 women (~ 146 with prevalent diabetes with 69.9% HIV +) of the Women's Interagency HIV Study. Prospective analyses were then conducted to determine associations of identified metabolites with incident diabetes over 12 years of follow-up in 694 participants (391 women from WIHS and 303 men from the Multicenter AIDS Cohort Study; 166 incident cases were recorded) with and without HIV infection. Mediation analyses were conducted to explore whether gut bacteria-diabetes associations are explained by altered metabolites and proteins.

RESULTS: Seven gut bacterial genera were identified to be associated with diabetes (FDR-q <  0.1), with positive associations for Shigella, Escherichia, Megasphaera, and Lactobacillus, and inverse associations for Adlercreutzia, Ruminococcus, and Intestinibacter. Importantly, the associations of most species, especially Adlercreutzia and Ruminococcus, were largely independent of antidiabetic medications use. Meanwhile, 18 proteins and 76 metabolites, including 3 microbially derived metabolites (trimethylamine N-oxide, phenylacetylglutamine (PAGln), imidazolepropionic acid (IMP)), 50 lipids (e.g., diradylglycerols (DGs) and triradylglycerols (TGs)) and 23 non-lipid metabolites, were associated with diabetes (FDR-q <  0.1), with the majority showing positive associations and more than half of them (59/76) associated with incident diabetes. In mediation analyses, several proteins, especially interleukin-18 receptor 1 and osteoprotegerin, IMP and PAGln partially mediate the observed bacterial genera-diabetes associations, particularly for those of Adlercreutzia and Escherichia. Many diabetes-associated metabolites and proteins were altered in HIV, but no effect modification on their associations with diabetes was observed by HIV.

CONCLUSION: Among individuals with and without HIV, multiple gut bacterial genera, blood metabolites, and proinflammatory proteins were associated with diabetes. The observed mediated effects by metabolites and proteins in genera-diabetes associations highlighted the potential involvement of inflammatory and metabolic perturbations in the link between gut dysbiosis and diabetes in the context of HIV infection.},
}

@article {pmid38643098,
year = {2024},
author = {Wang, Z and Wu, Y and Li, X and Ji, X and Liu, W},
title = {The gut microbiota facilitate their host tolerance to extreme temperatures.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {131},
pmid = {38643098},
issn = {1471-2180},
support = {31501175//National Natural Science Foundation of China/ ; RC342201//Talents in Anhui Agricultural University/ ; },
abstract = {BACKGROUND: Exposure to extreme cold or heat temperature is one leading cause of weather-associated mortality and morbidity in animals. Emerging studies demonstrate that the microbiota residing in guts act as an integral factor required to modulate host tolerance to cold or heat exposure, but common and unique patterns of animal-temperature associations between cold and heat have not been simultaneously examined. Therefore, we attempted to investigate the roles of gut microbiota in modulating tolerance to cold or heat exposure in mice.

RESULTS: The results showed that both cold and heat acutely change the body temperature of mice, but mice efficiently maintain their body temperature at conditions of chronic extreme temperatures. Mice adapt to extreme temperatures by adjusting body weight gain, food intake and energy harvest. Fascinatingly, 16 S rRNA sequencing shows that extreme temperatures result in a differential shift in the gut microbiota. Moreover, transplantation of the extreme-temperature microbiota is sufficient to enhance host tolerance to cold and heat, respectively. Metagenomic sequencing shows that the microbiota assists their hosts in resisting extreme temperatures through regulating the host insulin pathway.

CONCLUSIONS: Our findings highlight that the microbiota is a key factor orchestrating the overall energy homeostasis under extreme temperatures, providing an insight into the interaction and coevolution of hosts and gut microbiota.},
}

@article {pmid38642797,
year = {2024},
author = {Watanabe, M and Uematsu, M and Fujimoto, K and Hara, T and Yamamoto, M and Miyaoka, D and Yokota, C and Kamei, Y and Sugimoto, A and Kawasaki, N and Yabuno, T and Sato, N and Sato, S and Yamaguchi, K and Furukawa, Y and Tsuruta, D and Okada, F and Imoto, S and Uematsu, S},
title = {Targeted lysis of Staphylococcus hominis linked to axillary osmidrosis using bacteriophage-derived endolysin.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2024.03.039},
pmid = {38642797},
issn = {1523-1747},
}

@article {pmid38642768,
year = {2024},
author = {Li, Q and Yu, H and Peng, Y and Liu, R and Jing, Z and Wei, Y and Tu, S and Gao, H and Song, Y},
title = {Mitigated N2O emissions from submerged-plant-covered aquatic ecosystems on the Changjiang River Delta.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172592},
doi = {10.1016/j.scitotenv.2024.172592},
pmid = {38642768},
issn = {1879-1026},
abstract = {Submerged plants affect nitrogen cycling in aquatic ecosystems. However, whether and how submerged plants change nitrous oxide (N2O) production mechanism and emissions flux remains controversial. Current research primarily focuses on the feedback from N2O release to variation of substrate level and microbial communities. It is deficient in connecting the relative contribution of individual N2O production processes (i.e., the N2O partition). Here, we attempted to offer a comprehensive understanding of the N2O mitigation mechanism in aquatic ecosystems on the Changjiang River Delta according to stable isotopic techniques, metagenome-assembly genome analysis, and statistical analysis. We found that the submerged plant reduced 45 % of N2O emissions by slowing down the dissolved inorganic nitrogen conversion velocity to N2O in sediment (Vf-[DIN]sed). It was attributed to changing the N2O partition and suppressing the potential capacity of net N2O production (i.e., nor/nosZ). The dominated production processes showed a shift with increasing excess N2O. Meanwhile, distinct shift thresholds of planted and unplanted habitats reflected different mechanisms of stimulated N2O production. The hotspot zone of N2O production corresponded to high nor/nosZ and unsaturated oxygen (O2) in unplanted habitat. In contrast, planted habitat hotspot has lower nor/nosZ and supersaturated O2. O2 from photosynthesis critically impacted the activities of N2O producers and consumers. In summary, the presence of submerged plants is beneficial to mitigate N2O emissions from aquatic ecosystems.},
}

@article {pmid38642657,
year = {2024},
author = {Vacca, M and Celano, G and Serale, N and Costantino, G and Calabrese, FM and Calasso, M and De Angelis, M},
title = {Dynamic microbial and metabolic changes during Apulian Caciocavallo cheese-making and ripening produced according to a standardized protocol.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2023-24049},
pmid = {38642657},
issn = {1525-3198},
abstract = {The cheese microbiota plays a critical role in influencing its sensory and physicochemical properties. In this study, traditional Apulian Caciocavallo cheese coming from 4 different dairies in the same area and produced following standardized procedures have been examined, as well as the different bulk milks and natural whey starter cultures used. Moreover, considering the cheese wheels as the blocks of Caciocavallo cheeses as whole, these were characterized at different layers (i.e., core, under-rind, and rind) of the block using a multi-omics approach. In addition to physical-chemical characterization, culturomics, quantitative PCR, metagenomics, and metabolomics analysis, have been carried out post-salting and throughout ripening time (2 mo) to investigate the major shifts in the succession of the microbiota and flavor development. Culture-dependent and 16S rRNA metataxonomics results clearly clustered samples based on the microbiota biodiversity related to the production dairy plant as the result of the use of different NWS or intrinsic conditions of each production site. At the beginning of the ripening, cheeses were dominated by the Lactobacillus and, in 2 dairies (Art and SdC), Streptococcus genera associated with the NWS. The analysis allowed us to show that, although the diversity of identified genera did not change significantly between the rind, under-rind and core fractions of the same samples, there was an evolution in the relative abundance and absolute quantification, modifying and differentiating profiles during ripening. The qPCR mainly differentiated the temporal adaptation of those species originating from bulk milks and those provided by NWSs. The primary starter detected in NWS and cheese reassured the high relative concentration of 1-butanol, 2-butanol, 2-heptanol, 2-butanone, acetoin, delta-dodecalactone, hexanoic acid ethyl ester, octanoic acid ethyl ester, and VFFA during ripening, while cheeses displaying low abundances of Streptococcus and Lactococcus (dairy Del) have a lower total concentration of acetoin compared with Art and SdC. However, the sub-dominant strains and NSLAB present in cheeses are responsible for the production of secondary metabolites belonging to the chemical classes of ketones, alcohols, and organic acids, reaffirming the importance and relevance of autochthonous strains of each dairy plant although considering a delimited production area.},
}

@article {pmid38641693,
year = {2024},
author = {Chen, X and Yang, Y and Wang, J and Pan, C and Zhang, Z and Chen, S and Xie, S},
title = {Impacts of o-cresol spill on composition and function of river sediment and soil microbial communities.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {38641693},
issn = {1614-7499},
abstract = {o-Cresol is a toxic substance with strong irritating and corrosive effects on skin and mucous membranes. To date, information on the effects of o-cresol on microbial communities in the natural environment is very limited. In the present study, 16S rRNA sequencing and metagenomic technique were carried out to elucidate the effects of the o-cresol spill on microbial communities in river sediments and nearby soils. o-Cresol spill induced the increase in the relative abundance of phyla Planctomycetes and Gemmatimonadetes, suggesting their resilience to o-cresol-induced stress. Uncultured Gemmatimonadetes genera and the MND1 genus exhibited enrichment, while the Pseudomonas genus dominated across all samples, indicating their potential pivotal roles in adapting to the o-cresol spill. Moreover, o-cresol spill impaired the metabolic functions of microbes but triggered their defense mechanisms. Under o-cresol pressure, microbial functions related to carbon fixation were upregulated and functions associated with sulfur metabolism were downregulated. In addition, the o-cresol spill led to an increase in functional genes related to the conversion of o-cresol to 3-methylcatechol. Several genes involved in the degradation of aromatic compounds were also identified, potentially contributing to the biodegradation of o-cresol. This study provides fresh insights into the repercussions of an abrupt o-cresol spill on microbial communities in natural environments, shedding light on their adaptability, defense mechanisms, and biodegradation potential.},
}

@article {pmid38641305,
year = {2024},
author = {Chen, Y and Zhang, C and Chen, Z and Yang, Y and Lin, Z and Deng, Z and Wang, X},
title = {Fe(II)-driven spatiotemporal assembly of heterotrophic and anammox bacteria enhances simultaneous nitrogen and phosphorus removal for low-strength municipal wastewater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130713},
doi = {10.1016/j.biortech.2024.130713},
pmid = {38641305},
issn = {1873-2976},
abstract = {The mainstream anaerobic ammonium oxidation (anammox) faces considerable challenges with low-strength municipal wastewater. A Fe(Ⅱ)-amended partial denitrification coupled anammox (PD/A) process was conducted and achieved a long-term and efficient nitrogen and phosphorus removal, yielding effluent total nitrogen and phosphorus concentrations of 1.97 ± 1.03 mg/L and 0.23 ± 0.13 mg/L, respectively, which could well meet more stringent effluent discharge standard of some wastewater treatment plants in specific geographical locations, e.g., estuaries. Fe(Ⅱ)-driven vivianite formation provided key nucleuses for the optimization of the spatial distribution of heterotrophic and anammox bacteria with enhanced extracellular polymeric substances as key driving forces. Metagenomics analysis further revealed the increase of key genes, enhancing anammox bacteria homeostasis, which also bolstered the resistance to environmental perturbations. This study provided a comprehensive sight into the function of Fe(Ⅱ) in mainstream PD/A process, and explored a promising alternative for synergetic nitrogen and phosphorus removal for low-strength municipal wastewater treatment.},
}

@article {pmid38641105,
year = {2024},
author = {Lin, L and Xiong, J and Yue, T and Xu, W and Liu, L and Wang, F and Yang, S and Cao, W},
title = {Phosphorus starvation response genes and function coupling: A mechanism to regulate phosphorus availability in a subtropical estuary.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172575},
doi = {10.1016/j.scitotenv.2024.172575},
pmid = {38641105},
issn = {1879-1026},
abstract = {Phosphorus (P) plays an important role in regulating primary production in estuarine environments. However, knowledge of the P-functional gene composition of microbial communities and the mechanisms of microbial adaptation to changes in available P in estuaries remain limited. This study coupling 16 s rDNA and metagenomics sequencing was conducted to reveal the relationship between P cycling functional genes, microbial interactions, and P availability in the Jiulong River Estuary. The results showed that the relative abundance of P cycling functions genes was highest in winter, and lowest in summer. Spatially, the total relative abundance of P cycling functions genes was higher in the riverward than that in the seaward. P cycling functional microbial interactions and P cycling gene coupling were strongest in summer and in the seaward. Changes in both temperature and salinity had significant direct and indirect effects on P cycling function, and the influence of salinity on P cycling function was greater than that on the microbial community in the estuary. Salinity had significant direct negative effects on inorganic P-solubilization (IP), organic P-mineralization (OP), and P uptake and transport functions (PT). Whereas, salinity had a significant positive effect on P-starvation response regulation (PR) function. Thus, salinity and microbial communities regulate the soluble reactive phosphate concentrations in estuarine environments by strengthening internal coupling among P cycling functions, promoting PR function, and facilitating PT gene expression. PR is the most important predictors, PR, PT, and PR-PT together explained 38.56 % of the overall soluble reactive phosphorus (SRP) variation. Over 66 % of the explained SRP variations can be predicted by the PR, PT, and PR-PT functional genes. This finding improves the knowledge base of the microbial processes for P cycling and provides a foundation for eutrophication management strategies in the estuary.},
}

@article {pmid38640951,
year = {2024},
author = {Vezeau, N and Kahn, L},
title = {Current understanding and knowledge gaps regarding wildlife as reservoirs of antimicrobial resistance.},
journal = {American journal of veterinary research},
volume = {},
number = {},
pages = {1-9},
doi = {10.2460/ajvr.24.02.0040},
pmid = {38640951},
issn = {1943-5681},
abstract = {Antimicrobial resistance (AMR) is a serious health issue shared across all One Health domains. Wildlife species represent a key intersection of the animal and environmental domains. They are a relevant but understudied reservoir and route of spread for AMR throughout the environment. Most wildlife AMR research thus far has focused on avian species, terrestrial mammals, and a selection of aquatic and marine species. Pathogens often identified in terrestrial wildlife include enteric zoonotic organisms such as Eschericia coli and Salmonella spp, in addition to nonenterics such as Staphylococci. Resistances have been commonly identified to antimicrobials important in veterinary and human medicine, including β-lactams, tetracyclines, aminoglycosides, and macrolides. Our emerging understanding of the dynamics of AMR distribution across life on Earth provides further opportunities for us to assess the risk it poses to veterinary and human health. Future work will require prioritizing which wildlife most exacerbates and indicates AMR in domestic animals. However, decreasing prices and increasing ease for metagenomic sequencing allows for synergies with expanding wildlife viral disease surveillance. Improved understanding of how wildlife impacts veterinary and human healthcare may increase opportunities for related research funding and global equity in such research. The companion Currents in One Health article by Vezeau and Kahn, JAVMA, June 2024, addresses in further detail the routes of spread of AMR across different animal populations and actions that can be taken to mitigate AMR with special consideration for wildlife sources.},
}

@article {pmid38640860,
year = {2024},
author = {Dai, L and Liu, Z and Zhou, W and Zhang, L and Miao, M and Wang, L and Hua, H and Wang, B and Ji, G},
title = {Sijunzi decoction, a classical Chinese herbal formula, improves fatigue symptoms with changes in gut microbiota in chronic fatigue syndrome: A randomized, double-blind, placebo-controlled, multi-center clinical trial.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {129},
number = {},
pages = {155636},
doi = {10.1016/j.phymed.2024.155636},
pmid = {38640860},
issn = {1618-095X},
abstract = {BACKGROUD: Chronic fatigue syndrome (CFS) severely impact patients' quality of life and lacks well-acknowledged drug therapy. Sijunzi decoction (SJZD), a classical Chinese herbal formula, has been widely used for spleen deficiency syndrome like fatigue in China. However, there is a lack of evidence on the efficacy of SJZD in treating CFS.

PURPOSE: To evaluate the efficacy and safety of SJZD for CFS.

STUDY DESIGN: A multi-center, double-blinded, randomized controlled trial.

METHODS: Participants with definite diagnoses of CFS and spleen deficiency syndrome were randomly assigned in 1:1 ratio to receive SJZD or placebo granules for 2 months. The primary outcome was the change of Chalder fatigue questionnaire (CFQ) scoring after treatment. Other outcomes included changes in short form-36 physical function (SF36-PF) score, spleen deficiency scale score, Euroqol Questionnaire-Visual Analogue Scale (ED-VAS) score, and clinical global impression (CGI) evaluating by corresponding questionnaires. Fecal metagenome sequencing was conducted to explore the potential mechanism of SJZD effect.

