@article {pmid38622738,
year = {2024},
author = {Wu, LY and Wijesekara, Y and Piedade, GJ and Pappas, N and Brussaard, CPD and Dutilh, BE},
title = {Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {97},
pmid = {38622738},
issn = {1474-760X},
support = {Consolidator grant 865694//H2020 European Research Council/ ; Consolidator grant 865694//H2020 European Research Council/ ; 955974//H2020 Marie Skłodowska-Curie Actions/ ; grant ALWPP.2016.019//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; grant ALWPP.2016.019//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Benchmarking ; Metagenome ; Ecosystem ; Metagenomics/methods ; Computational Biology/methods ; Databases, Genetic ; *Viruses/genetics ; },
abstract = {BACKGROUND: As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identification tools have been developed for this task, making it challenging to choose the right tools, parameters, and cutoffs. As all these tools measure different biological signals, and use different algorithms and training and reference databases, it is imperative to conduct an independent benchmarking to give users objective guidance.

RESULTS: We compare the performance of nine state-of-the-art virus identification tools in thirteen modes on eight paired viral and microbial datasets from three distinct biomes, including a new complex dataset from Antarctic coastal waters. The tools have highly variable true positive rates (0-97%) and false positive rates (0-30%). PPR-Meta best distinguishes viral from microbial contigs, followed by DeepVirFinder, VirSorter2, and VIBRANT. Different tools identify different subsets of the benchmarking data and all tools, except for Sourmash, find unique viral contigs. Performance of tools improved with adjusted parameter cutoffs, indicating that adjustment of parameter cutoffs before usage should be considered.

CONCLUSIONS: Together, our independent benchmarking facilitates selecting choices of bioinformatic virus identification tools and gives suggestions for parameter adjustments to viromics researchers.},
}

*Benchmarking
Metagenome
Ecosystem
Metagenomics/methods
Computational Biology/methods
Databases, Genetic
*Viruses/genetics

@article {pmid38622589,
year = {2024},
author = {Gao, J and Yang, Y and Xiang, X and Zheng, H and Yi, X and Wang, F and Liang, Z and Chen, D and Shi, W and Wang, L and Wu, D and Feng, S and Huang, Q and Li, X and Shu, W and Chen, R and Zhong, N and Wang, Z},
title = {Human genetic associations of the airway microbiome in chronic obstructive pulmonary disease.},
journal = {Respiratory research},
volume = {25},
number = {1},
pages = {165},
pmid = {38622589},
issn = {1465-993X},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/diagnosis/genetics/complications ; *Microbiota/genetics ; Sputum ; Transcriptome ; Human Genetics ; Adaptor Proteins, Signal Transducing/genetics ; },
abstract = {Little is known about the relationships between human genetics and the airway microbiome. Deeply sequenced airway metagenomics, by simultaneously characterizing the microbiome and host genetics, provide a unique opportunity to assess the microbiome-host genetic associations. Here we performed a co-profiling of microbiome and host genetics with the identification of over 5 million single nucleotide polymorphisms (SNPs) through deep metagenomic sequencing in sputum of 99 chronic obstructive pulmonary disease (COPD) and 36 healthy individuals. Host genetic variation was the most significant factor associated with the microbiome except for geography and disease status, with its top 5 principal components accounting for 12.11% of the microbiome variability. Within COPD individuals, 113 SNPs mapped to candidate genes reported as genetically associated with COPD exhibited associations with 29 microbial species and 48 functional modules (P < 1 × 10[-5]), where Streptococcus salivarius exhibits the strongest association to SNP rs6917641 in TBC1D32 (P = 9.54 × 10[-8]). Integration of concurrent host transcriptomic data identified correlations between the expression of host genes and their genetically-linked microbiome features, including NUDT1, MAD1L1 and Veillonella parvula, TTLL9 and Stenotrophomonas maltophilia, and LTA4H and Haemophilus influenzae. Mendelian randomization analyses revealed a potential causal link between PARK7 expression and microbial type III secretion system, and a genetically-mediated association between COPD and increased relative abundance of airway Streptococcus intermedius. These results suggest a previously underappreciated role of host genetics in shaping the airway microbiome and provide fresh hypotheses for genetic-based host-microbiome interactions in COPD.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/diagnosis/genetics/complications
*Microbiota/genetics
Sputum
Transcriptome
Human Genetics
Adaptor Proteins, Signal Transducing/genetics

@article {pmid38621967,
year = {2024},
author = {Wang, ZH and Liu, S and Yang, G and Lu, ZY and Zhu, RQ and Li, Y and Shen, Y and Kang, LP and Chen, ML},
title = {[Effects of organic fertilizer from traditional Chinese medicine residues on growth and soil microbial community of Salvia miltiorrhiza by metagenomic technique].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {49},
number = {5},
pages = {1206-1216},
doi = {10.19540/j.cnki.cjcmm.20231213.101},
pmid = {38621967},
issn = {1001-5302},
mesh = {Soil/chemistry ; *Salvia miltiorrhiza/chemistry ; Fertilizers ; Medicine, Chinese Traditional ; Bacteria/genetics ; *Mycobiome ; Soil Microbiology ; },
abstract = {Soil microbiome is a key evaluation index of soil health. Previous studies have shown that organic fertilizer from traditional Chinese medicine(TCM)residues can improve the yield and quality of cultivated traditional Chinese medicinal materials. However, there are few reports on the effects of organic fertilizer from TCM residues on soil microbiome. Therefore, on the basis of evaluating the effects of organic fertilizer from TCM residues on the yield and quality of cultivated Salvia miltiorrhiza, the metagenomic sequencing technique was used to study the effects of organic fertilizer from TCM residues on rhizosphere microbiome community and function of cultivated S. miltiorrhiza. The results showed that:(1) the application of organic fertilizer from TCM residues promoted the growth of S. miltiorrhiza and the accumulation of active components, and the above-ground and underground dry weight and fresh weight of S. miltiorrhiza increased by 371.4%, 288.3%, 313.4%, and 151.9%. The increases of rosmarinic acid and salvianolic acid B were 887.0% and 183.0%.(2)The application of organic fertilizer from TCM residues significantly changed the rhizosphere bacterial and fungal community structures, and the microbial community composition was significantly different.(3)The relative abundance of soil-beneficial bacteria, such as Nitrosospira multiformis, Bacillus subtilis, Lysobacter enzymogenes, and Trichoderma was significantly increased by the application of organic fertilizer from TCM residues.(4)KEGG function prediction analysis showed that metabolism-related microorganisms were more easily enriched in the soil environment after organic fertilizer application. The abundance of functional genes related to nitrification and denitrification could also be increased after the application of organic fertilizer from TCM residues. The results of this study provide guidance for the future application of organic fertilizer from TCM residues in the cultivation of traditio-nal Chinese medicinal materials and enrich the content of green cultivation technology of traditional Chinese medicinal materials.},
}

Soil/chemistry
*Salvia miltiorrhiza/chemistry
Fertilizers
Medicine, Chinese Traditional
Bacteria/genetics
*Mycobiome
Soil Microbiology

@article {pmid38617453,
year = {2024},
author = {Chen, SJ and Zhang, DY and Wu, X and Zhang, FM and Cui, BT and Huang, YH and Zhang, ZL and Wang, R and Bai, FH},
title = {Washed microbiota transplantation for Crohn's disease: A metagenomic, metatranscriptomic, and metabolomic-based study.},
journal = {World journal of gastroenterology},
volume = {30},
number = {11},
pages = {1572-1587},
pmid = {38617453},
issn = {2219-2840},
mesh = {Humans ; Amino Acids ; *Antifibrinolytic Agents ; *Crohn Disease/diagnosis/therapy ; Escherichia coli ; Metagenome ; *Microbiota ; Prospective Studies ; },
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is a promising therapeutic approach for treating Crohn's disease (CD). The new method of FMT, based on the automatic washing process, was named as washed microbiota transplantation (WMT). Most existing studies have focused on observing the clinical phenomena. However, the mechanism of action of FMT for the effective management of CD-particularly in-depth multi-omics analysis involving the metagenome, metatranscriptome, and metabolome-has not yet been reported.

AIM: To assess the efficacy of WMT for CD and explore alterations in the microbiome and metabolome in response to WMT.

METHODS: We conducted a prospective, open-label, single-center clinical study. Eleven CD patients underwent WMT. Their clinical responses (defined as a decrease in their CD Activity Index score of > 100 points) and their microbiome (metagenome, metatranscriptome) and metabolome profiles were evaluated three months after the procedure.

RESULTS: Seven of the 11 patients (63.6%) showed an optimal clinical response three months post-WMT. Gut microbiome diversity significantly increased after WMT, consistent with improved clinical symptoms. Comparison of the metagenome and metatranscriptome analyses revealed consistent alterations in certain strains, such as Faecalibacterium prausnitzii, Roseburia intestinalis, and Escherichia coli. In addition, metabolomics analyses demonstrated that CD patients had elevated levels of various amino acids before treatment compared to the donors. However, levels of vital amino acids that may be associated with disease progression (e.g., L-glutamic acid, gamma-glutamyl-leucine, and prolyl-glutamine) were reduced after WMT.

CONCLUSION: WMT demonstrated therapeutic efficacy in CD treatment, likely due to the effective reconstruction of the patient's microbiome. Multi-omics techniques can effectively help decipher the potential mechanisms of WMT in treating CD.},
}

Humans
Amino Acids
*Antifibrinolytic Agents
*Crohn Disease/diagnosis/therapy
Escherichia coli
Metagenome
*Microbiota
Prospective Studies

@article {pmid38561162,
year = {2024},
author = {Ozsefil, IC and Miraloglu, IH and Ozbayram, EG and Ince, B and Ince, O},
title = {Bioaugmentation of anaerobic digesters with the enriched lignin-degrading microbial consortia through a metagenomic approach.},
journal = {Chemosphere},
volume = {355},
number = {},
pages = {141831},
doi = {10.1016/j.chemosphere.2024.141831},
pmid = {38561162},
issn = {1879-1298},
mesh = {*Lignin/metabolism ; Microbial Consortia ; Bioreactors ; Anaerobiosis ; *Microbiota ; Methane/metabolism ; Biofuels ; },
abstract = {The recalcitrance of lignin impedes the efficient utilization of lignocellulosic biomass, hindering the efficient production of biogas and value-added materials. Despite the emergence of anaerobic digestion as a superior alternative to the aerobic method for lignin processing, achieving its feasibility requires thorough characterization of lignin-degrading anaerobic microorganisms, assessment of their biomethane production potential, and a comprehensive understanding of the degradation pathway. This study aimed to address the aforementioned necessities by bioaugmenting seed sludge with three distinct enriched lignin-degrading microbial consortia at both 25 °C and 37 °C. Enhanced biomethane yields was detected in the bioaugmented digesters, while the highest production was observed as 188 mLN CH4 gVS[-1] in digesters operated at 37 °C. Moreover, methane yield showed a significant improvement in the samples at 37 °C ranging from 110% to 141% compared to the control, demonstrating the efficiency of the enriched lignin-degrading microbial community. Temperature and substrate were identified as key factors influencing microbial community dynamics. The observation that microbial communities tended to revert to the initial state after lignin depletion, indicating the stability of the overall microbiota composition in the digesters, is a promising finding for large-scale studies. Noteworthy candidates for lignin degradation, including Sporosarcina psychrophila, Comamonas aquatica, Shewanella baltica, Pseudomonas sp. C27, and Brevefilum fermentans were identified in the bioaugmented samples. PICRUSt2 predictions suggest that the pathway and specific proteins involved in anaerobic lignin degradation might share similarities with those engaged in the degradation of aromatic compounds.},
}

*Lignin/metabolism
Microbial Consortia
Bioreactors
Anaerobiosis
*Microbiota
Methane/metabolism
Biofuels