RESULTS: From June 2020 to July 2021, 105 of 127 participants completed the study at four hospitals in China. After a 2-month treatment, intention-to-treat (ITT) analysis found participants who received SJZD had larger reduction than placebo control (mean change 6.65 [standard deviation (SD) 6.11] points vs. 5.31 [SD 5.19] points; difference 1.34, 95 % confidence interval [CI] -0.65 to 3.33). Per-protocol (PP) analysis reported confirmative results with a significant difference between SJZD and placebo groups (2.24, 95 % CI 0.10 to 4.39). SJZD also significantly improved overall health status compared with placebo in per-protocol population (p = 0.009). No significant difference was found between groups in changes of SF36-PF, spleen deficiency scale scoring, and CGI. Fecal metagenome sequencing and correlation analyses indicated that the beneficial effect of SJZD may be related to the abundance change of Pediococcus acidilactici. No serious adverse event or abnormal laboratory test was found during the whole study.

CONCLUSION: Our results indicated that SJZD can improve fatigue symptom and overall health status in patients with CFS under good medication adherence. Potential therapeutic effects may be related to the regulation of gut microbiota. Large-scale trials with longer intervention period are encouraged to further support SJZD's application.

CLINICAL TRIAL REGISTRATION: (ID, ISRCTN23930966, URL = https://www.isrctn.com/ISRCTN23930966).},
}

@article {pmid38640816,
year = {2024},
author = {Yi, S and Song, H and Kim, WH and Lee, S and Guk, JH and Woo, J and Cho, S},
title = {Dynamics of microbiota and antimicrobial resistance in on-farm dairy processing plants using metagenomic and culture-dependent approaches.},
journal = {International journal of food microbiology},
volume = {417},
number = {},
pages = {110704},
doi = {10.1016/j.ijfoodmicro.2024.110704},
pmid = {38640816},
issn = {1879-3460},
abstract = {On-farm dairy processing plants, which are situated close to farms and larger dairy processing facilities, face unique challenges in maintaining environmental hygiene. This can impact various stages of dairy processing. These plants operate on smaller scales and use Low-Temperature-Long-Time (LTLT) pasteurization, making them more susceptible to microbial contamination through direct and indirect contact. Antimicrobial-resistant bacteria found on dairy farms pose risks to human health by potentially transferring resistance via dairy products. Our study aimed to investigate microbial distribution and antimicrobial resistance at four key stages: the farm, pre-pasteurization, post-pasteurization, and processing environments. We assessed microbial distribution by quantifying indicator bacteria and conducting metagenomic analysis. Antimicrobial resistance was examined by identifying resistance phenotypes and detecting resistance genes in bacterial isolates and metagenomes. Our results showed that the indicator bacteria were detected at all stages of on-farm dairy processing. We observed a significant reduction in aerobic microbes and coliforms post-pasteurization. However, contamination of the final dairy products increased, suggesting potential cross-contamination during post-pasteurization. Metagenomic analysis revealed that Pseudomonas, a representative psychrotrophic bacterium, was predominant in both the farm (24.1 %) and pre-pasteurization (65.9 %) stages, indicating microbial transfer from the farms to the processing plants. Post-pasteurization, Pseudomonas and other psychrotrophs like Acinetobacter and Enterobacteriaceae remained dominant. Core microbiota analysis identified 74 genera in total, including 13 psychrotrophic bacteria, across all stages. Of the 59 strains isolated from these plants, 49 were psychrotrophic. Antimicrobial resistance analysis showed that 74.6 % (44/59) of isolates were resistant to at least one antibiotic, with cefoxitin-, ampicillin-, amoxicillin-, and ticarcillin-resistant bacteria present at all stages. Identical antimicrobial resistance patterns were observed in isolates from serial stages of the same farm and season, suggesting bacterial transmission across stages. Additionally, 27.1 % (16/59) of isolates carried plasmid-mediated resistance genes, which were also detected in the metagenomes of non-isolated samples, indicating potential antimicrobial resistance gene transmission and their presence in uncultured bacteria. These findings reveal the persistence of antimicrobial-resistant psychrotrophic bacteria in on-farm dairy processing plants, which pose potential health risks via dairy consumption. Our study underscores the importance of both culture-dependent and culture-independent methods to fully understand their distribution and impact.},
}

@article {pmid38640749,
year = {2024},
author = {Gago, JF and Viver, T and Urdiain, M and Ferreira, E and Robledo, P and Rossello-Mora, R},
title = {Metagenomics of two aquifers with thermal anomalies in Mallorca Island, and proposal of new uncultivated taxa named following the rules of SeqCode.},
journal = {Systematic and applied microbiology},
volume = {47},
number = {2-3},
pages = {126506},
doi = {10.1016/j.syapm.2024.126506},
pmid = {38640749},
issn = {1618-0984},
abstract = {Groundwater offers an intriguing blend of distinctive physical and chemical conditions, constituting a challenge for microbial life. In Mallorca, the largest island of Balearic archipelago, harbours a variety of thermal anomalies (i.e., geothermal manifestation where surface aquifers exhibiting temperatures exceeding the regional average). The metagenomes of two aquifers in the centre and southern of the island showed Pseudomonadota to be the most represented phylum when using extracted 16S rRNA gene sequences. However, the microbial structures within and between aquifers were remarkably diverse but similar in their metabolic profiles as revealed by the metagenome-assembled genomes (MAGs) pointing to a prevalence of aerobic chemolithoautotrophic and heterotrophic metabolisms, especially in the Llucmajor aquifer. Also, some evidences of anaerobic lifestyles were detected, which would indicate that these environments either could suffer episodes of oxygen depletion or the anaerobes had been transported from deeper waters. We believe that the local environmental factors (temperature, external inputs or chemistry) seem to be more relevant than the connection and, eventually, transport of microbial cells within the aquifer in determining the highly divergent structures. Notably, most of the reconstructed genomes belonged to undescribed bacterial lineages and from them two high-quality MAGs could be classified as novel taxa named following the rules of the Code for Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Accordingly, we propose the new species and genus Costitxia debesea gen. nov., sp. nov., affiliated with the novel family Costitxiaceae fam. nov., order Costitxiales ord. nov. and class Costitxiia class. nov.; and the new new species and genus Lloretia debesea gen. nov. sp. nov. affiliated with the novel family Lloretiaceae fam. nov.},
}

@article {pmid38640670,
year = {2024},
author = {Kang, Y and Wang, J and Li, Z},
title = {Enhancing pollutants removal in hospital wastewater: Comparative analysis of PAC coagulation vs. bio-contact oxidation, highlighting the impact of outdated treatment plants.},
journal = {Journal of hazardous materials},
volume = {471},
number = {},
pages = {134340},
doi = {10.1016/j.jhazmat.2024.134340},
pmid = {38640670},
issn = {1873-3336},
abstract = {While the effectiveness of Poly-Aluminum Chloride (PAC) coagulation for pollutant removal has been documented across various wastewater scenarios, its specific application in hospital wastewater (HWW) treatment to remove conventional pollutants and hazardous genetic pollutants has not been studied. The research compared three hospital wastewater treatment plants (HWTPs) to address a knowledge gap, including the PAC coagulation-sodium hypochlorite disinfection process (PAC-HWTP), the biological contact oxidation-precipitation-sodium hypochlorite process (BCO-HWTP), and a system using outdated equipment with PAC coagulation (ODE-PAC-HWTP). Effluent compliance with national discharge standards is assessed, with BCO-HWTP meeting standards for direct or indirect discharge into natural aquatic environments. ODE-PAC-HWTP exceeds pretreatment standards for COD and BOD5 concentrations. PAC-HWTP effluent largely adheres to national pretreatment standards, enabling release into municipal sewers for further treatment. Metagenomic analysis reveals that PAC-HWTP exhibits higher removal efficiencies for antibiotic resistance genes, metal resistance genes, mobile genetic elements, and pathogens compared to BCO-HWTP and ODE-PAC-HWTP, achieving average removal rates of 45.13%, 57.54%, 80.61%, and 72.17%, respectively. These results suggests that when discharging treated HWW into municipal sewers for further processing, the use of PAC coagulation process is more feasible and cost-effective compared to BCO technologies. The analysis emphasizes the urgent need to upgrade outdated equipment HWTPs.},
}

@article {pmid38640440,
year = {2024},
author = {Bosch, J and Dobbler, PT and Větrovský, T and Tláskal, V and Baldrian, P and Brabcová, V},
title = {Decomposition of Fomes fomentatius fruiting bodies - transition of healthy living fungus into a decayed bacteria-rich habitat is primarily driven by Arthropoda.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {5},
pages = {},
doi = {10.1093/femsec/fiae044},
pmid = {38640440},
issn = {1574-6941},
support = {21-09334 J//Czech Science Foundation/ ; },
abstract = {Fomes fomentarius is a widespread, wood-rotting fungus of temperate, broadleaved forests. Although the fruiting bodies of F. fomentarius persist for multiple years, little is known about its associated microbiome or how these recalcitrant structures are ultimately decomposed. Here we used metagenomics and metatranscriptomics to analyse the microbial community associated with healthy living and decomposing F. fomentarius fruiting bodies to assess the functional potential of the fruiting body-associated microbiome and to determine the main players involved in fruiting body decomposition. F. fomentarius sequences in the metagenomes were replaced by bacterial sequences as the fruiting body decomposed. Most CAZymes expressed in decomposing fruiting bodies targeted components of the fungal cell wall with almost all chitin-targeting sequences, plus a high proportion of beta-glucan-targeting sequences, belonging to Arthropoda. We suggest that decomposing fruiting bodies of F. fomentarius represent a habitat rich in bacteria, while its decomposition is primarily driven by Arthropoda. Decomposing fruiting bodies thus represent a specific habitat supporting both microorganisms and microfauna.},
}

@article {pmid38640403,
year = {2024},
author = {Ekpruke, CD and Alford, R and Parker, E and Silveyra, P},
title = {Gonadal sex and chromosome complement influence the gut microbiome in a mouse model of allergic airway inflammation.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00003.2024},
pmid = {38640403},
issn = {1531-2267},
support = {R01HL159764//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R03HL141618//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; },
abstract = {Evidence abounds that gut microbiome components are associated with sex disparities in the immune system. However, it remains unclear whether the observed sex disparity in asthma incidence is associated with sex-dependent differences in immune-modulating gut microbiota, and/or its influence on allergic airway inflammatory processes. Using a mouse model of house dust mite (HDM)-induced allergic inflammation and the four core genotypes (FCG) model, we have previously reported sex differences in lung inflammatory phenotypes. Here, we investigated associations of gut microbiomes to these phenotypes by challenging FCG mice (XXM, XXF, XYM, XYF, n=7/group) withHDM (25 μg) or PBS intranasally for 5 weeks and collecting fecal samples. We extracted fecal DNA and analyzed the 16S microbiome via Targeted Metagenomic Sequencing. We compared alpha and beta diversity across genotypes and assessed the Firmicutes/Bacteroidetes ratio (F/B). When comparing baseline and after exposure for the FCG, we found that the gut F/B was only increased in the XXM genotype. We also found that alpha diversity was significantly increased in all FCG mice upon HDM challenge, with the highest increase in the XXF, and the lowest in the XXM genotypes. Similarly, beta diversity of the microbial community was also affected by challenge in a gonad- and chromosome-dependent manner. In summary, our results indicated that HDM treatment, gonads, and sex chromosomes significantly influence the gut microbial community composition. We concluded that allergic lung inflammation may be affected by the gut microbiome in a sex-dependent manner involving both hormonal and genetic influences.},
}

@article {pmid38640284,
year = {2024},
author = {Sun, C and Zhou, C and Wang, L and Wei, S and Shi, M and Li, J and Lin, L and Liu, X},
title = {Clinical application of metagenomic next-generation sequencing for the diagnosis of suspected infection in adults: A cross-sectional study.},
journal = {Medicine},
volume = {103},
number = {16},
pages = {e37845},
doi = {10.1097/MD.0000000000037845},
pmid = {38640284},
issn = {1536-5964},
abstract = {Metagenomic next-generation sequencing (mNGS) has become an available method for pathogen detection. The clinical application of mNGS requires further evaluation. We conducted a cross-sectional study of 104 patients with suspected infection between May 2019 and May 2021. The risk factors associated with infection were analyzed using univariate logistic analysis. The diagnostic performance of pathogens was compared between mNGS and conventional microbiological tests. About 104 patients were assigned into 3 groups: infected group (n = 69), noninfected group (n = 20), and unknown group (n = 15). With the composite reference standard (combined results of all microbiological tests, radiological testing results, and a summary of the hospital stay of the patient) as the gold standard, the sensitivity, specificity, positive predictive value, negative predictive value of mNGS was 84.9%, 50.0%, 88.6%, and 42.1%, respectively. Compared with conventional microbiological tests, mNGS could detect more pathogens and had obvious advantages in Mycobacterium tuberculosis, Aspergillus, and virus detection. Moreover, mNGS had distinct benefits in detecting mixed infections. Bacteria-fungi-virus mixed infections were the most common in patients with severe pneumonia. mNGS had a higher sensitivity than conventional microbiological tests, especially for M. tuberculosis, Aspergillus, viruses, and mixed infections. We suggest that mNGS should be used more frequently in the early diagnosis of pathogens in critically ill patients in the future.},
}

@article {pmid38640279,
year = {2024},
author = {Li, S and Li, S and Chen, D and Zhao, S and Liu, C and Zhang, R and Chen, Y and Guo, X and Song, X},
title = {Case report of a novel mutation in the TNC gene in Chinese patients with nonsyndromic hearing loss.},
journal = {Medicine},
volume = {103},
number = {16},
pages = {e37702},
doi = {10.1097/MD.0000000000037702},
pmid = {38640279},
issn = {1536-5964},
abstract = {RATIONALE: Hereditary hearing loss is known to exhibit a significant degree of genetic heterogeneity. Herein, we present a case report of a novel mutation in the tenascin-C (TNC) gene in Chinese patients with nonsyndromic hearing loss (NSHL).

PATIENT CONCERNS: This includes a young deaf couple and their 2-year-old baby.

DIAGNOSES: Based on the clinical information, hearing test, metagenomic next-generation sequencing (mNGS), Sanger sequencing, protein function and structure analysis, and model prediction, in our case, the study results revealed 2 heterozygous mutations in the TNC gene (c.2852C>T, p.Thr951Ile) and the TBC1 domain family member 24 (TBC1D24) gene (c.1570C>T, p.Arg524Trp). These mutations may be responsible for the hearing loss observed in this family. Notably, the heterozygous mutations in the TNC gene (c.2852C>T, p.Thr951Ile) have not been previously reported in the literature.

INTERVENTIONS: Avoid taking drugs that can cause deafness, wearing hearing AIDS, and cochlear implants.

OUTCOMES: Regular follow-up of family members is ongoing.