@article {pmid37231259,
year = {2024},
author = {Pinto, Y and Chakraborty, M and Jain, N and Bhatt, AS},
title = {Phage-inclusive profiling of human gut microbiomes with Phanta.},
journal = {Nature biotechnology},
volume = {42},
number = {4},
pages = {651-662},
pmid = {37231259},
issn = {1546-1696},
support = {R01AI14862302//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AI14375702//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1S10OD02014101//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 5T32HG000044-25//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; n/a//EIF | Stand Up To Cancer (SU2C)/ ; n/a//Alfred P. Sloan Foundation/ ; Dean's Fellowship//SU | School of Medicine, Stanford University (Stanford School of Medicine, Stanford University)/ ; NDSEG fellowship//U.S. Department of Defense (United States Department of Defense)/ ; },
mesh = {Adult ; Humans ; *Bacteriophages/genetics ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; *Viruses/genetics ; DNA Viruses/genetics ; },
abstract = {Due to technical limitations, most gut microbiome studies have focused on prokaryotes, overlooking viruses. Phanta, a virome-inclusive gut microbiome profiling tool, overcomes the limitations of assembly-based viral profiling methods by using customized k-mer-based classification tools and incorporating recently published catalogs of gut viral genomes. Phanta's optimizations consider the small genome size of viruses, sequence homology with prokaryotes and interactions with other gut microbes. Extensive testing of Phanta on simulated data demonstrates that it quickly and accurately quantifies prokaryotes and viruses. When applied to 245 fecal metagenomes from healthy adults, Phanta identifies ~200 viral species per sample, ~5× more than standard assembly-based methods. We observe a ~2:1 ratio between DNA viruses and bacteria, with higher interindividual variability of the gut virome compared to the gut bacteriome. In another cohort, we observe that Phanta performs equally well on bulk versus virus-enriched metagenomes, making it possible to study prokaryotes and viruses in a single experiment, with a single analysis.},
}

Adult
Humans
*Bacteriophages/genetics
*Gastrointestinal Microbiome/genetics
*Microbiota
*Viruses/genetics
DNA Viruses/genetics

@article {pmid38614128,
year = {2024},
author = {Li, C and Guo, X and He, Y and Wang, J and Hao, J and Liu, X},
title = {Cohabiting with ulcerative colitis patients decreases differences of gut microbiome between healthy individuals and the patients.},
journal = {Annals of medicine},
volume = {56},
number = {1},
pages = {2337712},
pmid = {38614128},
issn = {1365-2060},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colitis, Ulcerative/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Inflammation ; },
abstract = {Background: Ulcerative colitis (UC), which is characterized by chronic relapsing inflammation of the colon, results from a complex interaction of factors involving the host, environment, and microbiome. The present study aimed to investigate the gut microbial composition and metabolic variations in patients with UC and their spouses. Materials and Methods: Fecal samples were collected from 13 healthy spouses and couples with UC. 16S rRNA gene amplicon sequencing and metagenomics sequencing were used to analyze gut microbiota composition, pathways, gene expression, and enzyme activity, followed by the Kyoto Encyclopedia of Genes and Genomes. Results: We found that the microbiome diversity of couples with UC decreased, especially that of UC patients. Bacterial composition, such as Firmicutes, was altered between UC patients and healthy controls, but was not significantly different between UC patients and their spouses. This has also been observed in pathways, such as metabolism, genetic information processing, organismal systems, and human diseases. However, the genes and enzymes of spouses with UC were not significantly different from those of healthy individuals. Furthermore, the presence of Faecalibacterium correlated with oxidative phosphorylation, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, and the bacterial secretion system, showed a marked decline in the UC group compared with their spouses, but did not vary between healthy couples. Conclusion: Our study revealed that cohabitation with UC patients decreased differences in the gut microbiome between healthy individuals and patients. Not only was the composition and diversity of the microbiota diminished, but active pathways also showed some decline. Furthermore, Firmicutes, Faecalibacterium, and the four related pathways may be associated with the pathological state of the host rather than with human behavior.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Colitis, Ulcerative/genetics
RNA, Ribosomal, 16S/genetics
*Microbiota
Inflammation

@article {pmid38613119,
year = {2024},
author = {Zhou, Y and Zeng, Y and Wang, R and Pang, J and Wang, X and Pan, Z and Jin, Y and Chen, Y and Yang, Y and Ling, W},
title = {Resveratrol Improves Hyperuricemia and Ameliorates Renal Injury by Modulating the Gut Microbiota.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38613119},
issn = {2072-6643},
support = {81730090//National Natural Science Foundation of China/ ; 81973022//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Mice ; *Hyperuricemia/drug therapy ; *Gastrointestinal Microbiome ; Resveratrol/pharmacology ; Uric Acid ; Kidney Tubules ; Inflammation ; },
abstract = {Resveratrol (RES) has been reported to prevent hyperuricemia (HUA); however, its effect on intestinal uric acid metabolism remains unclear. This study evaluated the impact of RES on intestinal uric acid metabolism in mice with HUA induced by a high-fat diet (HFD). Moreover, we revealed the underlying mechanism through metagenomics, fecal microbiota transplantation (FMT), and 16S ribosomal RNA analysis. We demonstrated that RES reduced the serum uric acid, creatinine, urea nitrogen, and urinary protein levels, and improved the glomerular atrophy, unclear renal tubule structure, fibrosis, and renal inflammation. The results also showed that RES increased intestinal uric acid degradation. RES significantly changed the intestinal flora composition of HFD-fed mice by enriching the beneficial bacteria that degrade uric acid, reducing harmful bacteria that promote inflammation, and improving microbial function via the upregulation of purine metabolism. The FMT results further showed that the intestinal microbiota is essential for the effect of RES on HUA, and that Lactobacillus may play a key role in this process. The present study demonstrated that RES alleviates HFD-induced HUA and renal injury by regulating the gut microbiota composition and the metabolism of uric acid.},
}

Animals
Mice
*Hyperuricemia/drug therapy
*Gastrointestinal Microbiome
Resveratrol/pharmacology
Uric Acid
Kidney Tubules
Inflammation

@article {pmid38612976,
year = {2024},
author = {Fagunwa, O and Davies, K and Bradbury, J},
title = {The Human Gut and Dietary Salt: The Bacteroides/Prevotella Ratio as a Potential Marker of Sodium Intake and Beyond.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38612976},
issn = {2072-6643},
support = {FMoH/PTDF//Federal Government of Nigeria/ ; NA//University of Huddersfield/ ; publishing//Queen's University Belfast/ ; },
mesh = {Humans ; *Sodium Chloride, Dietary ; *Microbiota ; Bacteroides ; Bacteroidetes ; Firmicutes ; Prevotella ; Sodium ; },
abstract = {The gut microbiota is a dynamic ecosystem that plays a pivotal role in maintaining host health. The perturbation of these microbes has been linked to several health conditions. Hence, they have emerged as promising targets for understanding and promoting good health. Despite the growing body of research on the role of sodium in health, its effects on the human gut microbiome remain under-explored. Here, using nutrition and metagenomics methods, we investigate the influence of dietary sodium intake and alterations of the human gut microbiota. We found that a high-sodium diet (HSD) altered the gut microbiota composition with a significant reduction in Bacteroides and inverse increase in Prevotella compared to a low-sodium diet (LSD). However, there is no clear distinction in the Firmicutes/Bacteroidetes (F/B) ratio between the two diet types. Metabolic pathway reconstruction revealed the presence of sodium reabsorption genes in the HSD, but not LSD. Since it is currently difficult in microbiome studies to confidently associate the F/B ratio with what is considered healthy (e.g., low sodium) or unhealthy (e.g., high sodium), we suggest that the use of a genus-based ratio such as the Bacteroides/Prevotella (B/P) ratio may be more beneficial for the application of microbiome studies in health.},
}

Humans
*Sodium Chloride, Dietary
*Microbiota
Bacteroides
Bacteroidetes
Firmicutes
Prevotella
Sodium

@article {pmid38557040,
year = {2024},
author = {Li, C and Lü, F and Peng, W and He, PJ and Zhang, H},
title = {Functional Redundant Microbiome Enhanced Anaerobic Digestion Efficiency under Ammonium Inhibition Conditions.},
journal = {Environmental science & technology},
volume = {58},
number = {15},
pages = {6659-6669},
doi = {10.1021/acs.est.4c01227},
pmid = {38557040},
issn = {1520-5851},
mesh = {Anaerobiosis ; *Ammonium Compounds ; Bioreactors ; *Microbiota ; Metagenome ; Methane ; },
abstract = {Revealing the role of functional redundancy is of great importance considering its key role in maintaining the stability of microbial ecosystems in response to various disturbances. However, experimental evidence on this point is still lacking due to the difficulty in "manipulating" and depicting the degree of redundancy. In this study, manipulative experiments of functional redundancy were conducted by adopting the mixed inoculation strategy to evaluate its role in engineered anaerobic digestion systems under ammonium inhibition conditions. The results indicated that the functional redundancy gradient was successfully constructed and confirmed by evidence from pathway levels. All mixed inoculation groups exhibited higher methane production regardless of the ammonium level, indicating that functional redundancy is crucial in maintaining the system's efficiency. Further analysis of the metagenome-assembled genomes within different functional guilds revealed that the extent of redundancy decreased along the direction of the anaerobic digestion flow, and the role of functional redundancy appeared to be related to the stress level. The study also found that microbial diversity of key functional populations might play a more important role than their abundance on the system's performance under stress. The findings provide direct evidence and highlight the critical role of functional redundancy in enhancing the efficiency and stability of anaerobic digestion.},
}

Anaerobiosis
*Ammonium Compounds
Bioreactors
*Microbiota
Metagenome
Methane

@article {pmid38556024,
year = {2024},
author = {Chen, T and Liu, S and Zhang, S and Song, H and Zhuang, Y and Ma, J and Xiao, J and Wang, J and Ma, Y and Wang, Y and Wang, W and Li, S and Cao, Z},
title = {Initial diet shapes resistance-gene composition and fecal microbiome dynamics in young ruminants during nursing.},
journal = {The Science of the total environment},
volume = {926},
number = {},
pages = {172103},
doi = {10.1016/j.scitotenv.2024.172103},
pmid = {38556024},
issn = {1879-1026},
mesh = {Pregnancy ; Animals ; Cattle ; Female ; *Diet/veterinary ; Colostrum/chemistry ; Feces/microbiology ; Anti-Bacterial Agents/analysis ; *Microbiota ; Aminoglycosides ; Ruminants ; Animal Feed/analysis ; Animals, Newborn ; Milk/chemistry ; },
abstract = {This study was conducted to examine how colostrum pasteurization affects resistance genes and microbial communities in calf feces. Forty female Holstein calves were randomly assigned to either the control (CON) group, which received unheated colostrum, or the pasteurized colostrum (PAT) group. The calves body weight was measured weekly before morning feeding. Calf starter intake were measured and recorded daily before morning feeding. Samples of colostrum were collected before feeding. Blood was collected on d 1 and 70 before morning feeding. Ten calves were randomly selected from each group (n = 20 calves total) for fecal sampling on d 3, 28, 56 and 70 for subsequent DNA extraction and metagenomic sequencing. Total bacterial counts in the colostrum were markedly higher in the CON group than in the PAT group. Pasteurized colostrum administration substantially reduced the ARO diversity and diminishes the abundance of Enterobacteriaceae, thereby decreasing their contribution to resistance genes. Pasteurization also reduced glucoside hydrolase-66 activity in 3-day-old calves which led to an increase in the activity of aminoglycoside antibiotics, resulting in 52.63 % of PAT-enriched bacteria acquiring aminoglycoside resistance genes. However, from the perspective of overall microbial community, the proportion of aminoglycoside, beta-lactam and tetracycline resistance genes carried by microbial community in PAT group was lower than CON group (P < 0.05). Fecal samples from the PAT group contained greater abundances of Subdoligranulum (P < 0.05) and Lachnospiraceae_NK4A136_group (P < 0.05) on days 28 and 70 compared to CON. Network analysis and abundance variations of the different bacteria obtained by linear discriminant analysis effect size analysis showed that pasteurized colostrum feeding reduced the interactions among related bacteria and maintained stability of the hind-gut microbiome. In conclusion, these findings underscore the intricate interactions between early diet, calf resistance-gene transmission and microbial dynamics, which should be carefully considered in calf-rearing practices.},
}

Pregnancy
Animals
Cattle
Female
*Diet/veterinary
Colostrum/chemistry
Feces/microbiology
Anti-Bacterial Agents/analysis
*Microbiota
Aminoglycosides
Ruminants
Animal Feed/analysis
Animals, Newborn
Milk/chemistry

@article {pmid38554650,
year = {2024},
author = {Zhao, M and Liu, H and Liu, M and Yue, Z and Li, C and Liu, L and Li, F},
title = {Metagenomics and metabolomics reveal that gut microbiome adapts to the diet transition in Hyla rabbits.},
journal = {Microbiological research},
volume = {283},
number = {},
pages = {127705},
doi = {10.1016/j.micres.2024.127705},
pmid = {38554650},
issn = {1618-0623},
mesh = {Humans ; Animals ; Female ; Rabbits ; *Gastrointestinal Microbiome/genetics ; Metabolomics ; *Microbiota ; Diet ; Intestines ; Metagenomics ; },
abstract = {There is still a lack of longitudinal dynamic studies on the taxonomic features, functional reserves, and metabolites of the rabbit gut microbiome. An experiment was conducted to characterize the bacterial community of rabbits. By combining metagenomics and metabolomics, we have comprehensively analyzed the longitudinal dynamics of the rabbit gut microbiota and its effect on host adaptability. Our data reveal an overall increasing trend in microbial community and functional gene diversity and richness during the pre-harvest lifespan of rabbits. The introduction of solid feed is an important driving factor affecting rabbit gut microbiological compositions. Clostridium and Ruminococcus had significantly higher relative abundances in the solid feed stage. Further, the starch and fiber in solid feed promote the secretion of carbohydrate-degrading enzymes, which helps the host adapt to dietary changes. The rabbit gut microbiota can synthesize lysine, and the synthase is gradually enriched during the diet transformation. The gut microbiota of newborn rabbits has a higher abundance of lipid metabolism, which helps the host obtain more energy from breast milk lipids. The rabbit gut microbiota can also synthesize a variety of secondary bile acids after the introduction of solid feed. These findings provide a novel understanding of how the gut microbiota mediates adaptability to environment and diet in rabbits and provide multiple potential strategies for regulating intestinal health and promoting higher feed efficiency.},
}

Humans
Animals
Female
Rabbits
*Gastrointestinal Microbiome/genetics
Metabolomics
*Microbiota
Diet
Intestines
Metagenomics

@article {pmid38501864,
year = {2024},
author = {Xiong, C and K Singh, B and Zhu, Y-G and Hu, H-W and Li, P-P and Han, Y-L and Han, L-L and Zhang, Q-B and Wang, J-T and Liu, S-Y and Wu, C-F and Ge, A-H and Zhang, L-M and He, J-Z},
title = {Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development.},
journal = {mSystems},
volume = {9},
number = {4},
pages = {e0105523},
pmid = {38501864},
issn = {2379-5077},
support = {XDA28020101//Chinese Academy of Sciences (CAS)/ ; 42277289//National Natural Science Foundation of China (NSFC)/ ; 42207142//National Natural Science Foundation of China (NSFC)/ ; DP210102081//Australian Research Council (ARC)/ ; },
mesh = {*Microbiota/genetics ; Agriculture ; Soil/chemistry ; Nitrogen/analysis ; Crops, Agricultural/metabolism ; Plant Development ; },
abstract = {Plant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil-plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with Methylobacterium, Azospirillum, Bradyrhizobium, and Rhizobium. Furthermore, eight dominant taxa belonging to Azospirillum and Methylobacterium were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to Pseudomonas mendocina. Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.IMPORTANCEPlants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.},
}

*Microbiota/genetics
Agriculture
Soil/chemistry
Nitrogen/analysis
Crops, Agricultural/metabolism
Plant Development

@article {pmid38489588,
year = {2024},
author = {David, G and Bertolotti, A and Layer, R and Scofield, D and Hayward, A and Baril, T and Burnett, HA and Gudmunds, E and Jensen, H and Husby, A},
title = {Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations.},
journal = {Genome biology and evolution},
volume = {16},
number = {4},
pages = {},
pmid = {38489588},
issn = {1759-6653},
support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Genomics ; *Genome ; Metagenomics ; Polymorphism, Single Nucleotide ; },
abstract = {Comprehensive characterization of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation, reproducible and high-confidence structural variation callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus). To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of structural variants is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analyzing short-read-discovered structural variation data sets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence structural variation callsets.},
}

*Genomics
*Genome
Metagenomics
Polymorphism, Single Nucleotide

@article {pmid38484575,
year = {2024},
author = {Deepa, N and Chauhan, S and Singh, A},
title = {Unraveling the functional characteristics of endophytic bacterial diversity for plant growth promotion and enhanced secondary metabolite production in Pelargonium graveolens.},
journal = {Microbiological research},
volume = {283},
number = {},
pages = {127673},
doi = {10.1016/j.micres.2024.127673},
pmid = {38484575},
issn = {1618-0623},
mesh = {*Pelargonium ; Bacteria ; Endophytes ; Firmicutes ; Plants ; *Microbiota ; Plant Roots/microbiology ; },
abstract = {The rich diversity of microbial endophytic communities associated with plants, often referred to as the second genome, serves as a compelling illustration of efficient co-evolution. This noteworthy partnership plays a pivotal role in sustaining plant well-being and enhancing plant adaptability across diverse habitats. Therefore, examining the diversity of endophytic microbes associated with their particular host plant is valuable for gaining insights into the vast spectrum of plant-microbe interactions. The present experiments aimed at investigating the bacterial endophytic diversity in both root and shoot tissues of Pelargonium graveolens, employing culture dependent and culture independent high-throughput metagenomics approach. A total of 614 and 620 operational taxonomic units (OTUs), encompassing 291 and 229 genera, were identified in the shoot and root tissues of P. graveolens, respectively. Furthermore, the subsequent classification of OTUs revealed 15 highly abundant phyla, with Proteobacteria dominating both root and shoot tissues. Notably, an exceptionally high abundance of Firmicutes phyla was observed in the shoot compared to the root. Additionally, 30 bacterial endophytes from the root, stem, petiole, and leaves were isolated and molecularly characterized, unveiling a consistent pattern of diversity distribution between the root and shoot of P. graveolens. Upon screening all isolates for plant growth promoting traits, Pseudomonas oryzihabitans was found to be positive for major biochemical test like nitrogen fixation, phosphate solubilization etc. and on inoculation resulted in about two-fold increase in content of essential oil accompanied by a significant rise in the geraniol and citronellol content. Diving deep into the genetic constitution of P. oryzihabitans unveiled a substantial number of genes directly and indirectly contributing to the endophyte's capability in colonizing host plants effectively. In summary, data obtained from metagenomics and culture dependent approaches including glass house trials suggest potential bacterial endophytes suitable for field applications for yield enhancement and in planta secondary metabolite enhancement investigations.},
}

*Pelargonium
Bacteria
Endophytes
Firmicutes
Plants
*Microbiota
Plant Roots/microbiology

@article {pmid38470142,
year = {2024},
author = {Zhang, Z and Zhang, L and Zhang, L and Chu, H and Zhou, J and Ju, F},
title = {Diversity and distribution of biosynthetic gene clusters in agricultural soil microbiomes.},
journal = {mSystems},
volume = {9},
number = {4},
pages = {e0126323},
pmid = {38470142},
issn = {2379-5077},
support = {2024SSYS0032//The "Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; LR22D010001//Zhejiang Provincial Natural Science Foundation of China/ ; 22241603//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Soil/chemistry ; Phylogeny ; Soil Microbiology ; *Microbiota/genetics ; Bacteria/genetics ; Multigene Family/genetics ; },
abstract = {Bacterial secondary metabolites serve as an important source of molecules for drug discovery. They also play an important function in mediating the interactions of microbial producers with their living environment and surrounding organisms. However, little is known about the genetic novelty, distribution, and community-level impacts of soil bacterial biosynthetic potential on a large geographic scale. Here, we constructed the first catalog of 11,149 biosynthetic gene clusters (BGCs) from agricultural soils across China and unearthed hidden biosynthetic potential for new natural product discovery from the not-yet-cultivated soil bacteria. Notably, we revealed soil pH as the strongest environmental driver of BGC biogeography and predicted that soil acidification and global climate change could damage the biosynthetic potential of the soil microbiome. The co-occurrence network of bacterial genomes revealed two BGC-rich species, i.e., Nocardia niigatensis from Actinobacteriota and PSRF01 from Acidobacteriota, as the module hub and connector, respectively, indicating their keystone positions in the soil microbial communities. We also uncovered a dominant role of BGC-inferred biotic interactions over environmental drivers in structuring the soil microbiome. Overall, this study achieved novel insights into the BGC landscape in agricultural soils of China, substantially expanding our understanding of the diversity and novelty of bacterial secondary metabolism and the potential role of secondary metabolites in microbiota assembly.IMPORTANCEBacterial secondary metabolites not only serve as the foundation for numerous therapeutics (e.g., antibiotics and anticancer drugs), but they also play critical ecological roles in mediating microbial interactions (e.g., competition and communication). However, our knowledge of bacterial secondary metabolism is limited to only a small fraction of cultured strains, thus restricting our comprehensive understanding of their diversity, novelty, and potential ecological roles in soil ecosystems. Here, we used culture-independent metagenomics to explore biosynthetic potentials in agricultural soils of China. Our analyses revealed a high degree of genetic diversity and novelty within biosynthetic gene clusters in agricultural soil environments, offering valuable insights for biochemists seeking to synthesize novel bioactive products. Furthermore, we uncovered the pivotal role of BGC-rich species in microbial communities and the significant relationship between BGC richness and microbial phylogenetic turnover. This information emphasizes the importance of biosynthetic potential in the assembly of microbial communities.},
}

*Soil/chemistry
Phylogeny
Soil Microbiology
*Microbiota/genetics
Bacteria/genetics
Multigene Family/genetics