LESSONS: The genetic diagnosis of NSHL holds significant importance as it helps in making informed treatment decisions, providing prognostic information, and offering genetic counseling for the patient's family.},
}

@article {pmid38639388,
year = {2024},
author = {Dong, S and Yan, PF and Mezzari, MP and Abriola, LM and Pennell, KD and Cápiro, NL},
title = {Using Network Analysis and Predictive Functional Analysis to Explore the Fluorotelomer Biotransformation Potential of Soil Microbial Communities.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c00942},
pmid = {38639388},
issn = {1520-5851},
abstract = {Microbial transformation of per- and polyfluoroalkyl substances (PFAS), including fluorotelomer-derived PFAS, by native microbial communities in the environment has been widely documented. However, few studies have identified the key microorganisms and their roles during the PFAS biotransformation processes. This study was undertaken to gain more insight into the structure and function of soil microbial communities that are relevant to PFAS biotransformation. We collected 16S rRNA gene sequencing data from 8:2 fluorotelomer alcohol and 6:2 fluorotelomer sulfonate biotransformation studies conducted in soil microcosms under various redox conditions. Through co-occurrence network analysis, several genera, including Variovorax, Rhodococcus, and Cupriavidus, were found to likely play important roles in the biotransformation of fluorotelomers. Additionally, a metagenomic prediction approach (PICRUSt2) identified functional genes, including 6-oxocyclohex-1-ene-carbonyl-CoA hydrolase, cyclohexa-1,5-dienecarbonyl-CoA hydratase, and a fluoride-proton antiporter gene, that may be involved in defluorination. This study pioneers the application of these bioinformatics tools in the analysis of PFAS biotransformation-related sequencing data. Our findings serve as a foundational reference for investigating enzymatic mechanisms of microbial defluorination that may facilitate the development of efficient microbial consortia and/or pure microbial strains for PFAS biotransformation.},
}

@article {pmid38638899,
year = {2024},
author = {Pawano, O and Jenpuntarat, N and Streit, WR and Pérez-García, P and Pongtharangkul, T and Phinyocheep, P and Thayanukul, P and Euanorasetr, J and Intra, B},
title = {Exploring untapped bacterial communities and potential polypropylene-degrading enzymes from mangrove sediment through metagenomics analysis.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1347119},
pmid = {38638899},
issn = {1664-302X},
abstract = {The versatility of plastic has resulted in huge amounts being consumed annually. Mismanagement of post-consumption plastic material has led to plastic waste pollution. Biodegradation of plastic by microorganisms has emerged as a potential solution to this problem. Therefore, this study aimed to investigate the microbial communities involved in the biodegradation of polypropylene (PP). Mangrove soil was enriched with virgin PP sheets or chemically pretreated PP comparing between 2 and 4 months enrichment to promote the growth of bacteria involved in PP biodegradation. The diversity of the resulting microbial communities was accessed through 16S metagenomic sequencing. The results indicated that Xanthomonadaceae, unclassified Gaiellales, and Nocardioidaceae were promoted during the enrichment. Additionally, shotgun metagenomics was used to investigate enzymes involved in plastic biodegradation. The results revealed the presence of various putative plastic-degrading enzymes in the mangrove soil, including alcohol dehydrogenase, aldehyde dehydrogenase, and alkane hydroxylase. The degradation of PP plastic was determined using Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR), Scanning Electron Microscopy (SEM), and Water Contact Angle measurements. The FTIR spectra showed a reduced peak intensity of enriched and pretreated PP compared to the control. SEM images revealed the presence of bacterial biofilms as well as cracks on the PP surface. Corresponding to the FTIR and SEM analysis, the water contact angle measurement indicated a decrease in the hydrophobicity of PP and pretreated PP surface during the enrichment.},
}

@article {pmid38638832,
year = {2024},
author = {Filardo, S and Di Pietro, M and Sessa, R},
title = {Current progresses and challenges for microbiome research in human health: a perspective.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1377012},
pmid = {38638832},
issn = {2235-2988},
abstract = {It is becoming increasingly clear that the human microbiota, also known as "the hidden organ", possesses a pivotal role in numerous processes involved in maintaining the physiological functions of the host, such as nutrient extraction, biosynthesis of bioactive molecules, interplay with the immune, endocrine, and nervous systems, as well as resistance to the colonization of potential invading pathogens. In the last decade, the development of metagenomic approaches based on the sequencing of the bacterial 16s rRNA gene via Next Generation Sequencing, followed by whole genome sequencing via third generation sequencing technologies, has been one of the great advances in molecular biology, allowing a better profiling of the human microbiota composition and, hence, a deeper understanding of the importance of microbiota in the etiopathogenesis of different pathologies. In this scenario, it is of the utmost importance to comprehensively characterize the human microbiota in relation to disease pathogenesis, in order to develop novel potential treatment or preventive strategies by manipulating the microbiota. Therefore, this perspective will focus on the progress, challenges, and promises of the current and future technological approaches for microbiome profiling and analysis.},
}

@article {pmid38638830,
year = {2024},
author = {Narrowe, AB and Lemons, JMS and Mahalak, KK and Firrman, J and den Abbeele, PV and Baudot, A and Deyaert, S and Li, Y and Yu, LL and Liu, L},
title = {Targeted remodeling of the human gut microbiome using Juemingzi (Senna seed extracts).},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1296619},
pmid = {38638830},
issn = {2235-2988},
abstract = {The genus Senna contains globally distributed plant species of which the leaves, roots, and seeds have multiple traditional medicinal and nutritional uses. Notable chemical compounds derived from Senna spp. include sennosides and emodin which have been tested for antimicrobial effects in addition to their known laxative functions. However, studies of the effects of the combined chemical components on intact human gut microbiome communities are lacking. This study evaluated the effects of Juemingzi (Senna sp.) extract on the human gut microbiome using SIFR[®] (Systemic Intestinal Fermentation Research) technology. After a 48-hour human fecal incubation, we measured total bacterial cell density and fermentation products including pH, gas production and concentrations of short chain fatty acids (SCFAs). The initial and post-incubation microbial community structure and functional potential were characterized using shotgun metagenomic sequencing. Juemingzi (Senna seed) extracts displayed strong, taxon-specific anti-microbial effects as indicated by significant reductions in cell density (40%) and intra-sample community diversity. Members of the Bacteroidota were nearly eliminated over the 48-hour incubation. While generally part of a healthy gut microbiome, specific species of Bacteroides can be pathogenic. The active persistence of the members of the Enterobacteriaceae and selected Actinomycetota despite the reduction in overall cell numbers was demonstrated by increased fermentative outputs including high concentrations of gas and acetate with correspondingly reduced pH. These large-scale shifts in microbial community structure indicate the need for further evaluation of dosages and potential administration with prebiotic or synbiotic supplements. Overall, the very specific effects of these extracts may offer the potential for targeted antimicrobial uses or as a tool in the targeted remodeling of the gut microbiome.},
}

@article {pmid38638828,
year = {2024},
author = {Zhang, J and Hou, XY and Wang, JY and Lu, B},
title = {Case report: Cutaneous anthrax diagnosed using mNGS of a formalin-fixed paraffin-embedded tissue sample.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1329235},
pmid = {38638828},
issn = {2235-2988},
abstract = {The metagenomic next-generation sequencing (mNGS) method is preferred for genotyping useful for the identification of organisms, illumination of metabolic pathways, and determination of microbiota. It can accurately obtain all the nucleic acid information in the test sample. Anthrax is one of the most important zoonotic diseases, infecting mainly herbivores and occasionally humans. The disease has four typical clinical forms, cutaneous, gastrointestinal, inhalation, and injection, all of which may result in sepsis or meningitis, with cutaneous being the most common form. Here, we report a case of cutaneous anthrax diagnosed by mNGS in a butcher. Histopathology of a skin biopsy revealed PAS-positive bacilli. Formalin-fixed paraffin-embedded (FFPE) tissue sample was confirmed the diagnosis of anthrax by mNGS. He was cured with intravenous penicillin. To our knowledge, this is the first case of cutaneous anthrax diagnosed by mNGS using FFPE tissue. mNGS is useful for identifying pathogens that are difficult to diagnose with conventional methods, and FFPE samples are simple to manage. Compared with traditional bacterial culture, which is difficult to cultivate and takes a long time, mNGS can quickly and accurately help us diagnose anthrax, so that anthrax can be controlled in a timely manner and prevent the outbreak of epidemic events.},
}

@article {pmid38638824,
year = {2024},
author = {Ma, L and Zhu, C and Yan, T and Hu, Y and Zhou, J and Li, Y and Du, F and Zhou, J},
title = {Illumina and Nanopore sequencing in culture-negative samples from suspected lower respiratory tract infection patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1230650},
pmid = {38638824},
issn = {2235-2988},
abstract = {OBJECTIVE: To evaluate the diagnostic value of metagenomic sequencing technology based on Illumina and Nanopore sequencing platforms for patients with suspected lower respiratory tract infection whose pathogen could not be identified by conventional microbiological tests.

METHODS: Patients admitted to the Respiratory and Critical Care Medicine in Shanghai Ruijin Hospital were retrospectively studied from August 2021 to March 2022. Alveolar lavage or sputum was retained in patients with clinically suspected lower respiratory tract infection who were negative in conventional tests. Bronchoalveolar lavage fluid (BALF) samples were obtained using bronchoscopy. Sputum samples were collected, while BALF samples were not available due to bronchoscopy contraindications. Samples collected from enrolled patients were simultaneously sent for metagenomic sequencing on both platforms.

RESULTS: Thirty-eight patients with suspected LRTI were enrolled in this study, consisting of 36 parts of alveolar lavage and 2 parts of sputum. According to the infection diagnosis, 31 patients were confirmed to be infected with pathogens, while 7 patients were diagnosed with non-infectious disease. With regard to the diagnosis of infectious diseases, the sensitivity and specificity of Illumina and Nanopore to diagnose infection in patients were 80.6% vs. 93.5% and 42.9 vs. 28.6%, respectively. In patients diagnosed with bacterial, Mycobacterium, and fungal infections, the positive rates of Illumina and Nanopore sequencer were 71.4% vs. 78.6%, 36.4% vs. 90.9%, and 50% vs. 62.5%, respectively. In terms of pathogen diagnosis, the sensitivity and specificity of pathogens detected by Illumina and Nanopore were 55.6% vs. 77.8% and 42.9% vs. 28.6%, respectively. Among the patients treated with antibiotics in the last 2 weeks, 61.1% (11/18) and 77.8% (14/18) cases of pathogens were accurately detected by Illumina and Nanopore, respectively, among which 8 cases were detected jointly. The consistency between Illumina and diagnosis was 63.9% (23/36), while the consistency between Nanopore and diagnosis was 83.3% (30/36). Between Illumina and Nanopore sequencing methods, the consistency ratio was 55% (22/42) based on pathogen diagnosis.

CONCLUSION: Both platforms play a certain value in infection diagnosis and pathogen diagnosis of CMT-negative suspected LRTI patients, providing a theoretical basis for clinical accurate diagnosis and symptomatic treatment. The Nanopore platform demonstrated potential advantages in the identification of Mycobacterium and could further provide another powerful approach for patients with suspected Mycobacterium infection.},
}

@article {pmid38638639,
year = {2024},
author = {Girard, C and Chabrillat, T and Kerros, S and Fravalo, P and Thibodeau, A},
title = {Essential oils mix effect on chicks ileal and caecal microbiota modulation: a metagenomics sequencing approach.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1350151},
pmid = {38638639},
issn = {2297-1769},
abstract = {INTRODUCTION: Microbiota plays a pivotal role in promoting the health and wellbeing of poultry. Essential oils (EOs) serve as an alternative solution for modulating poultry microbiota. This study aimed to investigate, using amplicon sequencing, the effect of a complex and well-defined combination of EOs feed supplement on both ileal and caecal broiler microbiota, within the context of Salmonella and Campylobacter intestinal colonization.

MATERIAL AND METHODS: For this experiment, 150-day-old Ross chicks were randomly allocated to two groups: T+ (feed supplementation with EO mix 500 g/t) and T- (non-supplemented). At day 7, 30 birds from each group were orally inoculated with 10[6] CFU/bird of a Salmonella enteritidis and transferred to the second room, forming the following groups: TS+ (30 challenged birds receiving infeed EO mix at 500g/t) and TS- (30 challenged birds receiving a non-supplemented control feed). At day 14, the remaining birds in the first room were orally inoculated with 10[3] CFU/bird of two strains of Campylobacter jejuni, resulting in the formation of groups T+C+ and T-C+. Birds were sacrificed at day 7, D10, D14, D17, and D21. Ileal and caecal microbiota samples were analyzed using Illumina MiSeq sequencing. At D7 and D14, ileal alpha diversity was higher for treated birds (p <0.05).

RESULTS AND DISCUSSION: No significant differences between groups were observed in caecal alpha diversity (p>0.05). The ileal beta diversity exhibited differences between groups at D7 (p < 0.008), D10 (p = 0.029), D14 (p = 0.001) and D17 (p = 0.018), but not at D21 (p = 0.54). For all time points, the analysis indicated that 6 biomarkers were negatively impacted, while 10 biomarkers were positively impacted. Sellimonas and Weissella returned the lowest (negative) and highest (positive) coefficient, respectively. At each time point, treatments influenced caecal microbiota beta diversity (p < 0.001); 31 genera were associated with T+: 10 Ruminoccocaceae genera were alternatively more abundant and less abundant from D7, 7 Lachnospiraceae genera were alternatively more and less abundant from D10, 6 Oscillospiraceae genera were variable depending on the date and 4 Enterobacteriaceae differed from D7. During all the experiment, Campylobacter decreased in treated birds (p < 0.05). This study showed that EO mix modulates ileal and caecal microbiota composition both before and during challenge conditions, increasing alpha diversity, especially in ileum during the early stages of chick life.},
}

@article {pmid38638558,
year = {2024},
author = {Liu, M and Du, X and Chen, H and Bai, C and Lan, L},
title = {Systemic investigation of di-isobutyl phthalate (DIBP) exposure in the risk of cardiovascular via influencing the gut microbiota arachidonic acid metabolism in obese mice model.},
journal = {Regenerative therapy},
volume = {27},
number = {},
pages = {290-300},
pmid = {38638558},
issn = {2352-3204},
abstract = {Phthalate esters (PE), a significant class of organic compounds used in industry, can contaminate humans and animals by entering water and food chains. Recent studies demonstrate the influence of PE on the development and progression of heart diseases, particularly in obese people. Di-isobutyl phthalate (DIBP) was administered orally to normal and diet-induced obese mice in this research to assess cardiovascular risk. The modifications in the microbial composition and metabolites were examined using RNA sequencing and mass spectrometry analysis. Based on the findings, lean group rodents were less susceptible to DIBP exposure than fat mice because of their cardiovascular systems. Histopathology examinations of mice fed a high-fat diet revealed lesions and plagues that suggested a cardiovascular risk. In the chronic DIBP microbial remodeling metagenomics Faecalibaculum rodentium was the predominant genera in obese mice. According to metabolomics data, arachidonic acid (AA) metabolism changes caused by DIBP were linked to unfavorable cardiovascular events. Our research offers new understandings of the cardiovascular damage caused by DIBP exposure in obese people and raises the possibility that arachidonic acid metabolism could be used as a regulator of the gut microbiota to avert related diseases.},
}

@article {pmid38638167,
year = {2024},
author = {Hernandez, JM and Almeida, GBS and Portela, ACR and Cardoso, JF and Junior, ECS and Lucena, MSS and Nunes, MRT and Gabbay, YB and Silva, LD},
title = {Microbial Diversity in Children with Gastroenteritis in the Amazon Region of Brazil: Development and Validation of a Molecular Method for Complete Sequencing of Viral Genomes.},
journal = {Journal of genomics},
volume = {12},
number = {},
pages = {47-54},
pmid = {38638167},
issn = {1839-9940},
abstract = {INTRODUCTION: Metagenomic sequencing is a powerful tool that is widely used in laboratories worldwide for taxonomic characterization of microorganisms in clinical and environmental samples. In this study, we utilized metagenomics to investigate comprehensively the microbial diversity in fecal samples of children over a four-year period. Our methods were carefully designed to ensure accurate and reliable results.

MATERIAL AND METHODS: Validated and analyzed were metagenomic data obtained from sequencing 27 fecal samples from children under 10 years old with gastroenteritis over a four-year period (2012-2016). The fecal specimens were collected from patients who received care at public health facilities in the northern region of Brazil. Sequencing libraries were prepared from cDNA and sequenced on the Illumina HiSeq. Kraken-2 was utilized to classify bacterial taxonomy based on the 16S rRNA gene, using the Silva rRNA database. Additionally, the Diamond program was used for mapping to the non-redundant protein database (NR database). Phylogenomic analyses were conducted using Geneious R10 and MEGA X software, and Bayesian estimation of phylogeny was performed using the MrBayes program. The results indicate significant heterogeneity among norovirus strains, with evidence of recombination and point mutations. This study presents the first complete genome of parechovirus 8 in the region. Additionally, it describes the bacterial populations and bacteriophages present in feces, with a high abundance of Firmicutes and Proteobacteria, including an increased proportion of the Enterobacteriaceae family. The presented data demonstrate the genetic diversity of microbial populations and provide a comprehensive report on viral molecular characterization. These findings are relevant for genomic studies in gastrointestinal infections. The metagenomic approach is a powerful tool for investigating microbial diversity in children with gastroenteritis. However, further studies are imperative to conduct genomic analysis of identified bacterial strains and thoroughly analyze antimicrobial resistance genes.},
}

@article {pmid38637353,
year = {2024},
author = {Lin, L and Fang, J and Li, J and Tang, Y and Xin, T and Ouyang, N and Cai, W and Xie, L and Lu, S and Zhang, J},
title = {Metagenomic Next-Generation Sequencing Contributes to the Early Diagnosis of Mixed Infections in Central Nervous System.},
journal = {Mycopathologia},
volume = {189},
number = {3},
pages = {34},
pmid = {38637353},
issn = {1573-0832},
support = {81571970//Innovative Research Group Project of the National Natural Science Foundation of China/ ; },
abstract = {Central nervous system (CNS) infections represent a challenge due to the complexities associated with their diagnosis and treatment, resulting in a high incidence rate and mortality. Here, we presented a case of CNS mixed infection involving Candida and human cytomegalovirus (HCMV), successfully diagnosed through macrogenomic next-generation sequencing (mNGS) in China. A comprehensive review and discussion of previously reported cases were also provided. Our study emphasizes the critical role of early pathogen identification facilitated by mNGS, underscoring its significance. Notably, the integration of mNGS with traditional methods significantly enhances the diagnostic accuracy of CNS infections. This integrated approach has the potential to provide valuable insights for clinical practice, facilitating early diagnosis, allowing for treatment adjustments, and ultimately, improving the prognosis for patients with CNS infections.},
}

@article {pmid38637335,
year = {2024},
author = {Li, P and Qian, Z and Tao, Y},
title = {Application of metagenomic next-generation sequencing in the diagnosis of Bartonella neuroretinitis: a case report and literature review.},
journal = {Journal of ophthalmic inflammation and infection},
volume = {14},
number = {1},
pages = {17},
pmid = {38637335},
issn = {1869-5760},
abstract = {BACKGROUND: Cat-scratch disease (CSD) is caused by Bartonella henselae infection. In atypical cases of CSD, pathogen determination is challenging. We report a case of Bartonella neuroretinitis with neither a clear history of scratches nor typical general symptoms. The diagnosis was made using metagenomic next-generation sequencing (mNGS), a high-throughput sequencing technology.