@article {pmid38445871,
year = {2024},
author = {Cai, M and Zhang, C and Ndungu, CN and Liu, G and Liu, W and Zhang, Q},
title = {Linking ecosystem multifunctionality to microbial community features in rivers along a latitudinal gradient.},
journal = {mSystems},
volume = {9},
number = {4},
pages = {e0014724},
pmid = {38445871},
issn = {2379-5077},
support = {32022051//MOST | National Natural Science Foundation of China (NSFC)/ ; 32201387//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Rivers ; Rhizosphere ; Plants ; *Microbiota ; Soil/chemistry ; Nitrogen ; },
abstract = {Microorganisms regulate numerous ecosystem functions and show considerable differences along a latitudinal gradient. Although studies have revealed the latitudinal patterns of microbial community structure and single ecosystem function, the latitudinal patterns of ecosystem multifunctionality (EMF) and how microbial communities affect EMF along a latitudinal gradient remain unclear. Here, we collected channel sediments, riparian rhizosphere soils, and riparian bulk soils from 30 rivers across China and calculated EMF using 18 variables related to nitrogen cycling, nutrient pool, plant productivity, and water quality. We also determined microbial diversity (taxonomic and functional) and microbial network complexity using metagenomic sequencing. The results showed that EMF significantly decreased with increasing latitude in riparian rhizosphere and bulk soils but not in channel sediments. Microbial taxonomic and functional richness (observed species) in channel sediments were significantly higher in the low-latitude group than in the high-latitude group. However, microbial co-occurrence networks were more complex in the high-latitude group compared with the low-latitude group. Abiotic factors, primarily geographic and climatic factors, contributed more to EMF than microbial diversity and network complexity parameters in which only betweenness centralization had a significant relationship with EMF. Together, this study provides insight into the latitudinal pattern of EMF in rivers and highlights the importance of large-scale factors in explaining such latitudinal patterns.IMPORTANCEEcosystem multifunctionality (EMF) is the capacity of an ecosystem to provide multiple functions simultaneously. Microorganisms, as dominant drivers of belowground processes, have a profound effect on ecosystem functions. Although studies have revealed the latitudinal patterns of microbial community structure and single ecosystem function, the latitudinal patterns of EMF and how microbial communities affect EMF along a latitudinal gradient remain unclear. We collected channel sediments, riparian rhizosphere soils, and riparian bulk soils from 30 rivers along a latitudinal gradient across China and calculated EMF using 18 variables related to nitrogen cycling, nutrient pool, plant productivity, and water quality. This study fills a critical knowledge gap regarding the latitudinal patterns and drivers of EMF in river ecosystems and gives new insights into how microbial diversity and network complexity affect EMF from a metagenomic perspective.},
}

*Rivers
Rhizosphere
Plants
*Microbiota
Soil/chemistry
Nitrogen

@article {pmid38445870,
year = {2024},
author = {Yap, M and O'Sullivan, O and O'Toole, PW and Sheehan, JJ and Fenelon, MA and Cotter, PD},
title = {Seasonal and geographical impact on the Irish raw milk microbiota correlates with chemical composition and climatic variables.},
journal = {mSystems},
volume = {9},
number = {4},
pages = {e0129023},
pmid = {38445870},
issn = {2379-5077},
support = {16/RC/3835//Science Foundation Ireland (SFI)/ ; TC 2020 0028//Enterprise Ireland/ ; },
mesh = {Female ; Animals ; *Milk ; Seasons ; Bacteria ; *Microbiota ; Metagenome ; },
abstract = {UNLABELLED: Season and location have previously been shown to be associated with differences in the microbiota of raw milk, especially in milk from pasture-based systems. Here, we further advance research in this area by examining differences in the raw milk microbiota from several locations across Ireland over 12 months, and by investigating microbiota associations with climatic variables and chemical composition. Shotgun metagenomic sequencing was used to investigate the microbiota of raw milk collected from nine locations (n = 241). Concurrent chemical analysis of the protein, fat, lactose, total solids, nonprotein nitrogen contents, and titratable acidity (TA) of the same raw milk were performed. Although the raw milk microbiota was highly diverse, a core microbiota was found, with Pseudomonas_E, Lactococcus, Acinetobacter, and Leuconostoc present in all samples. Microbiota diversity significantly differed by season and location, with differences in seasonality and geography corresponding to 11.8% and 10.5% of the variation in the microbiota. Functional and antibiotic resistance profiles also varied across season and location. The analysis of other metadata revealed additional interactions, such as an association between mean daily air and grass temperatures with the abundance of spoilage taxa like Pseudomonas species. Correlations were identified between pathogenic, mastitis-related species, fat content, and the number of sun hours, suggesting a seasonal effect. Ultimately, this study expands our understanding of the interconnected nature of the microbiota, environment/climate variables, and chemical composition of raw milk and provides evidence of a season- and location-specific microbiota.

IMPORTANCE: The microbiota of raw milk is influenced by many factors that encourage or prevent the introduction and growth of both beneficial and undesirable microorganisms. The seasonal and geographical impacts on the microbial communities of raw milk have been previously seen, but the relationships with environmental factors and the chemical composition has yet to be investigated. In this year-long study, we found that while raw milk is highly diverse, a core microbiota was detected for Irish raw milk, with strong evidence of seasonal and geographical influence. We also found associations between groups of microorganisms, environmental factors, and milk composition, which expand current knowledge on the relationships between microbial and chemical composition and the climate. These results provide evidence for the development of a tool to allow for the prediction of raw milk quality and safety.},
}

Female
Animals
*Milk
Seasons
Bacteria
*Microbiota
Metagenome

@article {pmid38441971,
year = {2024},
author = {Kadlečková, D and Saláková, M and Erban, T and Tachezy, R},
title = {Discovery and characterization of novel DNA viruses in Apis mellifera: expanding the honey bee virome through metagenomic analysis.},
journal = {mSystems},
volume = {9},
number = {4},
pages = {e0008824},
pmid = {38441971},
issn = {2379-5077},
support = {QK1910018; MZE-RO0423//Ministerstvo Zemědělství (Ministry of Agriculture)/ ; LX22NPO5103//Ministerstvo Školství, Mládeže a Tělovýchovy (MŠMT)/ ; SVV 260679//Charles University/ ; 101102733//EU4H Project No.101102733 (DURABLE)/ ; },
mesh = {Bees ; Animals ; Virome/genetics ; Ecosystem ; DNA Viruses/genetics ; *Viruses ; Metagenome/genetics ; *Nudiviridae ; },
abstract = {To date, many viruses have been discovered to infect honey bees. In this study, we used high-throughput sequencing to expand the known virome of the honey bee, Apis mellifera, by identifying several novel DNA viruses. While the majority of previously identified bee viruses are RNA, our study reveals nine new genomes from the Parvoviridae family, tentatively named Bee densoviruses 1 to 9. In addition, we characterized a large DNA virus, Apis mellifera filamentous-like virus (AmFLV), which shares limited protein identities with the known Apis mellifera filamentous virus. The complete sequence of AmFLV, obtained by a combination of laboratory techniques and bioinformatics, spans 152,678 bp. Linear dsDNA genome encodes for 112 proteins, of which 49 are annotated. Another large virus we discovered is Apis mellifera nudivirus, which belongs to a group of Alphanudivirus. The virus has a length of 129,467 bp and a circular dsDNA genome, and has 106 protein encoding genes. The virus contains most of the core genes of the family Nudiviridae. This research demonstrates the effectiveness of viral binning in identifying viruses in honey bee virology, showcasing its initial application in this field.IMPORTANCEHoney bees contribute significantly to food security by providing pollination services. Understanding the virome of honey bees is crucial for the health and conservation of bee populations and also for the stability of the ecosystems and economies for which they are indispensable. This study unveils previously unknown DNA viruses in the honey bee virome, expanding our knowledge of potential threats to bee health. The use of the viral binning approach we employed in this study offers a promising method to uncovering and understanding the vast viral diversity in these essential pollinators.},
}

Bees
Animals
Virome/genetics
Ecosystem
DNA Viruses/genetics
*Viruses
Metagenome/genetics
*Nudiviridae

@article {pmid38441032,
year = {2024},
author = {Mancabelli, L and Milani, C and De Biase, R and Bocchio, F and Fontana, F and Lugli, GA and Alessandri, G and Tarracchini, C and Viappiani, A and De Conto, F and Nouvenne, A and Ticinesi, A and Bussolati, O and Meschi, T and Cecchi, R and Turroni, F and Ventura, M},
title = {Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation.},
journal = {mSystems},
volume = {9},
number = {4},
pages = {e0129423},
pmid = {38441032},
issn = {2379-5077},
support = {GR-2018-12365988//Ministero della Salute (Italy Ministry of Health)/ ; 20229LEB99//Ministero della Ricerca e dell'Universita/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Metagenome/genetics ; Bacteria/genetics ; Vitamins ; },
abstract = {UNLABELLED: The human gut microbiota is a dynamic community of microorganisms that undergo variable changes over the entire life span. To thoroughly investigate the possible fluctuations of the microbiota throughout human life, we performed a pooled analysis of healthy fecal samples across different age groups covering the entire human life span. Our study integrated data from 79 publicly available studies and new stool samples from an Italian cohort, i.e., the Parma Microbiota project, resulting in 6,653 samples processed through the shotgun metagenomic approach. This approach has allowed species-level taxonomic reconstruction of the gut microbiota and investigation of its metabolic potential across the human life span. From a taxonomic point of view, our findings confirmed and detailed at species-level accuracy that the microbial richness of the gut microbiota gradually increases in the first stage of life, becoming relatively stable during adolescence. Moreover, the analysis identified the potential core microbiota representative of distinct age groups, revealing age-related bacterial patterns and the continuous rearrangement of the microbiota in terms of relative abundances across the life span rather than the acquisition and loss of taxa. Furthermore, the shotgun approach provided insights into the functional contribution of the human gut microbiome. The metagenomic analysis revealed functional age-related differences, particularly in carbohydrate and fiber metabolism, suggesting a co-evolution of the microbiome assembly with diet. Additionally, we identified correlations between vitamin synthesis, such as thiamine and niacin, and early life, suggesting a potential role of the microbiome in human physiology, in particular in the functions of the host's nervous and immune systems.

IMPORTANCE: In this study, we provided comprehensive insights into the dynamic nature of the human gut microbiota across the human life span. In detail, we analyzed a large data set based on a shotgun metagenomic approach, combining public data sets and new samples from the Parma Microbiota project and obtaining a detailed overview of the possible relationship between gut microbiota development and aging. Our findings confirmed the main stages in microbial richness development and revealed specific core microbiota associated with different age stages. Moreover, the shotgun metagenomic approach allowed the disentangling of the functional changes in the microbiome across the human life span, particularly in diet-related metabolism, which is probably correlated to bacterial co-evolution with dietary habits. Notably, our study also uncovered positive correlations with vitamin synthesis in early life, suggesting a possible impact of the microbiota on human physiology.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Microbiota
Metagenome/genetics
Bacteria/genetics
Vitamins

@article {pmid38414315,
year = {2024},
author = {Torma, F and Kerepesi, C and Jókai, M and Babszki, G and Koltai, E and Ligeti, B and Kalcsevszki, R and McGreevy, KM and Horvath, S and Radák, Z},
title = {Alterations of the gut microbiome are associated with epigenetic age acceleration and physical fitness.},
journal = {Aging cell},
volume = {23},
number = {4},
pages = {e14101},
pmid = {38414315},
issn = {1474-9726},
support = {RRF-2.3.1-21-2022-00004//European Union/ ; 126823//Ministry of Innovation and Technology National Excellence Program/ ; OTKA142192//National Research, Development and Innovation Office/ ; OTKA146113//National Research, Development and Innovation Office/ ; TKP2021-EGA-37//Hungarian University Sport Science, Innovation and Technology Ministry, Hungary/ ; 2021-28//National Academy of Science, Hungary/ ; },
mesh = {Humans ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; Physical Fitness ; *Microbiota/genetics ; Acceleration ; Aging/genetics ; Epigenesis, Genetic ; DNA Methylation ; },
abstract = {Epigenetic clocks can measure aging and predict the incidence of diseases and mortality. Higher levels of physical fitness are associated with a slower aging process and a healthier lifespan. Microbiome alterations occur in various diseases and during the aging process, yet their relation to epigenetic clocks is not explored. To fill this gap, we collected metagenomic (from stool), epigenetic (from blood), and exercise-related data from physically active individuals and, by applying epigenetic clocks, we examined the relationship between gut flora, blood-based epigenetic age acceleration, and physical fitness. We revealed that an increased entropy in the gut microbiome of physically active middle-aged/old individuals is associated with accelerated epigenetic aging, decreased fitness, or impaired health status. We also observed that a slower epigenetic aging and higher fitness level can be linked to altered abundance of some bacterial species often linked to anti-inflammatory effects. Overall our data suggest that alterations in the microbiome can be associated with epigenetic age acceleration and physical fitness.},
}