CASE PRESENTATION: A female patient presented to the ophthalmologist with complaint of blurred vision in her right eye. Although with history of raising a cat, she reported no clear history of scratches or typical general symptoms, except a fever of unknown origin which resolved spontaneously. The best corrected visual acuity (BCVA) of the right eye was count fingers. Fundus examination showed optic disc oedema, macular exudates and inferior exudative retinal detachment. Laboratory examination results showed increased value of serum C-reactive protein and erythrocyte sedimentation rate. Ocular involvement of toxoplasmosis, syphilis and tuberculosis were excluded. To identify the possible causative pathogen of the disease, mNGS of aqueous humour sample was performed and 521 reads of B. henselae were identified. Serological test results further showed a positive immunoglobulin G (IgG) titre of 1:64. Taking the contact history, clinical manifestations, mNGS and serological results into consideration, the diagnosis of Bartonella neuroretinitis (ocular CSD) was made. After appropriate treatment, the BCVA of the right eye improved to 20/25 in the last follow-up. Fundus examination showed a normal optic disc and macula, and the exudates had reduced.

CONCLUSION: mNGS, a fast and unbiased method, can be used to detect B. henselae (if present) in intraocular fluid samples.; however, the results should be interpreted together with the clinical symptoms and other auxiliary test results.},
}

@article {pmid38630810,
year = {2024},
author = {Chen, J and Liu, C and Li, W and Zhang, W and Wang, Y and Clark, AG and Lu, J},
title = {From sub-Saharan Africa to China: Evolutionary history and adaptation of Drosophila melanogaster revealed by population genomics.},
journal = {Science advances},
volume = {10},
number = {16},
pages = {eadh3425},
pmid = {38630810},
issn = {2375-2548},
mesh = {Animals ; *Drosophila melanogaster/genetics ; *Metagenomics ; Genetic Variation ; Ecosystem ; Africa South of the Sahara ; China ; },
abstract = {Drosophila melanogaster is a widely used model organism for studying environmental adaptation. However, the genetic diversity of populations in Asia is poorly understood, leaving a notable gap in our knowledge of the global evolution and adaptation of this species. We sequenced genomes of 292 D. melanogaster strains from various ecological settings in China and analyzed them along with previously published genome sequences. We have identified six global genetic ancestry groups, despite the presence of widespread genetic admixture. The strains from China represent a unique ancestry group, although detectable differentiation exists among populations within China. We deciphered the global migration and demography of D. melanogaster, and identified widespread signals of adaptation, including genetic changes in response to insecticides. We validated the effects of insecticide resistance variants using population cage trials and deep sequencing. This work highlights the importance of population genomics in understanding the genetic underpinnings of adaptation, an effort that is particularly relevant given the deterioration of ecosystems.},
}

Animals
*Drosophila melanogaster/genetics
*Metagenomics
Genetic Variation
Ecosystem
Africa South of the Sahara
China

@article {pmid38637082,
year = {2024},
author = {Sonets, IV and Solovyev, MA and Ivanova, VA and Vasiluev, PA and Kachalkin, AV and Ochkalova, SD and Korobeynikov, AI and Razin, SV and Ulianov, SV and Tyakht, AV},
title = {Hi-C metagenomics facilitate comparative genome analysis of bacteria and yeast from spontaneous beer and cider.},
journal = {Food microbiology},
volume = {121},
number = {},
pages = {104520},
doi = {10.1016/j.fm.2024.104520},
pmid = {38637082},
issn = {1095-9998},
abstract = {Sequence-based analysis of fermented foods and beverages' microbiomes offers insights into their impact on taste and consumer health. High-throughput metagenomics provide detailed taxonomic and functional community profiling, but bacterial and yeast genome reconstruction and mobile genetic elements tracking are to be improved. We established a pipeline for exploring fermented foods microbiomes using metagenomics coupled with chromosome conformation capture (Hi-C metagenomics). The approach was applied to analyze a collection of spontaneously fermented beers and ciders (n = 12). The Hi-C reads were used to reconstruct the metagenome-assembled genomes (MAGs) of bacteria and yeasts facilitating subsequent comparative genomic analysis, assembly scaffolding and exploration of "plasmid-bacteria" links. For a subset of beverages, yeasts were isolated and characterized phenotypically. The reconstructed Hi-C MAGs primarily belonged to the Lactobacillaceae family in beers, along with Acetobacteraceae and Enterobacteriaceae in ciders, exhibiting improved quality compared to conventional metagenomic MAGs. Comparative genomic analysis of Lactobacillaceae Hi-C MAGs revealed clustering by niche and suggested genetic determinants of survival and probiotic potential. For Pediococcus damnosus, Hi-C-based networks of contigs enabled linking bacteria with plasmids. Analyzing phylogeny and accessory genes in the context of known reference genomes offered insights into the niche specialization of beer lactobacilli. The subspecies-level diversity of cider Tatumella spp. was disentangled using a Hi-C-based graph. We obtained highly complete yeast Hi-C MAGs primarily represented by Brettanomyces and Saccharomyces, with Hi-C-facilitated chromosome-level genome assembly for the former. Utilizing Hi-C metagenomics to unravel the genomic content of individual species can provide a deeper understanding of the ecological interactions within the food microbiome, aid in bioprospecting beneficial microorganisms, improving quality control and improving innovative fermented products.},
}

@article {pmid38637066,
year = {2024},
author = {Lee, AW and Ng, IC and Wong, EY and Wong, IT and Sze, RP and Chan, KY and So, TY and Zhang, Z and Ka-Yee Fung, S and Choi-Ying Wong, S and Tam, WY and Lao, HY and Lee, LK and Leung, JS and Chan, CT and Ng, TT and Zhang, J and Chow, FW and Leung, PH and Siu, GK},
title = {Comprehensive identification of pathogenic microbes and antimicrobial resistance genes in food products using nanopore sequencing-based metagenomics.},
journal = {Food microbiology},
volume = {121},
number = {},
pages = {104493},
doi = {10.1016/j.fm.2024.104493},
pmid = {38637066},
issn = {1095-9998},
abstract = {Foodborne pathogens, particularly antimicrobial-resistant (AMR) bacteria, remain a significant threat to global health. Given the limitations of conventional culture-based approaches, which are limited in scope and time-consuming, metagenomic sequencing of food products emerges as a promising solution. This method provides a fast and comprehensive way to detect the presence of pathogenic microbes and antimicrobial resistance genes (ARGs). Notably, nanopore long-read sequencing provides more accurate bacterial taxonomic classification in comparison to short-read sequencing. Here, we revealed the impact of food types and attributes (origin, retail place, and food processing methods) on microbial communities and the AMR profile using nanopore metagenomic sequencing. We analyzed a total of 260 food products, including raw meat, sashimi, and ready-to-eat (RTE) vegetables. Clostridium botulinum, Acinetobacter baumannii, and Vibrio parahaemolyticus were identified as the top three foodborne pathogens in raw meat and sashimi. Importantly, even with low pathogen abundance, higher percentages of samples containing carbapenem and cephalosporin resistance genes were identified in chicken and RTE vegetables, respectively. In parallel, our results demonstrated that fresh, peeled, and minced foods exhibited higher levels of pathogenic bacteria. In conclusion, this comprehensive study offers invaluable data that can contribute to food safety assessments and serve as a basis for quality indicators.},
}

@article {pmid38636877,
year = {2024},
author = {Lv, L and Chen, J and Wei, Z and Hao, P and Wang, P and Liu, X and Gao, W and Sun, L and Liang, J and Ren, Z and Zhang, G and Li, W},
title = {A new strategy for accelerating recovery of anaerobic granular sludge after low-temperature shock: In situ regulation of quorum sensing microorganisms embedded in polyvinyl alcohol sodium alginate.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130709},
doi = {10.1016/j.biortech.2024.130709},
pmid = {38636877},
issn = {1873-2976},
abstract = {Low-temperature could inhibit the performance of anaerobic granular sludge (AnGS). Quorum sensing (QS), as a communication mode between microorganisms, can effectively regulate AnGS. In this study, a kind of embedded particles (PVA/SA@Serratia) based on signal molecule secreting bacteria was prepared by microbial immobilization technology based on polyvinyl alcohol and sodium alginate to accelerate the recovery of AnGS system after low temperature. Low-temperature shock experiment verified the positive effect of PVA/SA@Serratia on restoring the COD removal rate and methanogenesis capacity of AnGS. Further analysis by metagenomics analysis showed that PVA/SA@Serratia stimulated higher QS activity and promoted the secretion of extracellular polymeric substance (EPS) in AnGS. The rapid construction of EPS protective layer effectively accelerated the establishment of a robust microbial community structure. PVA/SA@Serratia also enhanced multiple methanogenic pathways, including direct interspecies electron transfer. In conclusion, this study demonstrated that PVA/SA@Serratia could effectively strengthen AnGS after low-temperature shock.},
}

@article {pmid38636860,
year = {2024},
author = {Zhou, ZZ and Zhu, J and Yin, Y and Ding, LJ},
title = {Seasonal variations of profiles of antibiotic resistance genes and virulence factor genes in household dust from Beijing, China revealed by the metagenomics.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172542},
doi = {10.1016/j.scitotenv.2024.172542},
pmid = {38636860},
issn = {1879-1026},
abstract = {Household-related microbiome is closely related with human health. However, the knowledge about profiles of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) which are carried by microbes inside homes and their temporal dynamics are rather limited. Here we monitored the seasonal changes of bacterial community (especially pathogenic bacteria), ARGs, and VFGs in household dust samples during two years. Based on metagenomic sequencing, the dust-related bacterial pathogenic community, ARGs, and VFGs all harbored the lowest richness in spring among four seasons. Their structure (except that of VFGs) also exhibited remarkable differences among the seasons. The structural variations of ARGs and VFGs were almost explained by mobile genetic elements (MGEs), bacterial pathogens, and particulate matter-related factors, with MGEs explaining the most. Moreover, the total normalized abundance of ARGs or VFGs showed no significant change across the seasons. Results of metagenomic binning and microbial network both showed that several pathogenic taxa (e.g., Ralstonia pickettii) were strongly linked with numerous ARGs (mainly resistant to multidrug) and VFGs (mainly encoding motility) simultaneously. Overall, these findings underline the significance of MGEs in structuring ARGs and VFGs inside homes along with seasonal variations, suggesting that household dust is a neglected reservoir for ARGs and VFGs.},
}

@article {pmid38636642,
year = {2024},
author = {Wen, X and Cui, L and Lin, H and Zhu, W and Shao, Z and Wang, Y},
title = {Comparison of nitrification performance in SBR and SBBR with response to NaCl salinity shock: microbial structure and functional genes.},
journal = {Environmental research},
volume = {},
number = {},
pages = {118917},
doi = {10.1016/j.envres.2024.118917},
pmid = {38636642},
issn = {1096-0953},
abstract = {Ammonia removal by nitrifiers at the extremely high salinity poses a great challenge for saline wastewater treatment. Sequencing batch reactor (SBR) was conducted with a stepwise increase of salinity from 10 to 40 g-NaCl·L[-1], while sequencing batch biofilm reactor (SBBR) with one-step salinity enhancement, their nitrification performance, microbial structure and interaction were evaluated. Both SBR and SBBR can achieve high-efficiency nitrification (98% ammonia removal) at 40 g-NaCl·L[-1]. However, SBBR showed more stable nitrification performance than SBR at 40 g-NaCl·L[-1] after a shorter adaptation period of 4-15 d compared to previous studies. High-throughput sequencing and metagenomic analysis demonstrated that the abundance and capability of conventional ammonia-oxidizing bacteria (Nitrosomonas) were suppressed in SBBR relative to SBR. Gelidibacter, Anaerolineales were the predominant genus in SBBR, which were not found in SBR. NorB and nosZ responsible for reducing NO to N2O and reducing N2O to N2 respectively had s strong synergistic effect in SBBR. This study will provide a valuable reference for the startup of nitrification process within a short period of time under the extremely high NaCl salinity.},
}

@article {pmid38636618,
year = {2024},
author = {Ergunay, K and Bourke, BP and Reinbold-Wasson, DD and Caicedo-Quiroga, L and Vaydayko, N and Kirkitadze, G and Chunashvili, T and Tucker, CL and Linton, YM},
title = {Novel clades of tick-borne pathogenic nairoviruses in Europe.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105593},
doi = {10.1016/j.meegid.2024.105593},
pmid = {38636618},
issn = {1567-7257},
abstract = {Members of the Orthonairovirus genus (family Nairoviridae) include many tick-borne viruses of significant human and animal health impact, with several recently-documented pathogenic viruses lacking sufficient epidemiological information. We screened 215 adult ticks of seven species collected in Bulgaria, Georgia, Latvia and Poland for orthonairoviruses, followed by nanopore sequencing (NS) for genome characterization. Initial generic amplification revealed Sulina virus (SULV, Orthonairovirus sulinaense), for which an updated amplification assay was used, revealing an overall prevalence of 2.7% in Ixodes ricinus ticks from Latvia. Three complete and additional partial SULV genomes were generated, that consistently formed a separate, distinct clade with further intragroup divergence in the maximum likelihood analyses. Comparisons with previously described viruses from Romania exhibited similar genome topologies, albeit with divergent motifs and cleavage sites on the glycoprotein precursor. Preliminary evidence of recombination involving the S segment was documented, in addition to variations in predicted viral glycoproteins. Generic screening further identified Tacheng tick virus 1 (TCTV1, Orthonairovirus tachengense), with documented human infections, in Dermacentor reticulatus ticks from Poland, with a prevalence of 0.9%. Subsequent NS and assembly provided the first complete TCTV1 genome outside of China, where it was originally described. Phylogenetic analysis of virus genome segments revealed TCTV1-Poland as a discrete taxon within the TCTV1 cluster in the Orthonairovirus genus, representing a geographically segregated clade. Comparable genome topology with TCTV1 from China was observed, aside from minor variations in the M segment. Similar to SULV, TCTV1 exhibited several mismatches on previously described screening primer binding sites, likely to prevent amplification. These findings indicate presence of novel TCTV1 and SULV clades in Eastern Europe, confirming the expansion of orthonairoviruses with pathogenic potential.},
}

@article {pmid38636385,
year = {2024},
author = {Xu, L and Mao, T and Xia, M and Wu, W and Chen, J and Jiang, C and Zeng, T and Tian, Y and Lu, L and Cai, Z},
title = {New evidence for gut-muscle axis: Lactic acid bacteria-induced gut microbiota regulates duck meat flavor.},
journal = {Food chemistry},
volume = {450},
number = {},
pages = {139354},
doi = {10.1016/j.foodchem.2024.139354},
pmid = {38636385},
issn = {1873-7072},
abstract = {The interaction between gut microbiota and muscles through the gut-muscle axis has received increasing attention. This study attempted to address existing research gaps by investigating the effects of gut microbiota on meat flavor. Specifically, lactic acid bacteria were administered to ducks, and the results of e-nose and e-tongue showed significantly enhanced meat flavor in the treatment group. Further analyses using GC-MS revealed an increase in 6 characteristic volatile flavor compounds, including pentanal, hexanal, heptanal, 1-octen-3-ol, 2,3-octanedione, and 2-pentylfuran. Linoleic acid was identified as the key fatty acid that influences meat flavor. Metagenomic and transcriptomic results further confirmed that cecal microbiota affects the duck meat flavor by regulating the metabolic pathways of fatty acids and amino acids, especially ACACB was related to fatty acid biosynthesis and ACAT2, ALDH1A1 with fatty acid degradation. This study sheds light on a novel approach to improving the flavor of animal-derived food.},
}

@article {pmid38635882,
year = {2024},
author = {Al Radi, ZMA and Prins, FM and Collij, V and Vich Vila, A and Festen, EAM and Dijkstra, G and Weersma, RK and Klaassen, MAY and Gacesa, R},
title = {Exploring the Predictive Value of Gut Microbiome Signatures for Therapy Intensification in Patients With Inflammatory Bowel Disease: A 10-Year Follow-up Study.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izae064},
pmid = {38635882},
issn = {1536-4844},
support = {//Netherlands Organization for Scientific Research/ ; MLDS D16-14//Dutch Digestive Foundation/ ; },
abstract = {BACKGROUND: Inflammatory bowel diseases (IBDs) pose a significant challenge due to their diverse, often debilitating, and unpredictable clinical manifestations. The absence of prognostic tools to anticipate the future complications that require therapy intensification presents a substantial burden to patient private life and health. We aimed to explore whether the gut microbiome is a potential biomarker for future therapy intensification in a cohort of 90 IBD patients.