Humans
Middle Aged
*Gastrointestinal Microbiome/genetics
Physical Fitness
*Microbiota/genetics
Acceleration
Aging/genetics
Epigenesis, Genetic
DNA Methylation

@article {pmid38612702,
year = {2024},
author = {McDermott, G and Walsh, A and Crispie, F and Frost, S and Greally, P and Cotter, PD and O'Sullivan, O and Renwick, J},
title = {Insights into the Adolescent Cystic Fibrosis Airway Microbiome Using Shotgun Metagenomics.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
pmid = {38612702},
issn = {1422-0067},
support = {204814/Z/16/A/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Child ; Humans ; Adolescent ; *Cystic Fibrosis ; Staphylococcus aureus ; Biological Assay ; DNA, Ribosomal ; *Microbiota/genetics ; },
abstract = {Cystic fibrosis (CF) is an inherited genetic disorder which manifests primarily in airway disease. Recent advances in molecular technologies have unearthed the diverse polymicrobial nature of the CF airway. Numerous studies have characterised the genus-level composition of this airway community using targeted 16S rDNA sequencing. Here, we employed whole-genome shotgun metagenomics to provide a more comprehensive understanding of the early CF airway microbiome. We collected 48 sputum samples from 11 adolescents and children with CF over a 12-month period and performed shotgun metagenomics on the Illumina NextSeq platform. We carried out functional and taxonomic analysis of the lung microbiome at the species and strain levels. Correlations between microbial diversity measures and independent demographic and clinical variables were performed. Shotgun metagenomics detected a greater diversity of bacteria than culture-based methods. A large proportion of the top 25 most-dominant species were anaerobes. Samples dominated by Staphylococcus aureus and Prevotella melaninogenica had significantly higher microbiome diversity, while no CF pathogen was associated with reduced microbial diversity. There was a diverse resistome present in all samples in this study, with 57.8% agreement between shotgun metagenomics and culture-based methods for detection of resistance. Pathogenic sequence types (STs) of S. aureus, Pseudomonas aeruginosa, Haemophilus influenzae and Stenotrophomonas maltophilia were observed to persist in young CF patients, while STs of S. aureus were both persistent and shared between patients. This study provides new insight into the temporal changes in strain level composition of the microbiome and the landscape of the resistome in young people with CF. Shotgun metagenomics could provide a very useful one-stop assay for detecting pathogens, emergence of resistance and conversion to persistent colonisation in early CF disease.},
}

Child
Humans
Adolescent
*Cystic Fibrosis
Staphylococcus aureus
Biological Assay
DNA, Ribosomal
*Microbiota/genetics

@article {pmid38612577,
year = {2024},
author = {Feng, C and Li, N and Gao, G and He, Q and Kwok, LY and Zhang, H},
title = {Dynamic Changes of the Gut Microbiota and Its Functional Metagenomic Potential during the Development of Non-Small Cell Lung Cancer.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
pmid = {38612577},
issn = {1422-0067},
support = {NDYB2022-41//Research Initiation Project for Introducing Excellent Doctoral Talents from Inner Mongolia Agricultural University/ ; 2022YFD2100700//Research Fund for the National Key R&D Program of China/ ; U22A20540//National Natural Science Foundation of China/ ; 2021ZD0014//Inner Mongolia Science and Technology Major Projects/ ; CARS36//earmarked fund/ ; },
mesh = {Humans ; Animals ; Mice ; *Carcinoma, Non-Small-Cell Lung ; *Lung Neoplasms ; *Gastrointestinal Microbiome ; Biomarkers, Tumor ; Clostridiales ; },
abstract = {The gut microbiota plays a significant role in tumor pathogenesis by regulating the host metabolism and immune response, and there are few studies focused on tracking changes in the gut microbiota from the onset of lung cancer. Therefore, the aim of our study is combining preclinical and clinical research to thoroughly analyze the signatures of fecal microbiota in lung cancer, which will be useful for early diagnosis and predicting the therapeutic efficacy of lung cancer. The first part of this study analyzed the fecal metagenomic differences between patients with non-small cell lung cancer and healthy subjects, and the second part of this work constructed a murine lung cancer model to monitor changes in mouse fecal metagenomics and T cell immunology during lung cancer progression. We found that the fecal microbiota was altered in both humans and mice with lung cancer, characterized by a significantly reduced microbial diversity and number of beneficial microbes, with increases in potential pathogens. The fecal level of Akkermansia muciniphila and the gut metabolic module of the secondary bile acid metabolism were diminished in both humans and mice with lung cancer compared with healthy subjects. Splenomegaly was observed in the lung cancer mice. Flow cytometer analysis of the splenocytes revealed substantial alterations in the proportions of T cell subsets in the lung cancer mice, characterized by significant increases in CD4[+]Foxp3[+]CD25[+] T regulatory cells (p < 0.05) while significant decreases in CD3[+] T cells (p < 0.001), CD4[+] T cells (p < 0.001), and the CD4[+]/CD8[+] ratio (p < 0.01). Vertical and longitudinal analyses of the fecal microbiota of the two mouse groups identified some lung cancer biomarkers (including Acutalibacter timonensis, Lachnospiraceae bacterium NSJ-38 sp014337195, etc.). The fecal microbiota of the lung cancer mice had a reduced metagenomic potential for neurotransmitters (melatonin, γ-aminobutyric acid, and histamine) compared with healthy mice. In summary, this study found that the diversity, structure, and composition of gut microbiota vary between cancer and healthy conditions, ultimately leading to changes in the potential for functional metagenomics.},
}

Humans
Animals
Mice
*Carcinoma, Non-Small-Cell Lung
*Lung Neoplasms
*Gastrointestinal Microbiome
Biomarkers, Tumor
Clostridiales

@article {pmid38611776,
year = {2024},
author = {Szulc, J and Okrasa, M and Nowak, A and Ryngajłło, M and Nizioł, J and Kuźniar, A and Ruman, T and Gutarowska, B},
title = {Uncontrolled Post-Industrial Landfill-Source of Metals, Potential Toxic Compounds, Dust, and Pathogens in Environment-A Case Study.},
journal = {Molecules (Basel, Switzerland)},
volume = {29},
number = {7},
pages = {},
pmid = {38611776},
issn = {1420-3049},
support = {Phase IV of the National Program "Safety and working conditions improvement"//Ministry of Science and Higher Education and the National Centre for Research and Development/ ; 726/BN/D/2019-2021//Regional Found for Environmental Protection and Water Management in Lodz/ ; },
mesh = {Humans ; *Dust ; Caco-2 Cells ; Metals ; *Mercury ; Soil ; },
abstract = {The aim of this case study was the evaluation of the selected metals' concentration, potential toxic compound identification, cytotoxicity analysis, estimation of the airborne dust concentration, biodiversity, and number of microorganisms in the environment (leachate, soil, air) of the biggest uncontrolled post-industrial landfills in Poland. Based on the results obtained, preliminary solutions for the future management of post-industrial objects that have become an uncontrolled landfill were indicated. In the air, the PM1 fraction dominated, constituting 78.1-98.2% of the particulate matter. Bacterial counts were in the ranges of 9.33 × 10[1]-3.21 × 10[3] CFU m[-3] (air), 1.87 × 10[5]-2.30 × 10[6] CFU mL[-1] (leachates), and 8.33 × 10[4]-2.69 × 10[6] CFU g[-1] (soil). In the air, the predominant bacteria were Cellulosimicrobium and Stenotrophomonas. The predominant fungi were Mycosphaerella, Cladosporium, and Chalastospora. The main bacteria in the leachates and soils were Acinetobacter, Mortierella, Proteiniclasticum, Caloramator, and Shewanella. The main fungi in the leachates and soils were Lindtneria. Elevated concentrations of Pb, Zn, and Hg were detected. The soil showed the most pronounced cytotoxic potential, with rates of 36.55%, 63.08%, and 100% for the A-549, Caco-2, and A-549 cell lines. Nine compounds were identified which may be responsible for this cytotoxic effect, including 2,4,8-trimethylquinoline, benzo(f)quinoline, and 1-(m-tolyl)isoquinoline. The microbiome included bacteria and fungi potentially metabolizing toxic compounds and pathogenic species.},
}

Humans
*Dust
Caco-2 Cells
Metals
*Mercury
Soil

@article {pmid38609443,
year = {2024},
author = {Kholousi Adab, F and Mehdi Yaghoobi, M and Gharechahi, J},
title = {Enhanced crystalline cellulose degradation by a novel metagenome-derived cellulase enzyme.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {8560},
pmid = {38609443},
issn = {2045-2322},
mesh = {Animals ; Metagenome ; Camelus ; *Microbiota ; *Cellulase/genetics ; Cellulose ; },
abstract = {Metagenomics has revolutionized access to genomic information of microorganisms inhabiting the gut of herbivorous animals, circumventing the need for their isolation and cultivation. Exploring these microorganisms for novel hydrolytic enzymes becomes unattainable without utilizing metagenome sequencing. In this study, we harnessed a suite of bioinformatic analyses to discover a novel cellulase-degrading enzyme from the camel rumen metagenome. Among the protein-coding sequences containing cellulase-encoding domains, we identified and subsequently cloned and purified a promising candidate cellulase enzyme, Celcm05-2, to a state of homogeneity. The enzyme belonged to GH5 subfamily 4 and exhibited robust enzymatic activity under acidic pH conditions. It maintained hydrolytic activity under various environmental conditions, including the presence of metal ions, non-ionic surfactant Triton X-100, organic solvents, and varying temperatures. With an optimal temperature of 40 °C, Celcm05-2 showcased remarkable efficiency when deployed on crystalline cellulose (> 3.6 IU/mL), specifically Avicel, thereby positioning it as an attractive candidate for a myriad of biotechnological applications spanning biofuel production, paper and pulp processing, and textile manufacturing. Efficient biodegradation of waste paper pulp residues and the evidence of biopolishing suggested that Celcm05-2 can be used in the bioprocessing of cellulosic craft fabrics in the textile industry. Our findings suggest that the camel rumen microbiome can be mined for novel cellulase enzymes that can find potential applications across diverse biotechnological processes.},
}

Animals
Metagenome
Camelus
*Microbiota
*Cellulase/genetics
Cellulose

@article {pmid38609235,
year = {2024},
author = {Hou, Q and Wang, Y and Qu, D and Zhao, H and Tian, L and Zhou, J and Liu, J and Guo, Z},
title = {Microbial communities, functional, and flavor differences among three different-colored high-temperature Daqu: A comprehensive metagenomic, physicochemical, and electronic sensory analysis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {184},
number = {},
pages = {114257},
doi = {10.1016/j.foodres.2024.114257},
pmid = {38609235},
issn = {1873-7145},
mesh = {Temperature ; *Metagenome ; *Microbiota ; Cluster Analysis ; Electronics ; },
abstract = {High-temperature Daqu (HTD) is the starter for producing sauce-flavor Baijiu, with different-colored Daqu (white, yellow, and black) reflecting variations in fermentation chamber conditions, chemical reactions, and associated microbiota. Understanding the relationship between Daqu characteristics and flavor/taste is challenging yet vital for improving Baijiu fermentation. This study utilized metagenomic sequencing, physicochemical analysis, and electronic sensory evaluation to compare three different-colored HTD and their roles in fermentation. Fungi and bacteria dominated the HTD-associated microbiota, with fungi increasing as the fermentation temperature rose. The major fungal genera were Aspergillus (40.17%) and Kroppenstedtia (21.16%), with Aspergillus chevalieri (25.65%) and Kroppenstedtia eburnean (21.07%) as prevalent species. Microbial communities, functionality, and physicochemical properties, particularly taste and flavor, were color-specific in HTD. Interestingly, the microbial communities in different-colored HTDs demonstrated robust functional complementarity. White Daqu exhibited non-significantly higher α-diversity compared to the other two Daqu. It played a crucial role in breaking down substrates such as starch, proteins, hyaluronic acid, and glucan, contributing to flavor precursor synthesis. Yellow Daqu, which experienced intermediate temperature and humidity, demonstrated good esterification capacity and a milder taste profile. Black Daqu efficiently broke down raw materials, especially complex polysaccharides, but had inferior flavor and taste. Notably, large within-group variations in physicochemical quality and microbial composition were observed, highlighting limitations in color-based HTD quality assessment. Water content in HTD was associated with Daqu flavor, implicating its crucial role. This study revealed the complementary roles of the three HTD types in sauce-flavor Baijiu fermentation, providing valuable insights for product enhancement.},
}