METHODS: We conducted whole-genome metagenomics sequencing on fecal samples from these patients, allowing us to profile the taxonomic and functional composition of their gut microbiomes. Additionally, we conducted a retrospective analysis of patients' electronic records over a period of 10 years following the sample collection and classified patients into (1) those requiring and (2) not requiring therapy intensification. Therapy intensification included medication escalation, intestinal resections, or a loss of response to a biological treatment. We applied gut microbiome diversity analysis, dissimilarity assessment, differential abundance analysis, and random forest modeling to establish associations between baseline microbiome profiles and future therapy intensification.

RESULTS: We identified 12 microbial species (eg, Roseburia hominis and Dialister invisus) and 16 functional pathways (eg, biosynthesis of L-citrulline and L-threonine) with significant correlations to future therapy intensifications. Random forest models using microbial species and pathways achieved areas under the curve of 0.75 and 0.72 for predicting therapy intensification.

CONCLUSIONS: The gut microbiome is a potential biomarker for therapy intensification in IBD patients and personalized management strategies. Further research should validate our findings in other cohorts to enhance the generalizability of these results.},
}

@article {pmid38635629,
year = {2024},
author = {Wang, T and Weiss, A and You, L},
title = {A generic approach to infer community-level fitness of microbial genes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {17},
pages = {e2318380121},
doi = {10.1073/pnas.2318380121},
pmid = {38635629},
issn = {1091-6490},
support = {R01AI125604//HHS | National Institutes of Health (NIH)/ ; R01GM098642//HHS | National Institutes of Health (NIH)/ ; R01EB031869//HHS | National Institutes of Health (NIH)/ ; MCB-1937259//National Science Foundation (NSF)/ ; },
abstract = {The gene content in a metagenomic pool defines the function potential of a microbial community. Natural selection, operating on the level of genomes or genes, shapes the evolution of community functions by enriching some genes while depriving the others. Despite the importance of microbiomes in the environment and health, a general metric to evaluate the community-wide fitness of microbial genes remains lacking. In this work, we adapt the classic neutral model of species and use it to predict how the abundances of different genes will be shaped by selection, regardless of at which level the selection acts. We establish a simple metric that quantitatively infers the average survival capability of each gene in a microbiome. We then experimentally validate the predictions using synthetic communities of barcoded Escherichia coli strains undergoing neutral assembly and competition. We further show that this approach can be applied to publicly available metagenomic datasets to gain insights into the environment-function interplay of natural microbiomes.},
}

@article {pmid38635609,
year = {2024},
author = {Xu, R and Zhang, J and Zheng, J and Wu, Q},
title = {Allergic bronchopulmonary mycosis due to Schizophyllum commune in a patient with chronic hepatitis B.},
journal = {Journal of infection in developing countries},
volume = {18},
number = {3},
pages = {488-494},
doi = {10.3855/jidc.18024},
pmid = {38635609},
issn = {1972-2680},
abstract = {INTRODUCTION: Schizophyllum commune (S. commune) is an opportunistic pathogenic fungus and can cause infection of the respiratory system in immunocompromised hosts. Allergic bronchopulmonary mycosis (ABPM) is the major disease caused by S. commune. However, identification of S. commune using routine mycological diagnostic methods is difficult. It is easy to make mistakes in diagnosis and treatment, resulting in deterioration of the disease. We report the first case of ABPM due to S. commune in a Chinese patient with chronic hepatitis B.

CASE PRESENTATION: The patient presented cough, sputum and dyspnea for six months. The pathogen was missed during routine laboratory workup. We performed bronchoscopy examination and bronchoalveolar lavage. S. commune was identified by metagenomic next-generation sequencing (mNGS) of bronchial alveolar lavage fluid (BALF). Hence, the patient was immediately treated with 200 mg voriconazole twice daily (intravenous infusion) and 20 mg prednisone once a day (oral therapy), along with oral entecavir for hepatitis B. There was no recurrence of infection after the medication was discontinued.

CONCLUSIONS: S. commune infection should be considered in the diagnosis of patients with refractory cough, sputum and dyspnea, especially in immunocompromised individuals. The mNGS technique is an effective supplementary technique for the diagnosis of S. commune infection, enabling precise clinical decision-making and appropriate treatment. Most patients have good prognosis with a combination of proper antifungal therapy and hormonal therapy.},
}

@article {pmid38635587,
year = {2024},
author = {Ohdera, AH and Mansbridge, M and Wang, M and Naydenkov, P and Kamel, B and Goentoro, L},
title = {The microbiome of a Pacific moon jellyfish Aurelia coerulea.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0298002},
doi = {10.1371/journal.pone.0298002},
pmid = {38635587},
issn = {1932-6203},
abstract = {The impact of microbiome in animal physiology is well appreciated, but characterization of animal-microbe symbiosis in marine environments remains a growing need. This study characterizes the microbial communities associated with the moon jellyfish Aurelia coerulea, first isolated from the East Pacific Ocean and has since been utilized as an experimental system. We find that the microbiome of this Pacific Aurelia culture is dominated by two taxa, a Mollicutes and Rickettsiales. The microbiome is stable across life stages, although composition varies. Mining the host sequencing data, we assembled the bacterial metagenome-assembled genomes (MAGs). The bacterial MAGs are highly reduced, and predict a high metabolic dependence on the host. Analysis using multiple metrics suggest that both bacteria are likely new species. We therefore propose the names Ca. Mariplasma lunae (Mollicutes) and Ca. Marinirickettsia aquamalans (Rickettsiales). Finally, comparison with studies of Aurelia from other geographical populations suggests the association with Ca. Mariplasma lunae occurs in Aurelia from multiple geographical locations. The low-diversity microbiome of Aurelia provides a relatively simple system to study host-microbe interactions.},
}

@article {pmid38635326,
year = {2024},
author = {Wang, M and Rieber, L and van Baaren, J and Morgan, M and Merrett, S and McDowell, I and Bowen, T},
title = {Diverse Class 2 CRISPR Effectors as Active Nucleases with Expanded Targeting Capabilities.},
journal = {The CRISPR journal},
volume = {7},
number = {2},
pages = {120-130},
doi = {10.1089/crispr.2023.0058},
pmid = {38635326},
issn = {2573-1602},
abstract = {CRISPR-Cas systems have proven effective in a variety of applications due to their ease of use and relatively high editing efficiency. Yet, any individual CRISPR-Cas system has inherent limitations, necessitating a diversity of RNA-guided nucleases to suit applications with distinct needs. We searched through metagenomic sequences to identify RNA-guided nucleases and found enzymes from diverse CRISPR-Cas types and subtypes, the most promising of which we developed into gene-editing platforms. Based on prior annotations of the metagenomic sequences, we establish the likely taxa and sampling locations where Class 2 CRISPR-Cas systems active in eukaryotes may be found. The newly discovered systems show robust capabilities as gene editors and base editors.},
}

@article {pmid38635321,
year = {2024},
author = {Wang, M and Lkhagva, E and Kim, S and Zhai, C and Islam, MM and Kim, HJ and Hong, ST},
title = {The gut microbe pair of Oribacterium sp. GMB0313 and Ruminococcus sp. GMB0270 confers complete protection against SARS-CoV-2 infection by activating CD8+ T cell-mediated immunity.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2342497},
doi = {10.1080/19490976.2024.2342497},
pmid = {38635321},
issn = {1949-0984},
abstract = {Despite the potential protective role of the gut microbiome against COVID-19, specific microbes conferring resistance to COVID-19 have not yet been identified. In this work, we aimed to identify and validate gut microbes at the species level that provide protection against SARS-CoV-2 infection. To identify gut microbes conferring protection against COVID-19, we conducted a fecal microbiota transplantation (FMT) from an individual with no history of COVID-19 infection or immunization into a lethal COVID-19 hamster model. FMT from this COVID-19-resistant donor resulted in significant phenotypic changes related to COVID-19 sensitivity in the hamsters. Metagenomic analysis revealed distinct differences in the gut microbiome composition among the hamster groups, leading to the identification of two previously unknown bacterial species: Oribacterium sp. GMB0313 and Ruminococcus sp. GMB0270, both associated with COVID-19 resistance. Subsequently, we conducted a proof-of-concept confirmation animal experiment adhering to Koch's postulates. Oral administration of this gut microbe pair, Oribacterium sp. GMB0313 and Ruminococcus sp. GMB0270, to the hamsters provided complete protection against SARS-CoV-2 infection through the activation of CD8+ T cell mediated immunity. The prophylactic efficacy of the gut microbe pair against SARS-CoV-2 infection was comparable to, or even superior to, current mRNA vaccines. This strong prophylactic efficacy suggests that the gut microbe pair could be developed as a host-directed universal vaccine for all betacoronaviruses, including potential future emerging viruses.},
}

@article {pmid38634770,
year = {2024},
author = {Lee, I and Jo, JW and Woo, HJ and Suk, KT and Lee, SS and Kim, BS},
title = {Proton pump inhibitors increase the risk of carbapenem-resistant Enterobacteriaceae colonization by facilitating the transfer of antibiotic resistance genes among bacteria in the gut microbiome.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2341635},
doi = {10.1080/19490976.2024.2341635},
pmid = {38634770},
issn = {1949-0984},
abstract = {Carbapenem-resistant Enterobacteriaceae (CRE) pose a global health threat; however, there is still limited understanding of the risk factors and underlying mechanisms of CRE colonization in the gut microbiome. We conducted a matched case-control study involving 282 intensive care unit patients to analyze influencing covariates on CRE colonization. Subsequently, their effects on the gut microbiome were analyzed in a subset of 98 patients (47 CRE carriers and 51 non-CRE carriers) using whole metagenome sequences. The concomitant use of proton pump inhibitors (PPIs) and antibiotics was a significant risk factor for CRE colonization. The gut microbiome differed according to PPI administration, even within the CRE and non-CRE groups. Moreover, the transfer of mobile genetic elements (MGEs) harboring carbapenem resistance genes (CRGs) between bacteria was higher in the PPI-treated group than in the PPI-not-treated group among CRE carriers. The concomitant use of PPIs and antibiotics significantly alters the gut microbiome and increases the risk of CRE colonization by facilitating the transfer of CRGs among bacteria of the gut microbiome. Based on these findings, improved stewardship of PPIs as well as antibiotics can provide strategies to reduce the risk of CRE colonization, thereby potentially improving patient prognosis.},
}

@article {pmid38633703,
year = {2024},
author = {Arisan, D and Moya-Beltrán, A and Rojas-Villalobos, C and Issotta, F and Castro, M and Ulloa, R and Chiacchiarini, PA and Díez, B and Martín, AJM and Ñancucheo, I and Giaveno, A and Johnson, DB and Quatrini, R},
title = {Acidithiobacillia class members originating at sites within the Pacific Ring of Fire and other tectonically active locations and description of the novel genus 'Igneacidithiobacillus'.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1360268},
pmid = {38633703},
issn = {1664-302X},
abstract = {Recent studies have expanded the genomic contours of the Acidithiobacillia, highlighting important lacunae in our comprehension of the phylogenetic space occupied by certain lineages of the class. One such lineage is 'Igneacidithiobacillus', a novel genus-level taxon, represented by 'Igneacidithiobacillus copahuensis' VAN18-1[T] as its type species, along with two other uncultivated metagenome-assembled genomes (MAGs) originating from geothermally active sites across the Pacific Ring of Fire. In this study, we investigate the genetic and genomic diversity, and the distribution patterns of several uncharacterized Acidithiobacillia class strains and sequence clones, which are ascribed to the same 16S rRNA gene sequence clade. By digging deeper into this data and contributing to novel MAGs emerging from environmental studies in tectonically active locations, the description of this novel genus has been consolidated. Using state-of-the-art genomic taxonomy methods, we added to already recognized taxa, an additional four novel Candidate (Ca.) species, including 'Ca. Igneacidithiobacillus chanchocoensis' (mCHCt20-1[TS]), 'Igneacidithiobacillus siniensis' (S30A2[T]), 'Ca. Igneacidithiobacillus taupoensis' (TVZ-G3 [TS]), and 'Ca. Igneacidithiobacillus waiarikiensis' (TVZ-G4 [TS]). Analysis of published data on the isolation, enrichment, cultivation, and preliminary microbiological characterization of several of these unassigned or misassigned strains, along with the type species of the genus, plus the recoverable environmental data from metagenomic studies, allowed us to identify habitat preferences of these taxa. Commonalities and lineage-specific adaptations of the seven species of the genus were derived from pangenome analysis and comparative genomic metabolic reconstruction. The findings emerging from this study lay the groundwork for further research on the ecology, evolution, and biotechnological potential of the novel genus 'Igneacidithiobacillus'.},
}

@article {pmid38633701,
year = {2024},
author = {Jia, Y and He, C and Lahm, M and Chen, Q and Powers, L and Gonsior, M and Chen, F},
title = {A pilot study suggests the correspondence between SAR202 bacteria and dissolved organic matter in the late stage of a year-long microcosm incubation.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1357822},
pmid = {38633701},
issn = {1664-302X},
abstract = {SAR202 bacteria are abundant in the marine environment and they have been suggested to contribute to the utilization of recalcitrant organic matter (RDOM) within the ocean's biogeochemical cycle. However, this functional role has only been postulated by metagenomic studies. During a one-year microcosm incubation of an open ocean microbial community with lysed Synechococcus and its released DOM, SAR202 became relatively more abundant in the later stage (after day 30) of the incubation. Network analysis illustrated a high degree of negative associations between SAR202 and a unique group of molecular formulae (MFs) in phase 2 (day 30 to 364) of the incubation, which is empirical evidence that SAR202 bacteria are major consumers of the more oxygenated, unsaturated, and higher-molecular-weight MFs. Further investigation of the SAR202-associated MFs suggested that they were potentially secondary products arising from initial heterotrophic activities following the amendment of labile Synechococcus-derived DOM. This pilot study provided a preliminary observation on the correspondence between SAR202 bacteria and more resistant DOM, further supporting the hypothesis that SAR202 bacteria play important roles in the degradation of RDOM and thus the ocean's biogeochemical cycle.},
}

@article {pmid38633306,
year = {2024},
author = {Zhang, L and Liu, X and Fan, B and Chen, J and Chen, J and Li, Q and Wu, X},
title = {Microbiome features in bronchoalveolar lavage fluid of patients with idiopathic inflammatory myopathy-related interstitial lung disease.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1338947},
pmid = {38633306},
issn = {2296-858X},
abstract = {BACKGROUND: Interstitial lung disease (ILD) is a common complication of idiopathic inflammatory myopathy (IIM), which is one of the connective tissue diseases (CTD). It can lead to poor prognosis and increased mortality. However, the distribution and role of the lower respiratory tract (LRT) microbiome in patients with IIM-ILD remains unclear. This study aimed to investigate the microbial diversity and community differences in bronchoalveolar lavage fluid (BALF) in patients with IIM-ILD.

METHODS: From 28 June 2021 to 26 December 2023, 51 individual BALF samples were enrolled, consisting of 20 patients with IIM-ILD, 16 patients with other CTD-ILD (including 8 patients with SLE and 8 with RA) and 15 patients with CAP. The structure and function of microbiota in BALF were identified by metagenomic next-generation sequencing (mNGS).