Temperature
*Metagenome
*Microbiota
Cluster Analysis
Electronics

@article {pmid38609223,
year = {2024},
author = {Ma, J and Qian, C and Hu, Q and Zhang, J and Gu, G and Liang, X and Zhang, L},
title = {The bacteriome-coupled phage communities continuously contract and shift to orchestrate the traditional rice vinegar fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {184},
number = {},
pages = {114244},
doi = {10.1016/j.foodres.2024.114244},
pmid = {38609223},
issn = {1873-7145},
mesh = {Humans ; *Oryza ; Acetic Acid ; Fermentation ; *Bacteriophages/genetics ; *Microbiota/genetics ; },
abstract = {Amounts of microbiome studies have uncovered the microbial communities of traditional food fermentations, while in which the phageome development with time is poorly understood. Here, we conducted a study to decipher both phageome and bacteriome of the traditional rice vinegar fermentation. The vinegar phageomes showed significant differences in the alpha diversity, network density and clustering coefficient over time. Peduoviridae had the highest relative abundance. Moreover, the phageome negatively correlated to the cognate bacteriome in alpha diversity, and undergone constantly contracting and shifting across the temporal scale. Nevertheless, 257 core virial clusters (VCs) persistently occurred with time whatever the significant impacts imposed by the varied physiochemical properties. Glycoside hydrolase (GH) and glycosyltransferase (GT) families genes displayed the higher abundances across all samples. Intriguingly, diversely structuring of toxin-antitoxin systems (TAs) and CRISPR-Cas arrays were frequently harbored by phage genomes. Their divergent organization and encoding attributes underlie the multiple biological roles in modulation of network and/or contest of phage community as well as bacterial host community. This phageome-wide mapping will fuel the current insights of phage community ecology in other traditional fermented ecosystems that are challenging to decipher.},
}

Humans
*Oryza
Acetic Acid
Fermentation
*Bacteriophages/genetics
*Microbiota/genetics

@article {pmid38606341,
year = {2024},
author = {Eitel, M and Osigus, HJ and Brenzinger, B and Wörheide, G},
title = {Beauty in the beast - Placozoan biodiversity explored through molluscan predator genomics.},
journal = {Ecology and evolution},
volume = {14},
number = {4},
pages = {e11220},
pmid = {38606341},
issn = {2045-7758},
abstract = {The marine animal phylum Placozoa is characterized by a poorly explored cryptic biodiversity combined with very limited knowledge of their ecology. While placozoans are typically found as part of the epibenthos of coastal waters, known placozoan predators, namely small, shell-less sea slugs belonging to the family Rhodopidae (Mollusca: Gastropoda: Heterobranchia), inhabit the interstitium of seafloor sediment. In order to gain further insights into this predator-prey relationship and to expand our understanding of placozoan ecological niches, we screened publicly available whole-body metagenomic data from two rhodopid specimens collected from coastal sediments. Our analysis not only revealed the signatures of three previously unknown placozoan lineages in these sea slug samples but also enabled the assembly of three complete and two partial mitochondrial chromosomes belonging to four previously described placozoan genera, substantially extending the picture of placozoan biodiversity. Our findings further refine the molecular phylogeny of the Placozoa, corroborate the recently established taxonomic ranks in this phylum, and provide molecular support that known placozoan clades should be referred to as genera. We finally discuss the main finding of our study - the presence of placozoans in the sea floor sediment interstitium - in the context of their ecological, biological, and natural history implications.},
}

@article {pmid38605401,
year = {2024},
author = {Feng, X and Li, H},
title = {Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {92},
pmid = {38605401},
issn = {1474-760X},
support = {R01HG010040/HG/NHGRI NIH HHS/United States ; U01HG010961/HG/NHGRI NIH HHS/United States ; },
mesh = {*Metagenome ; *Microbiota/genetics ; Algorithms ; Bacteria/genetics ; Metagenomics/methods ; },
abstract = {BACKGROUND: In the metagenomic assembly of a microbial community, abundant species are often thought to assemble well given their deeper sequencing coverage. This conjuncture is rarely tested or evaluated in practice. We often do not know how many abundant species are missing and do not have an approach to recover them.

RESULTS: Here, we propose k-mer based and 16S RNA based methods to measure the completeness of metagenome assembly. We show that even with PacBio high-fidelity (HiFi) reads, abundant species are often not assembled, as high strain diversity may lead to fragmented contigs. We develop a novel reference-free algorithm to recover abundant metagenome-assembled genomes (MAGs) by identifying circular assembly subgraphs. Complemented with a reference-free genome binning heuristics based on dimension reduction, the proposed method rescues many abundant species that would be missing with existing methods and produces competitive results compared to those state-of-the-art binners in terms of total number of near-complete genome bins.

CONCLUSIONS: Our work emphasizes the importance of metagenome completeness, which has often been overlooked. Our algorithm generates more circular MAGs and moves a step closer to the complete representation of microbial communities.},
}

*Metagenome
*Microbiota/genetics
Algorithms
Bacteria/genetics
Metagenomics/methods

@article {pmid38600101,
year = {2024},
author = {Ma, X and Wen, G and Zhao, Z and Lu, L and Li, T and Gao, N and Han, G},
title = {Alternations in the human skin, gut and vaginal microbiomes in perimenopausal or postmenopausal Vulvar lichen sclerosus.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {8429},
pmid = {38600101},
issn = {2045-2322},
support = {YN2021QX02//Peking University International Hospital/ ; },
mesh = {Female ; Humans ; *Vulvar Lichen Sclerosus/pathology ; Postmenopause ; Perimenopause ; Quality of Life ; *Microbiota ; Arrhythmias, Cardiac ; Vagina/pathology ; },
abstract = {Vulvar lichen sclerosus (VLS) is a chronic and progressive dermatologic condition that can cause physical dysfunction, disfigurement, and impaired quality of life. However, the etiology of VLS remains unknown. The vulvar skin, intestinal and vaginal microbiomes have been postulated to play important roles in the pathogenesis of this disease. The aim of this study was to compare the compositional characteristics of the vulvar skin, vagina, and gut microbiota between perimenopausal or postmenopausal VLS patients and healthy controls. The study involved six perimenopausal or postmenopausal VLS patients which were based on characteristic clinical manifestations and histologic confirmation and five healthy controls. The pruritus severity of each patient was evaluated using the NRS scale, and the dermatology-specific health-related quality of life was assessed using the Skindex-16. Metagenomic sequencing was performed, and the results were analyzed for alpha and beta diversity. LEfSe analysis were used to investigate the microbial alterations in vulvar skin, gut and vagina. KEGG databases were used to analyze differences in functional abundance. The study found significant differences in alpha diversity between the two groups in stool and vaginal samples (P < 0.05). Patients with VLS had a higher abundance of Enterobacter cloacae, Flavobacterium_branchiophilum, Mediterranea_sp._An20, Parabacteroides_johnsoniiand Streptococcus_bovimastitidis on the vulvar skin, while Corynebacterium_sp._zg-913 was less abundant compared to the control group. The relative abundance of Sphingomonas_sp._SCN_67_18, Sphingobium_sp._Ant17, and Pontibacter_sp_BT213 was significantly higher in the gut samples of patients with VLS.Paenibacillus_popilliae,Gemella_asaccharolytica, and Coriobacteriales_bacterium_DNF00809 compared to the control group. Additionally, the vaginal samples of patients with VLS exhibited a significantly lower relative abundance of Bacteroidales_bacterium_43_8, Bacteroides_sp._CAG:20, Blautia_sp._AM28-10, Fibrobacter_sp._UWB16, Lachnospiraceae_bacterium_AM25-39, Holdemania_filiformis, Lachnospiraceae_bacterium_GAM79, and Tolumonas_sp. Additionally, the butyrate-producing bacterium SS3/4 showed a significant difference compared to the controls. The study found a negative relationship between Sphingobium_sp._Ant17 in stool and Skindex-16 (P < 0.05), while Mediterranea_sp._An20 had a positive correlation with Skindex-16 (P < 0.05) in the skin. Additionally, our functional analysis revealed alterations in Aminoacyl_tRNA_biosynthesis, Glutathione_metabolism, the pentose phosphate pathway, and Alanine__aspartate_and_glutamate_metabolism in the VLS patient group. The study suggests that perimenopausal or postmenopausal patients with VLS have a modified microbiome in the vulvar skin, gut, and vagina. This modification is linked to abnormal energy metabolism, increased oxidative stress, and abnormal amino acid metabolism.},
}

Female
Humans
*Vulvar Lichen Sclerosus/pathology
Postmenopause
Perimenopause
Quality of Life
*Microbiota
Arrhythmias, Cardiac
Vagina/pathology

@article {pmid38599113,
year = {2024},
author = {Pilkington, LI and Kerner, W and Bertoldi, D and Larcher, R and Lee, SA and Goddard, MR and Albanese, D and Franceschi, P and Fedrizzi, B},
title = {Integration and holistic analysis of multiple multidimensional soil data sets.},
journal = {Talanta},
volume = {274},
number = {},
pages = {125954},
doi = {10.1016/j.talanta.2024.125954},
pmid = {38599113},
issn = {1873-3573},
abstract = {Complex matrices such as soil have a range of measurable characteristics, and thus data to describe them can be considered multidimensional. These characteristics can be strongly influenced by factors that introduce confounding effects that hinder analyses. Traditional statistical approaches lack the flexibility and granularity required to adequately evaluate such matrices, particularly those with large dataset of varying data types (i.e. quantitative non-compositional, quantitative compositional). We present a statistical workflow designed to effectively analyse complex, multidimensional systems, even in the presence of confounding variables. The developed methodology involves exploratory analysis to identify the presence of confounding variables, followed by data decomposition (including strategies for both compositional and non-compositional quantitative data) to minimise the influence of these confounding factors such as sampling site/location. These data processing methods then allow for common patterns to be highlighted in the data, including the identification of biomarkers and determination of non-trivial associations between variables. We demonstrate the utility of this statistical workflow by jointly analysing the chemical composition and fungal biodiversity of New Zealand vineyard soils that have been managed with either organic low-input or conventional input approaches. By applying this pipeline, we were able to identify biomarkers that distinguish viticultural soil from both approaches and also unearth links and associations between the chemical and metagenomic profiles. While soil is an example of a system that can require this type of statistical methodology, there are a range of biological and ecological systems that are challenging to analyse due to the complex interplay of global and local effects. Utilising our developed pipeline will greatly enhance the way that these systems can be studied and the quality and impact of insight gained from their analysis.},
}

@article {pmid38598617,
year = {2024},
author = {Gilbert, JA and Alverdy, J},
title = {Where do the pathogens that cause surgical site infections come from?.},
journal = {Science translational medicine},
volume = {16},
number = {742},
pages = {eado1449},
doi = {10.1126/scitranslmed.ado1449},
pmid = {38598617},
issn = {1946-6242},
mesh = {Humans ; *Surgical Wound Infection/drug therapy ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Microbiota ; },
abstract = {A study from Long et al. shows that many pathogens that cause surgical site infections during spine surgery come from the patient's own microbiome, suggesting a paradigm shift in the understanding of surgical site infections that questions the effectiveness of current enhanced sterility and antibiotic protocols.},
}

Humans
*Surgical Wound Infection/drug therapy
Anti-Bacterial Agents/pharmacology/therapeutic use
*Microbiota

@article {pmid38569543,
year = {2024},
author = {Li, C and Stražar, M and Mohamed, AMT and Pacheco, JA and Walker, RL and Lebar, T and Zhao, S and Lockart, J and Dame, A and Thurimella, K and Jeanfavre, S and Brown, EM and Ang, QY and Berdy, B and Sergio, D and Invernizzi, R and Tinoco, A and Pishchany, G and Vasan, RS and Balskus, E and Huttenhower, C and Vlamakis, H and Clish, C and Shaw, SY and Plichta, DR and Xavier, RJ},
title = {Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria.},
journal = {Cell},
volume = {187},
number = {8},
pages = {1834-1852.e19},
doi = {10.1016/j.cell.2024.03.014},
pmid = {38569543},
issn = {1097-4172},
mesh = {Humans ; *Bacteria/metabolism ; *Cardiovascular Diseases/metabolism ; *Cholesterol/analysis/blood/metabolism ; Feces/chemistry ; *Gastrointestinal Microbiome ; Longitudinal Studies ; Metabolome ; Metabolomics ; RNA, Ribosomal, 16S/metabolism ; },
abstract = {Accumulating evidence suggests that cardiovascular disease (CVD) is associated with an altered gut microbiome. Our understanding of the underlying mechanisms has been hindered by lack of matched multi-omic data with diagnostic biomarkers. To comprehensively profile gut microbiome contributions to CVD, we generated stool metagenomics and metabolomics from 1,429 Framingham Heart Study participants. We identified blood lipids and cardiovascular health measurements associated with microbiome and metabolome composition. Integrated analysis revealed microbial pathways implicated in CVD, including flavonoid, γ-butyrobetaine, and cholesterol metabolism. Species from the Oscillibacter genus were associated with decreased fecal and plasma cholesterol levels. Using functional prediction and in vitro characterization of multiple representative human gut Oscillibacter isolates, we uncovered conserved cholesterol-metabolizing capabilities, including glycosylation and dehydrogenation. These findings suggest that cholesterol metabolism is a broad property of phylogenetically diverse Oscillibacter spp., with potential benefits for lipid homeostasis and cardiovascular health.},
}

Humans
*Bacteria/metabolism
*Cardiovascular Diseases/metabolism
*Cholesterol/analysis/blood/metabolism
Feces/chemistry
*Gastrointestinal Microbiome
Longitudinal Studies
Metabolome
Metabolomics
RNA, Ribosomal, 16S/metabolism

@article {pmid38531781,
year = {2024},
author = {Jiang, X and Li, H and Ma, J and Li, H and Ma, X and Tang, Y and Li, J and Chi, X and Deng, Y and Zeng, S and Liu, Z},
title = {Role of Type VI secretion system in pathogenic remodeling of host gut microbiota during Aeromonas veronii infection.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38531781},
issn = {1751-7370},
support = {32160038//National Natural Science Foundation of China/ ; 2020WNLOKF019//Open Project Program of Wuhan National Laboratory for Optoelectronics/ ; },
mesh = {*Type VI Secretion Systems/genetics ; *Gastrointestinal Microbiome/physiology ; Aeromonas veronii/genetics ; Symbiosis ; Ecosystem ; Bacterial Proteins/genetics ; },
abstract = {Intestinal microbial disturbance is a direct cause of host disease. The bacterial Type VI secretion system (T6SS) often plays a crucial role in the fitness of pathogenic bacteria by delivering toxic effectors into target cells. However, its impact on the gut microbiota and host pathogenesis is poorly understood. To address this question, we characterized a new T6SS in the pathogenic Aeromonas veronii C4. First, we validated the secretion function of the core machinery of A. veronii C4 T6SS. Second, we found that the pathogenesis and colonization of A. veronii C4 is largely dependent on its T6SS. The effector secretion activity of A. veronii C4 T6SS not only provides an advantage in competition among bacteria in vitro, but also contributes to occupation of an ecological niche in the nutritionally deficient and anaerobic environment of the host intestine. Metagenomic analysis showed that the T6SS directly inhibits or eliminates symbiotic strains from the intestine, resulting in dysregulated gut microbiome homeostasis. In addition, we identified three unknown effectors, Tse1, Tse2, and Tse3, in the T6SS, which contribute to T6SS-mediated bacterial competition and pathogenesis by impairing targeted cell integrity. Our findings highlight that T6SS can remodel the host gut microbiota by intricate interplay between T6SS-mediated bacterial competition and altered host immune responses, which synergistically promote pathogenesis of A. veronii C4. Therefore, this newly characterized T6SS could represent a general interaction mechanism between the host and pathogen, and may offer a potential therapeutic target for controlling bacterial pathogens.},
}

*Type VI Secretion Systems/genetics
*Gastrointestinal Microbiome/physiology
Aeromonas veronii/genetics
Symbiosis
Ecosystem
Bacterial Proteins/genetics

@article {pmid38519112,
year = {2024},
author = {Deng, Y and Yang, S and Zhang, L and Chen, C and Cheng, X and Hou, C},
title = {Chronic bee paralysis virus exploits host antimicrobial peptides and alters gut microbiota composition to facilitate viral infection.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38519112},
issn = {1751-7370},
support = {31811530276//National Natural Science Foundation of China/ ; CAAS-ASTIP-2023//Agricultural Science, Technology Innovation Program of CAAS/ ; Y2021YJ25//Central Public-interest Scientific Institution Basal Research Fund/ ; },
mesh = {Bees ; Animals ; *RNA Viruses/physiology ; *Gastrointestinal Microbiome ; Antimicrobial Peptides ; *Insect Viruses/physiology ; *Viruses ; *Virus Diseases ; Paralysis ; },
abstract = {The significance of gut microbiota in regulating animal immune response to viral infection is increasingly recognized. However, how chronic bee paralysis virus (CBPV) exploits host immune to disturb microbiota for its proliferation remains elusive. Through histopathological examination, we discovered that the hindgut harbored the highest level of CBPV, and displayed visible signs of damages. The metagenomic analysis showed that a notable reduction in the levels of Snodgrassella alvi and Lactobacillus apis, and a significant increase in the abundance of the opportunistic pathogens such as Enterobacter hormaechei and Enterobacter cloacae following CBPV infection. Subsequent co-inoculation experiments showed that these opportunistic pathogens facilitated the CBPV proliferation, leading to accelerated mortality in bees and exacerbation of bloated abdomen symptoms after CBPV infection. The expression level of antimicrobial peptide (AMP) was found to be significantly up-regulated by over 1000 times in response to CBPV infection, as demonstrated by subsequent transcriptome and quantitative real-time PCR investigations. In particular, through correlation analysis and a bacteriostatic test revealed that the AMPs did not exhibit any inhibitory effect against the two opportunistic pathogens. However, they did demonstrate inhibitory activity against S. alvi and L. apis. Our findings provide different evidence that the virus infection may stimulate and utilize the host's AMPs to eradicate probiotic species and facilitate the proliferation of opportunistic bacteria. This process weakens the intestinal barrier and ultimately resulting in the typical bloated abdomen.},
}

Bees
Animals
*RNA Viruses/physiology
*Gastrointestinal Microbiome
Antimicrobial Peptides
*Insect Viruses/physiology
*Viruses
*Virus Diseases
Paralysis

@article {pmid38383853,
year = {2024},
author = {Ma, B and Wang, Y and Zhao, K and Stirling, E and Lv, X and Yu, Y and Hu, L and Tang, C and Wu, C and Dong, B and Xue, R and Dahlgren, RA and Tan, X and Dai, H and Zhu, YG and Chu, H and Xu, J},
title = {Biogeographic patterns and drivers of soil viromes.},
journal = {Nature ecology & evolution},
volume = {8},
number = {4},
pages = {717-728},
pmid = {38383853},
issn = {2397-334X},
support = {41721007//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42090060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42277283//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41991334//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Soil/chemistry ; Ecosystem ; Virome ; Soil Microbiology ; Ecology ; *Viruses/genetics ; },
abstract = {Viruses are crucial in shaping soil microbial functions and ecosystems. However, studies on soil viromes have been limited in both spatial scale and biome coverage. Here we present a comprehensive synthesis of soil virome biogeographic patterns using the Global Soil Virome dataset (GSV) wherein we analysed 1,824 soil metagenomes worldwide, uncovering 80,750 partial genomes of DNA viruses, 96.7% of which are taxonomically unassigned. The biogeography of soil viral diversity and community structure varies across different biomes. Interestingly, the diversity of viruses does not align with microbial diversity and contrasts with it by showing low diversity in forest and shrubland soils. Soil texture and moisture conditions are further corroborated as key factors affecting diversity by our predicted soil viral diversity atlas, revealing higher diversity in humid and subhumid regions. In addition, the binomial degree distribution pattern suggests a random co-occurrence pattern of soil viruses. These findings are essential for elucidating soil viral ecology and for the comprehensive incorporation of viruses into soil ecosystem models.},
}

*Soil/chemistry
Ecosystem
Virome
Soil Microbiology
Ecology
*Viruses/genetics

@article {pmid38191834,
year = {2024},
author = {Ashiqueali, SA and Chaudhari, D and Zhu, X and Noureddine, S and Siddiqi, S and Garcia, DN and Gostynska, A and Stawny, M and Rubis, B and Zanini, BM and Mansoor, MAM and Schneider, A and Naser, SA and Yadav, H and Masternak, MM},
title = {Fisetin modulates the gut microbiota alongside biomarkers of senescence and inflammation in a DSS-induced murine model of colitis.},
journal = {GeroScience},
volume = {46},
number = {3},
pages = {3085-3103},
pmid = {38191834},
issn = {2509-2723},
support = {R56 AG074499/AG/NIA NIH HHS/United States ; R56 AG074499/GF/NIH HHS/United States ; },
mesh = {Female ; Animals ; Mice ; *Gastrointestinal Microbiome ; Disease Models, Animal ; *Colitis/chemically induced/drug therapy/metabolism ; Inflammation ; *Inflammatory Bowel Diseases/microbiology ; Biomarkers ; *MicroRNAs ; *Flavonols ; },
abstract = {Colitis, a subtype of inflammatory bowel disease (IBD), is a multifactorial disorder characterized by chronic inflammation of the colon. Among various experimental models used in the study of IBD, the chemical colitogenic dextran sulfate sodium (DSS) is most commonly employed to induce colitis in vivo. In the search for new therapeutic strategies, Fisetin, a flavonoid found in many fruits and vegetables, has recently garnered attention for its senolytic properties. Female mice were administered 2.5% DSS in sterile drinking water and were subsequently treated with Fisetin or vehicle by oral gavage. DSS significantly upregulated beta-galactosidase activity in colonic proteins, while Fisetin remarkably inhibited its activity to baseline levels. Particularly, qPCR revealed that the senescence and inflammation markers Vimentin and Ptgs2 were elevated by DSS exposure with Fisetin treatment inhibiting the expression of p53, Bcl2, Cxcl1, and Mcp1, indicating that the treatment reduced senescent cell burden in the DSS targeted intestine. Alongside, senescence and inflammation associated miRNAs miR-149-5p, miR-96-5p, miR-34a-5p, and miR-30e-5p were significantly inhibited by DSS exposure and restored by Fisetin treatment, revealing novel targets for the treatment of IBDs. Metagenomics was implemented to assess impacts on the microbiota, with DSS increasing the prevalence of bacteria in the phyla Bacteroidetes. Meanwhile, Fisetin restored gut health through increased abundance of Akkermansia muciniphila, which is negatively correlated with senescence and inflammation. Our study suggests that Fisetin mitigates DSS-induced colitis by targeting senescence and inflammation and restoring beneficial bacteria in the gut indicating its potential as a therapeutic intervention for IBDs.},
}