RESULTS: The community evenness of LRT microbiota within the IIM-ILD group was marginally lower compared to the other CTD-ILD and CAP groups. Nonetheless, there were no noticeable differences. The species community structure was similar among the three groups, based on the Bray-Curtis distance between the samples. At the level of genus, the IIM-ILD group displayed a considerably higher abundance of Pseudomonas and Corynebacterium in comparison to the CAP group (p < 0.01, p < 0.05). At the species level, we found that the relative abundance of Pseudomonas aeruginosa increased significantly in the IIM-ILD group compared to the CAP group (p < 0.05). Additionally, the relative abundance of Prevotella pallens was significantly higher in other CTD-ILD groups compared to that in the IIM-ILD group (p < 0.05). Of all the clinical indicators examined in the correlation analysis, ferritin level demonstrated the strongest association with LRT flora, followed by Serum interleukin-6 level (p < 0.05).

CONCLUSION: Our research has identified particular LRT microorganisms that were found to be altered in the IIM-ILD group and were significantly associated with immune function and inflammatory markers in patients. The lower respiratory tract microbiota has potential in the diagnosis and treatment of IIM-ILD.},
}

@article {pmid38632606,
year = {2024},
author = {Liu, X and Zeng, X and Li, X and Xin, S and Zhang, F and Liu, F and Zeng, Y and Wu, J and Zou, Y and Xiong, X},
title = {Landscapes of gut bacterial and fecal metabolic signatures and their relationship in severe preeclampsia.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {360},
pmid = {38632606},
issn = {1479-5876},
support = {82160298//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Preeclampsia is a pregnancy-specific disease leading to maternal and perinatal morbidity. Hypertension and inflammation are the main characteristics of preeclampsia. Many factors can lead to hypertension and inflammation, including gut microbiota which plays an important role in hypertension and inflammation in humans. However, alterations to the gut microbiome and fecal metabolome, and their relationships in severe preeclampsia are not well known. This study aims to identify biomarkers significantly associated with severe preeclampsia and provide a knowledge base for treatments regulating the gut microbiome.

METHODS: In this study, fecal samples were collected from individuals with severe preeclampsia and healthy controls for shotgun metagenomic sequencing to evaluate changes in gut microbiota composition. Quantitative polymerase chain reaction analysis was used to validate the reliability of our shotgun metagenomic sequencing results. Additionally, untargeted metabolomics analysis was performed to measure fecal metabolome concentrations.

RESULTS: We identified several Lactobacillaceae that were significantly enriched in the gut of healthy controls, including Limosilactobacillus fermentum, the key biomarker distinguishing severe preeclampsia from healthy controls. Limosilactobacillus fermentum was significantly associated with shifts in KEGG Orthology (KO) genes and KEGG pathways of the gut microbiome in severe preeclampsia, such as flagellar assembly. Untargeted fecal metabolome analysis found that severe preeclampsia had higher concentrations of Phenylpropanoate and Agmatine. Increased concentrations of Phenylpropanoate and Agmatine were associated with the abundance of Limosilactobacillus fermentum. Furthermore, all metabolites with higher abundances in healthy controls were enriched in the arginine and proline metabolism pathway.

CONCLUSION: Our research indicates that changes in metabolites, possibly due to the gut microbe Limosilactobacillus fermentum, can contribute to the development of severe preeclampsia. This study provides insights into the interaction between gut microbiome and fecal metabolites and offers a basis for improving severe preeclampsia by modulating the gut microbiome.},
}

@article {pmid38632536,
year = {2024},
author = {Mao, JY and Li, DK and Zhang, D and Yang, QW and Long, Y and Cui, N},
title = {Utility of paired plasma and drainage fluid mNGS in diagnosing acute intra-abdominal infections with sepsis.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {409},
pmid = {38632536},
issn = {1471-2334},
support = {No. 2022-PUMCH-A-219//National High Level Hospital Clinical Research Funding/ ; No. 2022-PUMCH-B-126//National High Level Hospital Clinical Research Funding/ ; 2022YFC2009803//National Key R&D Program of China/ ; No. 82072226//National Natural Science Foundation of China/ ; (CIFMS) 2021-I2M-1-062//CAMS Innovation Fund for Medical Sciences/ ; No. Z201100005520049//Beijing Municipal Science and Technology Commission/ ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has been increasingly applied in sepsis. We aimed to evaluate the diagnostic and therapeutic utility of mNGS of paired plasma and peritoneal drainage (PD) fluid samples in comparison to culture-based microbiological tests (CMTs) among critically ill patients with suspected acute intra-abdominal infections (IAIs).

METHODS: We conducted a prospective study from October 2021 to December 2022 enrolling septic patients with suspected IAIs (n = 111). Pairwise CMTs and mNGS of plasma and PD fluid were sent for pathogen detection. The mNGS group underwent therapeutic regimen adjustment based on mNGS results for better treatment. The microbial community structure, clinical features, antibiotic use and prognoses of the patients were analyzed.

RESULTS: Higher positivity rates were observed with mNGS versus CMTs for both PD fluid (90.0% vs. 48.3%, p < 0.005) and plasma (76.7% vs. 1.6%, p < 0.005). 90% of enrolled patients had clues of suspected pathogens combining mNGS and CMT methods. Gram-negative pathogens consist of most intra-abdominal pathogens, including a great variety of anaerobes represented by Bacteroides and Clostridium. Patients with matched plasma- and PD-mNGS results had higher mortality and sepsis severity. Reduced usage of carbapenem (30.0% vs. 49.4%, p < 0.05) and duration of anti-MRSA treatment (5.1 ± 3.3 vs. 7.0 ± 8.4 days, p < 0.05) was shown in the mNGS group in our study.

CONCLUSIONS: Pairwise plasma and PD fluid mNGS improves microbiological diagnosis compared to CMTs for acute IAI. Combining plasma and PD mNGS could predict poor prognosis. mNGS may enable optimize empirical antibiotic use.},
}

@article {pmid38629078,
year = {2024},
author = {Lancaster, AK and Single, RM and Mack, SJ and Sochat, V and Mariani, MP and Webster, GD},
title = {PyPop: a mature open-source software pipeline for population genomics.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1378512},
pmid = {38629078},
issn = {1664-3224},
mesh = {*Metagenomics ; *Software ; Genetics, Population ; Haplotypes ; Genotype ; },
abstract = {Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs Ewens-Watterson tests for selection, estimates haplotype frequencies, measures linkage disequilibrium, and tests significance. Standardized means of performing these tests is key for contemporary studies of evolutionary biology and population genetics, and these tests are central to genetic studies of disease association as well. Here, we present PyPop 1.0.0, a new major release of the package, which implements new features using the more robust infrastructure of GitHub, and is distributed via the industry-standard Python Package Index. New features include implementation of the asymmetric linkage disequilibrium measures and, of particular interest to the immunogenetics research communities, support for modern nomenclature, including colon-delimited allele names, and improvements to meta-analysis features for aggregating outputs for multiple populations. Code available at: https://zenodo.org/records/10080668 and https://github.com/alexlancaster/pypop.},
}

*Metagenomics
*Software
Genetics, Population
Haplotypes
Genotype

@article {pmid38632404,
year = {2024},
author = {Hossain, AA and Pigli, YZ and Baca, CF and Heissel, S and Thomas, A and Libis, VK and Burian, J and Chappie, JS and Brady, SF and Rice, PA and Marraffini, LA},
title = {DNA glycosylases provide antiviral defence in prokaryotes.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {38632404},
issn = {1476-4687},
abstract = {Bacteria have adapted to phage predation by evolving a vast assortment of defence systems[1]. Although anti-phage immunity genes can be identified using bioinformatic tools, the discovery of novel systems is restricted to the available prokaryotic sequence data[2]. Here, to overcome this limitation, we infected Escherichia coli carrying a soil metagenomic DNA library[3] with the lytic coliphage T4 to isolate clones carrying protective genes. Following this approach, we identified Brig1, a DNA glycosylase that excises α-glucosyl-hydroxymethylcytosine nucleobases from the bacteriophage T4 genome to generate abasic sites and inhibit viral replication. Brig1 homologues that provide immunity against T-even phages are present in multiple phage defence loci across distinct clades of bacteria. Our study highlights the benefits of screening unsequenced DNA and reveals prokaryotic DNA glycosylases as important players in the bacteria-phage arms race.},
}

@article {pmid38631646,
year = {2024},
author = {Muscarella, SM and Alduina, R and Badalucco, L and Capri, FC and Di Leto, Y and Gallo, G and Laudicina, VA and Paliaga, S and Mannina, G},
title = {Water reuse of treated domestic wastewater in agriculture: Effects on tomato plants, soil nutrient availability and microbial community structure.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172259},
doi = {10.1016/j.scitotenv.2024.172259},
pmid = {38631646},
issn = {1879-1026},
abstract = {The reuse of treated wastewater (TWW) in agriculture for crop irrigation is desirable. Crop responses to irrigation with TWW depend on the characteristics of TWW and on intrinsic and extrinsic soil properties. The aim of this study was to assess the response of tomato (Solanum lycopersicum L.) cultivated in five different soils to irrigation with TWW, compared to tap water (TAP) and an inorganic NPK solution (IFW). In addition, since soil microbiota play many important roles in plant growth, a metataxonomic analysis was performed to reveal the prokaryotic community structures of TAP, TWW and IFW treated soil, respectively. A 56-days pot experiment was carried out. Plant biometric parameters, and chemical, biochemical and microbiological properties of different soils were investigated. Shoot and root dry and fresh weights, as well as plant height, were the highest in plants irrigated with IFW followed by those irrigated with TWW, and finally with TAP water. Plant biometric parameters were positively affected by soil total organic carbon (TOC) and nitrogen (TN). Electrical conductivity was increased by TWW and IFW, being such an increase proportional to clay and TOC. Soil available P was not affected by TWW, whereas mineral N increased following their application. Total microbial biomass, as well as, main microbial groups were positively affected by TOC and TN, and increased according to the following order: IFW > TWW > TAP. However, the fungi-to-bacteria ratio was lowered in soil irrigated with TWW because of its adverse effect on fungi. The germicidal effect of sodium hypochlorite on soil microorganisms was affected by soil pH. Nutrients supplied by TWW are not sufficient to meet the whole nutrients requirement of tomato, thus integration by fertilization is required. Bacteria were more stimulated than fungi by TWW, thus leading to a lower fungi-to-bacteria ratio. Interestingly, IFW and TWW treatment led to an increased abundance of Proteobacteria and Acidobacteria phyla and Balneimonas, Rubrobacter, and Steroidobacter genera. This soil microbiota structure modulation paralleled a general decrement of fungi versus bacteria abundance ratio, the increment of electrical conductivity and nitrogen content of soil and an improvement of tomato growth. Finally, the potential adverse effect of TWW added with sodium chloride on soil microorganisms depends on soil pH.},
}

@article {pmid38631637,
year = {2024},
author = {Zhang, D and Liu, F and Al, MA and Yang, Y and Yu, H and Li, M and Wu, K and Niu, M and Wang, C and He, Z and Yan, Q},
title = {Nitrogen and sulfur cycling and their coupling mechanisms in eutrophic lake sediment microbiomes.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172518},
doi = {10.1016/j.scitotenv.2024.172518},
pmid = {38631637},
issn = {1879-1026},
abstract = {Microorganisms play important roles in the biogeochemical cycles of lake sediment. However, the integrated metabolic mechanisms governing nitrogen (N) and sulfur (S) cycling in eutrophic lakes remain poorly understood. Here, metagenomic analysis of field and bioreactor enriched sediment samples from a typical eutrophic lake were applied to elucidate the metabolic coupling of N and S cycling. Our results showed significant diverse genes involved in the pathways of dissimilatory sulfur metabolism, denitrification and dissimilatory nitrate reduction to ammonium (DNRA). The N and S associated functional genes and microbial groups generally showed significant correlation with the concentrations of NH4[+], NO2[-] and SO4[2], while with relatively low effects from other environmental factors. The gene-based co-occurrence network indicated clear cooperative interactions between N and S cycling in the sediment. Additionally, our analysis identified key metabolic processes, including the coupled dissimilatory sulfur oxidation (DSO) and DNRA as well as the association of thiosulfate oxidation complex (SOX systems) with denitrification pathway. However, the enriched N removal microorganisms in the bioreactor ecosystem demonstrated an additional electron donor, incorporating both the SOX systems and DSO processes. Metagenome-assembled genomes-based ecological model indicated that carbohydrate metabolism is the key linking factor for the coupling of N and S cycling. Our findings uncover the coupling mechanisms of microbial N and S metabolism, involving both inorganic and organic respiration pathways in lake sediment. This study will enhance our understanding of coupled biogeochemical cycles in lake ecosystems.},
}

@article {pmid38631472,
year = {2024},
author = {Wong, MH and Minkina, T and Vasilchenko, N and Sushkova, S and Delegan, Y and Ranjan, A and Saxena, P and Tarigholizadeh, S and Dudnikova, T and Barbashev, A and Maksimov, A and Faenson, A and Kızılkaya, R},
title = {Assessment of Antibiotic Resistance Genes in Soils Polluted by Chemical and Technogenic Ways with Poly-Aromatic Hydrocarbons and Heavy Metals.},
journal = {Environmental research},
volume = {},
number = {},
pages = {118949},
doi = {10.1016/j.envres.2024.118949},
pmid = {38631472},
issn = {1096-0953},
abstract = {Anthropogenic activities are leaving lots of chemical footprints on the soil. It alters the physiochemical characteristics of the soil thereby modifying the natural soil microbiome. The prevalence of antimicrobial-resistance microbes in polluted soil has gained attention due to its obvious public health risks. This study focused on assessing the prevalence and distribution of antibiotic-resistance genes in polluted soil ecosystems impacted by industrial enterprises in southern Russia. Metagenomic analysis was conducted on soil samples collected from polluted sites using various approaches, and the prevalence of antibiotic-resistance genes was investigated. The results revealed that efflux-encoding pump sequences were the most widely represented group of genes, while genes whose products replaced antibiotic targets were less represented. The level of soil contamination increased, and there was an increase in the total number of antibiotic-resistance genes in proteobacteria, but a decrease in actinobacteria. The study proposed an optimal mechanism for processing metagenomic data in polluted soil ecosystems, which involves mapping raw reads by the KMA method, followed by a detailed study of specific genes. The study's conclusions provide valuable insights into the prevalence and distribution of antibiotic-resistance genes in polluted soils and have been illustrated in heat maps.},
}

@article {pmid38631413,
year = {2024},
author = {Ravichandran, A and Sivapackiyam, J and Periasamy, S},
title = {Oral bacterial insights from a comparative study between healthy and comorbid diseased human individuals.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {106643},
doi = {10.1016/j.micpath.2024.106643},
pmid = {38631413},
issn = {1096-1208},
abstract = {The human oral cavity is colonized by a diverse microbial community, which includes both native and transient colonizers. The microbial composition is crucial for maintaining oral homeostasis, but due to overgrowth or imbalances of these microbial communities, dysbiosis can occur. There is a lack of understanding of the research of native and transient colonizers in the oral cavity of the Indian subpopulation Therefore, in our present study, we explored the role and prevalence of transient and native colonizers between healthy and comorbid oral diseased human individuals. Culture-dependent techniques and culture-independent 16Sr DNA metagenomic analyses were employed to isolate and study the interactions of native and transient colonizers from human oral samples. Among the 66 human individuals of both healthy and comorbid individuals, the most abundant isolate was found to be Bacillus amyloliquefaciens MCC 4424. In addition, the more prevalent culturable isolate from the healthy samples was Streptococcus salivarius MTCC 13009, whereas in comorbid samples Staphylococcus pasteuri MTCC 13076, Rothia dentocariosa MTCC 13010 and Pseudomonas aeruginosa MTCC 13077 were prevalent to a greater extent. 16S rDNA metagenomic analyses revealed the prevalence and abundance of genera such as Bacteroidetes and Proteobacteria in healthy individuals; consequently, Fusobacteria and Firmicutes were observed mostly in comorbid individuals. The significant differences in bacterial population density were observed in terms of Shannon index (p = 0.5145) and Simpson index (p = 0.9061) between the healthy and comorbid groups. B. amyloliquefaciens MCC 4424 exhibits antagonistic behavior when grown as a dual species with native and transient colonizers. This result is very consistent with the findings of antibiofilm studies using confocal laser scanning microscopy, which revealed a significant reduction in biofilm biovolume (73%) and maximum thickness (80%) and an increase in the rough coefficient of biofilms (30%). Our data suggested that B. amyloliquefaciens MCC 4424 can be a native colonizer of Indian sub-populations. It may act as a novel candidate for oral healthcare applications and greatly aids in the regulation of transient species in the oral cavity.},
}

@article {pmid38631239,
year = {2024},
author = {Yu, Y and Trottmann, NF and Schärer, MR and Fenner, K and Robinson, SL},
title = {Substrate promiscuity of xenobiotic-transforming hydrolases from stream biofilms impacted by treated wastewater.},
journal = {Water research},
volume = {256},
number = {},
pages = {121593},
doi = {10.1016/j.watres.2024.121593},
pmid = {38631239},
issn = {1879-2448},
abstract = {Organic contaminants enter aquatic ecosystems from various sources, including wastewater treatment plant effluent. Freshwater biofilms play a major role in the removal of organic contaminants from receiving water bodies, but knowledge of the molecular mechanisms driving contaminant biotransformations in complex stream biofilm (periphyton) communities remains limited. Previously, we demonstrated that biofilms in experimental flume systems grown at higher ratios of treated wastewater (WW) to stream water displayed an increased biotransformation potential for a number of organic contaminants. We identified a positive correlation between WW percentage and biofilm biotransformation rates for the widely-used insect repellent, N,N-diethyl-meta-toluamide (DEET) and a number of other wastewater-borne contaminants with hydrolyzable moieties. Here, we conducted deep shotgun sequencing of flume biofilms and identified a positive correlation between WW percentage and metagenomic read abundances of DEET hydrolase (DH) homologs. To test the causality of this association, we constructed a targeted metagenomic library of DH homologs from flume biofilms. We screened our complete metagenomic library for activity with four different substrates, including DEET, and a subset thereof with 183 WW-related organic compounds. The majority of active hydrolases in the metagenomic library preferred aliphatic and aromatic ester substrates while, remarkably, only a single reference enzyme was capable of DEET hydrolysis. Of the 626 total enzyme-substrate combinations tested, approximately 5% were active enzyme-substrate pairs. Metagenomic DH family homologs revealed a broad substrate promiscuity spanning 22 different compounds when summed across all enzymes tested. We biochemically characterized the most promiscuous and active enzymes identified based on metagenomic analysis from uncultivated Rhodospirillaceae and Planctomycetaceae. In addition to characterizing new DH family enzymes, we exemplified a framework for linking metagenome-guided hypothesis generation with experimental validation. Overall, this study expands the scope of known enzymatic contaminant biotransformations for metagenomic hydrolases from WW-receiving stream biofilm communities.},
}

@article {pmid38631236,
year = {2024},
author = {Wu, H and Nie, WB and Tan, X and Xie, GJ and Qu, H and Zhang, X and Xian, Z and Dai, J and Yang, C and Chen, Y},
title = {Different oxygen affinities of methanotrophs and Comammox Nitrospira inform an electrically induced symbiosis for nitrogen loss.},
journal = {Water research},
volume = {256},
number = {},
pages = {121606},
doi = {10.1016/j.watres.2024.121606},
pmid = {38631236},
issn = {1879-2448},
abstract = {Aerobic methanotrophs establish a symbiotic association with denitrifiers to facilitate the process of aerobic methane oxidation coupled with denitrification (AME-D). However, the symbiosis has been frequently observed in hypoxic conditions continuing to pose an enigma. The present study has firstly characterized an electrically induced symbiosis primarily governed by Methylosarcina and Hyphomicrobium for the AME-D process in a hypoxic niche caused by Comammox Nitrospira. The kinetic analysis revealed that Comammox Nitrospira exhibited a higher apparent oxygen affinity compared to Methylosarcina. While the coexistence of comammox and AME-D resulted in an increase in methane oxidation and nitrogen loss rates, from 0.82 ± 0.10 to 1.72 ± 0.09 mmol CH4 d[-1] and from 0.59 ± 0.04 to 1.30 ± 0.15 mmol N2 d[-1], respectively. Furthermore, the constructed microbial fuel cells demonstrated a pronounced dependence of the biocurrents on AME-D due to oxygen competition, suggesting the involvement of direct interspecies electron transfer in the AME-D process under hypoxic conditions. Metagenomic and metatranscriptomic analysis revealed that Methylosarcina efficiently oxidized methane to formaldehyde, subsequently generating abundant NAD(P)H for nitrate reduction by Hyphomicrobium through the dissimilatory RuMP pathway, leading to CO2 production. This study challenges the conventional understanding of survival mechanism employed by AME-D symbionts, thereby contributing to the characterization responsible for limiting methane emissions and promoting nitrogen removal in hypoxic regions.},
}

@article {pmid38631226,
year = {2024},
author = {Rubin-Blum, M and Makovsky, Y and Rahav, E and Belkin, N and Antler, G and Sisma-Ventura, G and Herut, B},
title = {Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea.},
journal = {Marine environmental research},
volume = {198},
number = {},
pages = {106497},
doi = {10.1016/j.marenvres.2024.106497},
pmid = {38631226},
issn = {1879-0291},
abstract = {Discharge of gas-rich brines fuels productive chemosynthetic ecosystems in the deep sea. In these salty, methanic and sulfidic brines, microbial communities adapt to specific niches along the physicochemical gradients. However, the molecular mechanisms that underpin these adaptations are not fully known. Using metagenomics, we investigated the dense (∼10[6] cell ml[-1]) microbial communities that occupy small deep-sea brine pools found in the Southeastern Mediterranean Sea (1150 m water depth, ∼22 °C, ∼60 PSU salinity, sulfide, methane, ammonia reaching millimolar levels, and oxygen usually depleted), reaching high productivity rates of 685 μg C L[-1] d[-1] ex-situ. We curated 266 metagenome-assembled genomes of bacteria and archaea from the several pools and adjacent sediment-water interface, highlighting the dominance of a single Sulfurimonas, which likely fuels its autotrophy using sulfide oxidation or inorganic sulfur disproportionation. This lineage may be dominant in its niche due to genome streamlining, limiting its metabolic repertoire, particularly by using a single variant of sulfide: quinone oxidoreductase. These primary producers co-exist with ANME-2c archaea that catalyze the anaerobic oxidation of methane. Other lineages can degrade the necromass aerobically (Halomonas and Alcanivorax), or anaerobically through fermentation of macromolecules (e.g., Caldatribacteriota, Bipolaricaulia, Chloroflexota, etc). These low-abundance organisms likely support the autotrophs, providing energy-rich H2, and vital organics such as vitamin B12.},
}

@article {pmid38632506,
year = {2024},
author = {Alkathiry, HA and Alghamdi, SQ and Sinha, A and Margos, G and Stekolnikov, AA and Alagaili, AN and Darby, AC and Makepeace, BL and Khoo, JJ},
title = {Microbiome and mitogenomics of the chigger mite Pentidionis agamae: potential role as an Orientia vector and associations with divergent clades of Wolbachia and Borrelia.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {380},
pmid = {38632506},
issn = {1471-2164},
abstract = {BACKGROUND: Trombiculid mites are globally distributed, highly diverse arachnids that largely lack molecular resources such as whole mitogenomes for the elucidation of taxonomic relationships. Trombiculid larvae (chiggers) parasitise vertebrates and can transmit bacteria (Orientia spp.) responsible for scrub typhus, a zoonotic febrile illness. Orientia tsutsugamushi causes most cases of scrub typhus and is endemic to the Asia-Pacific Region, where it is transmitted by Leptotrombidium spp. chiggers. However, in Dubai, Candidatus Orientia chuto was isolated from a case of scrub typhus and is also known to circulate among rodents in Saudi Arabia and Kenya, although its vectors remain poorly defined. In addition to Orientia, chiggers are often infected with other potential pathogens or arthropod-specific endosymbionts, but their significance for trombiculid biology and public health is unclear.

RESULTS: Ten chigger species were collected from rodents in southwestern Saudi Arabia. Chiggers were pooled according to species and screened for Orientia DNA by PCR. Two species (Microtrombicula muhaylensis and Pentidionis agamae) produced positive results for the htrA gene, although Ca. Orientia chuto DNA was confirmed by Sanger sequencing only in P. agamae. Metagenomic sequencing of three pools of P. agamae provided evidence for two other bacterial associates: a spirochaete and a Wolbachia symbiont. Phylogenetic analysis of 16S rRNA and multi-locus sequence typing genes placed the spirochaete in a clade of micromammal-associated Borrelia spp. that are widely-distributed globally with no known vector. For the Wolbachia symbiont, a genome assembly was obtained that allowed phylogenetic localisation in a novel, divergent clade. Cytochrome c oxidase I (COI) barcodes for Saudi Arabian chiggers enabled comparisons with global chigger diversity, revealing several cases of discordance with classical taxonomy. Complete mitogenome assemblies were obtained for the three P. agamae pools and almost 50 SNPs were identified, despite a common geographic origin.

CONCLUSIONS: P. agamae was identified as a potential vector of Ca. Orientia chuto on the Arabian Peninsula. The detection of an unusual Borrelia sp. and a divergent Wolbachia symbiont in P. agamae indicated links with chigger microbiomes in other parts of the world, while COI barcoding and mitogenomic analyses greatly extended our understanding of inter- and intraspecific relationships in trombiculid mites.},
}

@article {pmid38632370,
year = {2024},
author = {Sterzi, L and Nodari, R and Di Marco, F and Ferrando, ML and Saluzzo, F and Spitaleri, A and Allahverdi, H and Papaleo, S and Panelli, S and Rimoldi, SG and Batisti Biffignandi, G and Corbella, M and Cavallero, A and Prati, P and Farina, C and Cirillo, DM and Zuccotti, G and Bandi, C and Comandatore, F},
title = {Genetic barriers more than environmental associations explain Serratia marcescens population structure.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {468},
pmid = {38632370},
issn = {2399-3642},
abstract = {Bacterial species often comprise well-separated lineages, likely emerged and maintained by genetic isolation and/or ecological divergence. How these two evolutionary actors interact in the shaping of bacterial population structure is currently not fully understood. In this study, we investigate the genetic and ecological drivers underlying the evolution of Serratia marcescens, an opportunistic pathogen with high genomic flexibility and able to colonise diverse environments. Comparative genomic analyses reveal a population structure composed of five deeply-demarcated genetic clusters with open pan-genome but limited inter-cluster gene flow, partially explained by Restriction-Modification (R-M) systems incompatibility. Furthermore, a large-scale research on hundred-thousands metagenomic datasets reveals only a partial habitat separation of the clusters. Globally, two clusters only show a separate gene composition coherent with ecological adaptations. These results suggest that genetic isolation has preceded ecological adaptations in the shaping of the species diversity, an evolutionary scenario coherent with the Evolutionary Extended Synthesis.},
}

@article {pmid38632042,
year = {2024},
author = {Coskun, ÖK and Gomez-Saez, GV and Beren, M and Özcan, D and Günay, SD and Elkin, V and Hoşgörmez, H and Einsiedl, F and Eisenreich, W and Orsi, WD},
title = {Quantifying genome specific carbon fixation in a 750 meter deep subsurface hydrothermal microbial community.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae062},
pmid = {38632042},
issn = {1574-6941},
abstract = {Dissolved inorganic carbon has been hypothesized to stimulate microbial chemoautotrophic activity as a biological sink in the carbon cycle of deep subsurface environments. Here, we tested this hypothesis using quantitative DNA stable isotope probing of metagenome assembled genomes (MAGs) at multiple 13C-labeled bicarbonate concentrations in hydrothermal fluids from a 750 meter deep subsurface aquifer in the Biga Peninsula (Turkey). The diversity of microbial populations assimilating 13C-labeled bicarbonate was significantly different at higher bicarbonate concentrations, and could be linked to four separate carbon fixation pathways encoded within 13C-labeled MAGs. Microbial populations encoding the Calvin-Benson-Bassham cycle had the highest contribution to carbon fixation across all bicarbonate concentrations tested, spanning 1-10 mM. However, out of all the active carbon fixation pathways detected, MAGs affiliated with the phylum Aquificae encoding the reverse tricarboxylic acid (rTCA) pathway were the only microbial populations that exhibited an increased 13C-bicarbonate assimilation under increasing bicarbonate concentrations. Our study provides the first experimental data supporting predictions that increased bicarbonate concentrations may promote chemoautotrophy via the rTCA cycle and its biological sink for deep subsurface inorganic carbon.},
}

@article {pmid38630611,
year = {2024},
author = {Roy, G and Prifti, E and Belda, E and Zucker, JD},
title = {Deep learning methods in metagenomics: a review.},
journal = {Microbial genomics},
volume = {10},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001231},
pmid = {38630611},
issn = {2057-5858},
abstract = {The ever-decreasing cost of sequencing and the growing potential applications of metagenomics have led to an unprecedented surge in data generation. One of the most prevalent applications of metagenomics is the study of microbial environments, such as the human gut. The gut microbiome plays a crucial role in human health, providing vital information for patient diagnosis and prognosis. However, analysing metagenomic data remains challenging due to several factors, including reference catalogues, sparsity and compositionality. Deep learning (DL) enables novel and promising approaches that complement state-of-the-art microbiome pipelines. DL-based methods can address almost all aspects of microbiome analysis, including novel pathogen detection, sequence classification, patient stratification and disease prediction. Beyond generating predictive models, a key aspect of these methods is also their interpretability. This article reviews DL approaches in metagenomics, including convolutional networks, autoencoders and attention-based models. These methods aggregate contextualized data and pave the way for improved patient care and a better understanding of the microbiome's key role in our health.},
}

@article {pmid38630394,
year = {2024},
author = {Balázs, B and Boros, Á and Pankovics, P and Nagy, G and Szekeres, S and Urbán, P and Reuter, G},
title = {Detection and complete genome characterization of a genogroup X (GX) sapovirus (family Caliciviridae) from a golden jackal (Canis aureus) in Hungary.},
journal = {Archives of virology},
volume = {169},
number = {5},
pages = {100},
pmid = {38630394},
issn = {1432-8798},
abstract = {In this study, a novel genotype of genogroup X (GX) sapovirus (family Caliciviridae) was detected in the small intestinal contents of a golden jackal (Canis aureus) in Hungary and characterised by viral metagenomics and next-generation sequencing techniques. The complete genome of the detected strain, GX/Dömsöd/DOCA-11/2020/HUN (PP105600), is 7,128 nt in length. The ORF1- and ORF2-encoded viral proteins (NSP, VP1, and VP2) have 98%, 95%, and 88% amino acid sequence identity to the corresponding proteins of genogroup GX sapoviruses from domestic pigs, but the nucleic acid sequence identity values for their genes are significantly lower (83%, 77%, and 68%). During an RT-PCR-based epidemiological investigation of additional jackal and swine samples, no other GX strains were detected, but a GXI sapovirus strain, GXI/Tótfalu/WBTF-10/2012/HUN (PP105601), was identified in a faecal sample from a wild boar (Sus scrofa). We report the detection of members of two likely underdiagnosed groups of sapoviruses (GX and GXI) in a golden jackal and, serendipitously, in a wild boar in Europe.},
}

@article {pmid38630379,
year = {2024},
author = {Sharafi, R and Salehi Jouzani, G and Karimi, E and Ghanavati, H and Kowsari, M},
title = {Integrating bioprocess and metagenomics studies to enhance humic acid production from rice straw.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {6},
pages = {173},
pmid = {38630379},
issn = {1573-0972},
support = {2-05-05-017-960740//Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)/ ; 2-05-05-017-960740//Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)/ ; 2-05-05-017-960740//Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)/ ; 2-05-05-017-960740//Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)/ ; 2-05-05-017-960740//Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)/ ; },
abstract = {Rice straw burning annually (millions of tons) leads to greenhouse gas emissions, and an alternative solution is producing humic acid with high added-value. This study aimed to examine the influence of a microbial consortium and other additives (chicken manure, urea, olive mill waste, zeolite, and biochar) on the composting process of rice straw and the subsequent production of humic acid. Results showed that among the fungal species, Thermoascus aurantiacus exhibited the most prominent impact in expediting maturation and improving compost quality, and Bacillus subtilis was the most abundant bacterial species based on metagenomics analysis. The highest temperature, C/N ratio reduction, and amount of humic acid production (Respectively in lab 61 °C, 54.67%, 298 g kg[-1] and in pilot level 65 °C, 72.11%, 310 g kg[-1]) were related to treatments containing these microorganisms and other additives except urea. Consequently, T. aurantiacus and B. subtilis can be employed on an industrial scale as compost additives to further elevate quality. Functional analysis showed that the bacterial enzymes in the treatments had the highest metabolic activities, including carbohydrate and amino acid metabolism compared to the control. The maximum enzymatic activities were in the thermophilic phase in treatments which were significantly higher than that in the control. The research emphasizes the importance of identifying and incorporating enzymatically active strains that are suitable for temperature conditions, alongside the native strains in decomposing materials. This strategy significantly improves the composting process and yields high-quality humic acid during the thermophilic phase.},
}

@article {pmid38630153,
year = {2024},
author = {Salam, LB},
title = {Metagenomic investigations into the microbial consortia, degradation pathways, and enzyme systems involved in the biodegradation of plastics in a tropical lentic pond sediment.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {6},
pages = {172},
pmid = {38630153},
issn = {1573-0972},
abstract = {The exploitation of exciting features of plastics for diverse applications has resulted in significant plastic waste generation, which negatively impacts environmental compartments, metabolic processes, and the well-being of aquatic ecosystems biota. A shotgun metagenomic approach was deployed to investigate the microbial consortia, degradation pathways, and enzyme systems involved in the degradation of plastics in a tropical lentic pond sediment (APS). Functional annotation of the APS proteome (ORFs) using the PlasticDB database revealed annotation of 1015 proteins of enzymes such as depolymerase, esterase, lipase, hydrolase, nitrobenzylesterase, chitinase, carboxylesterase, polyesterase, oxidoreductase, polyamidase, PETase, MHETase, laccase, alkane monooxygenase, among others involved in the depolymerization of the plastic polymers. It also revealed that polyethylene glycol (PEG), polyhydroxyalkanoates (PHA), polyhydroxybutyrate (PHB), polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), polyethylene terephthalate (PET), and nylon have the highest number of annotated enzymes. Further annotation using the KEGG GhostKOALA revealed that except for terephthalate, all the other degradation products of the plastic polymers depolymerization such as glyoxylate, adipate, succinate, 1,4-butanediol, ethylene glycol, lactate, and acetaldehyde were further metabolized to intermediates of the tricarboxylic acid cycle. Taxonomic characterization of the annotated proteins using the AAI Profiler and BLASTP revealed that Pseudomonadota members dominate most plastic types, followed by Actinomycetota and Acidobacteriota. The study reveals novel plastic degraders from diverse phyla hitherto not reported to be involved in plastic degradation. This suggests that plastic pollution in aquatic environments is prevalent with well-adapted degrading communities and could be the silver lining in mitigating the impacts of plastic pollution in aquatic environments.},
}

@article {pmid38629898,
year = {2024},
author = {Li, W and He, Y and Li, Y and Li, X and Bian, T and Liu, T and Liu, X and Jiang, W},
title = {Metagenomic next-generation sequencing for the diagnosis of neurobrucellosis.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {},
doi = {10.2217/fmb-2023-0177},
pmid = {38629898},
issn = {1746-0921},
support = {XJZT19MJ21//Discipline Promotion Project of Xijing Hospital/ ; },
abstract = {Objective: This study investigates the application of metagenomic next-generation sequencing (mNGS) in the diagnosis of neurobrucellosis (NB). Methods: We retrospectively analyzed patients diagnosed with NB who underwent cerebrospinal fluid (CSF) mNGS testing in Xijing Hospital from 2015 to 2021. Results: Among the 20 individuals included in the study, the serum rose bengal test was positive in 11 out of 16 cases, serum agglutination test was positive in 13 out of 16 cases, CSF culture was positive in 6 out of 11 cases, and CSF mNGS tests were positive in 18 out of 20 cases. Conclusion: CSF mNGS demonstrates superior sensitivity; therefore, it is recommended to collect CSF for mNGS testing prior to antibiotic therapy when NB is suspected.},
}

@article {pmid38629830,
year = {2024},
author = {Castro, AE and Montecillo, AD and Villanueva, RMD and Obusan, MCM},
title = {Bacterial community profiles of select tributaries of Laguna Lake in the Philippines.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0116123},
doi = {10.1128/mra.01161-23},
pmid = {38629830},
issn = {2576-098X},
abstract = {Laguna Lake is known for its ecological, economic, and cultural importance. Effects of urbanization and accumulation of emerging pollutants have been associated with its water quality; however, the microbial ecology of its tributaries remains to be explored. We report bacterial community profiles from shotgun metagenomes of its select tributary waters.},
}

@article {pmid38629119,
year = {2024},
author = {Mason, B and Cervena, B and Frias, L and Goossens, B and Hasegawa, H and Keuk, K and Langgeng, A and Majewski, K and Matsumoto, T and Matsuura, K and Mendonça, R and Okamoto, M and Peter, S and Petrzelkova, KJ and Sipangkui, S and Xu, Z and Pafco, B and MacIntosh, AJJ},
title = {Novel insight into the genetic diversity of strongylid nematodes infecting South-East and East Asian primates.},
journal = {Parasitology},
volume = {},
number = {},
pages = {1-9},
doi = {10.1017/S0031182024000386},
pmid = {38629119},
issn = {1469-8161},
support = {15H04283//Japan Society for the Promotion of Science/ ; 16H06181//Japan Society for the Promotion of Science/ ; 20H03333//Japan Society for the Promotion of Science/ ; 24770232//Japan Society for the Promotion of Science/ ; 446//Japan Society for the Promotion of Science/ ; 22-16475S//Grantová Agentura České Republiky/ ; },
abstract = {With many non-human primates (NHPs) showing continued population decline, there is an ongoing need to better understand their ecology and conservation threats. One such threat is the risk of disease, with various bacterial, viral and parasitic infections previously reported to have damaging consequences for NHP hosts. Strongylid nematodes are one of the most commonly reported parasitic infections in NHPs. Current knowledge of NHP strongylid infections is restricted by their typical occurrence as mixed infections of multiple genera, which are indistinguishable through traditional microscopic approaches. Here, modern metagenomics approaches were applied for insight into the genetic diversity of strongylid infections in South-East and East Asian NHPs. We hypothesized that strongylid nematodes occur in mixed communities of multiple taxa, dominated by Oesophagostomum, matching previous findings using single-specimen genetics. Utilizing the Illumina MiSeq platform, ITS-2 strongylid metabarcoding was applied to 90 samples from various wild NHPs occurring in Malaysian Borneo and Japan. A clear dominance of Oesophagostomum aculeatum was found, with almost all sequences assigned to this species. This study suggests that strongylid communities of Asian NHPs may be less species-rich than those in African NHPs, where multi-genera communities are reported. Such knowledge contributes baseline data, assisting with ongoing monitoring of health threats to NHPs.},
}

@article {pmid38628865,
year = {2024},
author = {Zhu, Q and Cui, J and Liu, S and Wei, S and Wu, Q and You, Y},
title = {Synbiotic regulates gut microbiota in patients with lupus nephritis: an analysis using metagenomic and metabolome sequencing.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1295378},
pmid = {38628865},
issn = {1664-302X},
abstract = {OBJECTIVE: To investigate the changes in gut microbes and their metabolites after administering synbiotics to patients with new-onset lupus nephritis (LN) treated using a conventional method and provide a theoretical basis for finding new targets for the diagnosis and treatment of LN.

METHODS: In this study, a total of 12 participants were divided into the lupus and synbiotic groups. Stool samples and clinical data were collected before and after treatment for metagenomic, nontargeted metabolomic, and statistical analyses.

RESULTS: The relative abundances of the pathogenic bacteria Prevotella, Bacteroides, and Enterobacteriaceae_unclassified decreased after synbiotic treatment, whereas the abundances of Actinobacteria and Firmicutes increased. Further, the Firmicutes to Bacteroidetes ratio increased; however, the difference was not statistically significant (p > 0.05). α diversity analysis showed no significant differences in the intestinal microbial richness and diversity index of patients with LN between the groups before and after treatment (p > 0.05). β analysis showed the differences in the community structure between the samples of the two groups before and after treatment. Linear discriminant analysis effect size and receiver operating characteristic curve analyses revealed that Negativicutes (AUC = 0.9722) and Enterobacteriaceae_unclassified (AUC = 0.9722) were the best predictors of the lupus and synbiotic groups, respectively, before and after treatment. Joint analyses revealed that amino acid biosynthesis, aminoacyl-tRNA biosynthesis, purine metabolism, and other metabolic pathways may be involved in the changes in the metabolic function of patients with LN after the addition of synbiotics. Spearman's correlation analysis revealed the interaction between clinical features and flora, and flora exhibited a complex biological network regulatory relationship.

CONCLUSION: Synbiotics regulate the metabolic functions of intestinal microorganisms in patients with LN and play a role in various biological functions. Synbiotic supplements may be safe and promising candidates for patients with LN.},
}

@article {pmid38628241,
year = {2024},
author = {Yuan, L and Lai, LM and Zhu, X and Rui, Z and Liu, Y and Chen, Q},
title = {Haemophilus aphrophilus and Eikenella corrodens Coinfection of Brain: An Unusual Case from China.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {1439-1445},
pmid = {38628241},
issn = {1178-6973},
abstract = {BACKGROUND: The HACEK group comprises Haemophilus spp., Aggregatibacter actinomycetemcomitans, Cardiobacterium hominis, Eikenella corrodens, and Kingella kingae, are Gram-negative bacteria that are slow-growing and fastidious. These organisms are common causes of culture-negative endocarditis. However, brain abscesses caused by Haemophilus aphrophilus and E. corrodens have been rarely reported. The case we describe, which was promptly identified and successfully treated, will be meaningful for the diagnosis and treatment of such infectious diseases.

CASE PRESENTATION: Herein, we report a case of brain abscess in a young man who was infected with Haemophilus aphrophilus and E. corrodens. The patient was admitted to the hospital with sudden onset of vomiting, coma, and fever. Magnetic resonance imaging (MRI) of the brain and cerebrospinal fluid cell counts suggested cerebral abscess, he underwent drainage of the abscess and empirical antimicrobial therapy of meropenem (2 g every 8 hours) and linezolid (0.6 g every 12 hours) for more than 10 days without significant improvement. Metagenomic next-generation sequencing (mNGS) of drainage fluid and matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) detection for isolated bacteria from samples suggested the presence of H. aphrophilus and E. corrodens. After 7 weeks of ceftriaxone (2 g every 12 hours) and meropenem (2 g every 8 hours) intravenously, the patient was discharged with a normal temperature and brain MRI showed improvement of the lesion.

CONCLUSION: Similar cases reported in previous studies were always associated with bacterial blood dissemination after dental surgery or myocarditis; however, the patient in our case had no any associated risk factors. As far as we know, this is the only case of central nervous system infection caused by H. aphrophilus and E. corrodens that has utilized combined mNGS and MALDI-TOF MS in the diagnosis.},
}

@article {pmid38628239,
year = {2024},
author = {Li, S and Han, X and Ma, J and Huang, GH and Yang, ST and Wang, CM},
title = {Study on mNGS Technique in Diagnosing Pneumocystis jirovecii Pneumonia in Non-HIV-Infected Patients.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {1397-1405},
pmid = {38628239},
issn = {1178-6973},
abstract = {OBJECTIVE: To investigate the value of metagenomic Next-Generation Sequencing (mNGS) in diagnosing Pneumocystis jirovecii pneumonia (PJP) in non-human immunodeficiency virus (HIV)-infected patients.

METHODS: In this retrospective study, non-HIV-infected patients with PJP and those diagnosed with non-PJP from August 2022 to December 2024 were selected as subjects. The presence of Pneumocystis jirovecii (PJ) and other co-pathogens in bronchoalveolar lavage fluid (BALF) was analyzed, and the diagnostic efficacy of NGS, polymerase chain reaction (PCR) and serum 1,3-β-D-glucan (BDG) in PJP was compared with the reference standard of clinical compound diagnosis.

RESULTS: Eighty-nine non-HIV-infected patients were recruited, with dyspnea as the primary symptom (69.66%) and solid malignant tumor as the most common underlying disease (20.22%). Taking clinical compound diagnosis as the reference standard, the sensitivity, specificity, negative predictive value and positive predictive value of mNGS were higher than those detected by PCR and serum BDG. Among 42 non-HIV-infected patients with PJP who underwent mNGS and conventional pathogen detection of BALF, 6 had simple PJ infection and 36 had combined PJ infection. The detection rate of mNGS in mixed infections was significantly higher than that of conventional pathogen detection (85.71 vs 61.70%, P = 0.012). A total of 127 pathogens were detected in BALF using mNGS, among which fungi had the highest detection rate (46.46%). The fungi, viruses and bacteria detected were mainly Pneumocystis jirovecii, human gammaherpesvirus 4 and Acinetobacter baumannii.

CONCLUSION: mNGS is highly effective in diagnosing non-HIV-infected patients with PJP and exhibits ideal performance in the detection of co-pathogens. In addition, it has certain value for clinical diagnosis and guidance of targeted anti-infective drug treatment.},
}

@article {pmid38627869,
year = {2024},
author = {Ortiz Sanjuán, JM and Argüello, H and Cabrera-Rubio, R and Crispie, F and Cotter, PD and Garrido, JJ and Ekhlas, D and Burgess, CM and Manzanilla, EG},
title = {Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {18},
pmid = {38627869},
issn = {2524-4671},
support = {0376//Teagasc Walsh Scholarship Programme/ ; 0376//Teagasc Walsh Scholarship Programme/ ; BEAGAL-18-106//Spanish Government (Ministerio de Educación y Formación Profesional)/ ; },
abstract = {BACKGROUND: Post weaning diarrhoea (PWD) causes piglet morbidity and mortality at weaning and is a major driver for antimicrobial use worldwide. New regulations in the EU limit the use of in-feed antibiotics (Ab) and therapeutic zinc oxide (ZnO) to prevent PWD. New approaches to control PWD are needed, and understanding the role of the microbiota in this context is key. In this study, shotgun metagenome sequencing was used to describe the taxonomic and functional evolution of the faecal microbiota of the piglet during the first two weeks post weaning within three experimental groups, Ab, ZnO and no medication, on commercial farms using antimicrobials regularly in the post weaning period.

RESULTS: Diversity was affected by day post weaning (dpw), treatment used and diarrhoea but not by the farm. Microbiota composition evolved towards the dominance of groups of species such as Prevotella spp. at day 14dpw. ZnO inhibited E. coli overgrowth, promoted higher abundance of the family Bacteroidaceae and decreased Megasphaera spp. Animals treated with Ab exhibited inconsistent taxonomic changes across time points, with an overall increase of Limosilactobacillus reuteri and Megasphaera elsdenii. Samples from non-medicated pigs showed virulence-related functions at 7dpw, and specific ETEC-related virulence factors were detected in all samples presenting diarrhoea. Differential microbiota functions of pigs treated with ZnO were related to sulphur and DNA metabolism, as well as mechanisms of antimicrobial and heavy metal resistance, whereas Ab treated animals exhibited functions related to antimicrobial resistance and virulence.

CONCLUSION: Ab and particularly ZnO maintained a stable microbiota composition and functionality during the two weeks post weaning, by limiting E. coli overgrowth, and ultimately preventing microbiota dysbiosis. Future approaches to support piglet health should be able to reproduce this stable gut microbiota transition during the post weaning period, in order to maintain optimal gut physiological and productive conditions.},
}

@article {pmid38627868,
year = {2024},
author = {Ho, M and Nguyen, HN and Van Hoang, M and Bui, TTT and Vu, BQ and Dinh, THT and Vo, HTM and Blaydon, DC and Eldirany, SA and Bunick, CG and Bui, CB},
title = {Altered skin microbiome, inflammation, and JAK/STAT signaling in Southeast Asian ichthyosis patients.},
journal = {Human genomics},
volume = {18},
number = {1},
pages = {38},
pmid = {38627868},
issn = {1479-7364},
support = {K08AR070290/AR/NIAMS NIH HHS/United States ; },
abstract = {BACKGROUND: Congenital ichthyosis (CI) is a collective group of rare hereditary skin disorders. Patients present with epidermal scaling, fissuring, chronic inflammation, and increased susceptibility to infections. Recently, there is increased interest in the skin microbiome; therefore, we hypothesized that CI patients likely exhibit an abnormal profile of epidermal microbes because of their various underlying skin barrier defects. Among recruited individuals of Southeast Asian ethnicity, we performed skin meta-genomics (i.e., whole-exome sequencing to capture the entire multi-kingdom profile, including fungi, protists, archaea, bacteria, and viruses), comparing 36 CI patients (representing seven subtypes) with that of 15 CI age-and gender-matched controls who had no family history of CI.

RESULTS: This case-control study revealed 20 novel and 31 recurrent pathogenic variants. Microbiome meta-analysis showed distinct microbial populations, decreases in commensal microbiota, and higher colonization by pathogenic species associated with CI; these were correlated with increased production of inflammatory cytokines and Th17- and JAK/STAT-signaling pathways in peripheral blood mononuclear cells. In the wounds of CI patients, we identified specific changes in microbiota and alterations in inflammatory pathways, which are likely responsible for impaired wound healing.

CONCLUSIONS: Together, this research enhances our understanding of the microbiological, immunological, and molecular properties of CI and should provide critical information for improving therapeutic management of CI patients.},
}