Female
Animals
Mice
*Gastrointestinal Microbiome
Disease Models, Animal
*Colitis/chemically induced/drug therapy/metabolism
Inflammation
*Inflammatory Bowel Diseases/microbiology
Biomarkers
*MicroRNAs
*Flavonols

@article {pmid37000389,
year = {2024},
author = {Ganesan, R and Gupta, H and Jeong, JJ and Sharma, SP and Won, SM and Oh, KK and Yoon, SJ and Han, SH and Yang, YJ and Baik, GH and Bang, CS and Kim, DJ and Suk, KT},
title = {Characteristics of microbiome-derived metabolomics according to the progression of alcoholic liver disease.},
journal = {Hepatology international},
volume = {18},
number = {2},
pages = {486-499},
pmid = {37000389},
issn = {1936-0541},
support = {NRF-2018M3A9F3020956//Ministry of National Defense/ ; NRF-2019R1I1A3A01060447//Ministry of National Defense/ ; NRF-2020R1A6A1A03043026//Ministry of National Defense/ ; P0020622//Korea Institute for Advancement of Technology/ ; },
mesh = {Humans ; Propionates ; RNA, Ribosomal, 16S/genetics ; *Liver Diseases, Alcoholic ; Liver Cirrhosis, Alcoholic ; *Gastrointestinal Microbiome ; Indoles ; Bile Acids and Salts ; },
abstract = {BACKGROUND AND AIM: The prevalence and severity of alcoholic liver disease (ALD) are increasing. The incidence of alcohol-related cirrhosis has risen up to 2.5%. This study aimed to identify novel metabolite mechanisms involved in the development of ALD in patients. The use of gut microbiome-derived metabolites is increasing in targeted therapies. Identifying metabolic compounds is challenging due to the complex patterns that have long-term effects on ALD. We investigated the specific metabolite signatures in ALD patients.

METHODS: This study included 247 patients (heathy control, HC: n = 62, alcoholic fatty liver, AFL; n = 25, alcoholic hepatitis, AH; n = 80, and alcoholic cirrhosis, AC, n = 80) identified, and stool samples were collected. 16S rRNA sequencing and metabolomics were performed with MiSeq sequencer and liquid chromatography coupled to time-of-flight-mass spectrometry (LC-TOF-MS), respectively. The untargeted metabolites in AFL, AH, and AC samples were evaluated by multivariate statistical analysis and metabolic pathotypic expression. Metabolic network classifiers were used to predict the pathway expression of the AFL, AH, and AC stages.

RESULTS: The relative abundance of Proteobacteria was increased and the abundance of Bacteroides was decreased in ALD samples (p = 0.001) compared with that in HC samples. Fusobacteria levels were higher in AH samples (p = 0.0001) than in HC samples. Untargeted metabolomics was applied to quantitatively screen 103 metabolites from each stool sample. Indole-3-propionic acid levels are significantly lower in AH and AC (vs. HC, p = 0.001). Indole-3-lactic acid (ILA: p = 0.04) levels were increased in AC samples. AC group showed an increase in indole-3-lactic acid (vs. HC, p = 0.040) level. Compared with that in HC samples, the levels of short-chain fatty acids (SCFAs: acetic acid, butyric acid, propionic acid, iso-butyric acid, and iso-valeric acid) and bile acids (lithocholic acids) were significantly decreased in AC. The pathways of linoleic acid metabolism, indole compounds, histidine metabolism, fatty acid degradation, and glutamate metabolism were closely associated with ALD metabolism.

CONCLUSIONS: This study identified that microbial metabolic dysbiosis is associated with ALD-related metabolic dysfunction. The SCFAs, bile acids, and indole compounds were depleted during ALD progression.

CLINICAL TRIAL: Clinicaltrials.gov, number NCT04339725.},
}

Humans
Propionates
RNA, Ribosomal, 16S/genetics
*Liver Diseases, Alcoholic
Liver Cirrhosis, Alcoholic
*Gastrointestinal Microbiome
Indoles
Bile Acids and Salts

@article {pmid38597375,
year = {2024},
author = {Arunan, B and Talukdar, D and Swain, S and Varadarajan, A and Sarda, R and Singh, G and Nischal, N and Soneja, M and Bakshi, S and Jana, P and Tanwar, S and Sikka, K and Verma, H and Subramanian, A and Xess, I and Wig, N and Das, B and Ray, A},
title = {Metagenomic insights into fungal community composition of the nasopharyngeal region of COVID-19 associated mucormycosis patients from India.},
journal = {Journal of medical virology},
volume = {96},
number = {4},
pages = {e29601},
doi = {10.1002/jmv.29601},
pmid = {38597375},
issn = {1096-9071},
support = {//All-India Institute of Medical Sciences Intramural Grant/ ; RAD-22017/19/2022-KGD-DBT//Department of Biotechnology (DBT), Govt. of India/ ; },
mesh = {Humans ; *Mucormycosis/epidemiology ; *Mycobiome ; *COVID-19 ; Nose ; India/epidemiology ; },
abstract = {Coronavirus disease 2019 (COVID-19) associated mucormycosis (CAM) was reported predominantly from India during the second wave of COVID-19 and has a high mortality rate. The present study aims to understand the fungal community composition of the nasopharyngeal region of CAM-infected individuals and compare it with severe COVID-19 patients and healthy controls. The fungal community composition was decoded by analyzing the sequence homology of the internal transcribed spacer-2-(ITS-2) region of metagenomic DNA extracted from the upper respiratory samples. The alpha-diversity indices were found to be significantly altered in CAM patients (p < 0.05). Interestingly, a higher abundance of Candida africana, Candida haemuloni, Starmerella floris, and Starmerella lactiscondensi was observed exclusively in CAM patients. The interindividual changes in mycobiome composition were well supported by beta-diversity analysis (p < 0.05). The current study provides insights into the dysbiosis of the nasal mycobiome during CAM infection. In conclusion, our study shows that severe COVID-19 and CAM are associated with alteration in mycobiome as compared to healthy controls. However, the sequential alteration in the fungal flora which ultimately leads to the development of CAM needs to be addressed by future studies.},
}

Humans
*Mucormycosis/epidemiology
*Mycobiome
*COVID-19
Nose
India/epidemiology

@article {pmid38594375,
year = {2024},
author = {Poulsen, CS and Hesse, D and Fernandes, GR and Hansen, TH and Kern, T and Linneberg, A and Van Espen, L and Jørgensen, T and Nielsen, T and Alibegovic, AC and Matthijnssens, J and Pedersen, O and Vestergaard, H and Hansen, T and Andersen, MK},
title = {Characterization of the gut bacterial and viral microbiota in latent autoimmune diabetes in adults.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {8315},
pmid = {38594375},
issn = {2045-2322},
support = {1S25720N//Fonds voor Wetenschappelijk Onderzoek/ ; po0115//The Danish Diabetes Academy/ ; DFF-5053-00159//Danish Council for Independent Research/ ; },
mesh = {Adult ; Humans ; *Diabetes Mellitus, Type 1/genetics ; *Diabetes Mellitus, Type 2/genetics ; *Latent Autoimmune Diabetes in Adults/genetics ; *Gastrointestinal Microbiome/genetics ; Adenosine Deaminase ; RNA, Ribosomal, 16S/genetics ; Intercellular Signaling Peptides and Proteins ; Insulin ; *Glucose Intolerance ; },
abstract = {Latent autoimmune diabetes in adults (LADA) is a heterogeneous disease characterized by autoantibodies against insulin producing pancreatic beta cells and initial lack of need for insulin treatment. The aim of the present study was to investigate if individuals with LADA have an altered gut microbiota relative to non-diabetic control subjects, individuals with type 1 diabetes (T1D), and individuals with type 2 diabetes (T2D). Bacterial community profiling was performed with primers targeting the variable region 4 of the 16S rRNA gene and sequenced. Amplicon sequence variants (ASVs) were generated with DADA2 and annotated to the SILVA database. The gut virome was sequenced, using a viral particle enrichment and metagenomics approach, assembled, and quantified to describe the composition of the viral community. Comparison of the bacterial alpha- and beta-diversity measures revealed that the gut bacteriome of individuals with LADA resembled that of individuals with T2D. Yet, specific genera were found to differ in abundance in individuals with LADA compared with T1D and T2D, indicating that LADA has unique taxonomical features. The virome composition reflected the stability of the most dominant order Caudovirales and the families Siphoviridae, Podoviridae, and Inoviridae, and the dominant family Microviridae. Further studies are needed to confirm these findings.},
}

Adult
Humans
*Diabetes Mellitus, Type 1/genetics
*Diabetes Mellitus, Type 2/genetics
*Latent Autoimmune Diabetes in Adults/genetics
*Gastrointestinal Microbiome/genetics
Adenosine Deaminase
RNA, Ribosomal, 16S/genetics
Intercellular Signaling Peptides and Proteins
Insulin
*Glucose Intolerance

@article {pmid38594362,
year = {2024},
author = {Lateef, AA and Azeez, AA and Ren, W and Hamisu, HS and Oke, OA and Asiegbu, FO},
title = {Bacterial biota associated with the invasive insect pest Tuta absoluta (Meyrick).},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {8268},
pmid = {38594362},
issn = {2045-2322},
support = {Grant number 4400T-2002//Maa- ja MetsätalousministeriÖ/ ; },
mesh = {Animals ; *Moths/physiology ; RNA, Ribosomal, 16S/genetics ; Insecta ; Larva/physiology ; *Microbiota ; *Solanum lycopersicum ; Bacteria/genetics ; },
abstract = {Tuta absoluta (the tomato pinworm) is an invasive insect pest with a highly damaging effect on tomatoes causing between 80 and 100% yield losses if left uncontrolled. Resistance to chemical pesticides have been reported in some T. absoluta populations. Insect microbiome plays an important role in the behavior, physiology, and survivability of their host. In a bid to explore and develop an alternative control method, the associated microbiome of this insect was studied. In this study, we unraveled the bacterial biota of T. absoluta larvae and adults by sequencing and analyzing the 16S rRNA V3-V4 gene regions using Illumina NovaSeq PE250. Out of 2,092,015 amplicon sequence variants (ASVs) recovered from 30 samples (15 larvae and 15 adults), 1,268,810 and 823,205 ASVs were obtained from the larvae and adults, respectively. A total of 433 bacterial genera were shared between the adults and larval samples while 264 and 139 genera were unique to the larvae and adults, respectively. Amplicon metagenomic analyses of the sequences showed the dominance of the phylum Proteobacteria in the adult samples while Firmicutes and Proteobacteria dominated in the larval samples. Linear discriminant analysis effect size (LEfSe) comparison revealed the genera Pseudomonas, Delftia and Ralstonia to be differentially enriched in the adult samples while Enterococcus, Enterobacter, Lactococcus, Klebsiella and Wiessella were differentially abundant in the larvae. The diversity indices showed that the bacterial communities were not different between the insect samples collected from different geographical regions. However, the bacterial communities significantly differed based on the sample type between larvae and adults. A co-occurrence network of significantly correlated taxa revealed a strong interaction between the microbial communities. The functional analysis of the microbiome using FAPROTAX showed that denitrification, arsenite oxidation, methylotrophy and methanotrophy as the active functional groups of the adult and larvae microbiomes. Our results have revealed the core taxonomic, functional, and interacting microbiota of T. absoluta and these indicate that the larvae and adults harbor a similar but transitory set of bacteria. The results provide a novel insight and a basis for exploring microbiome-based biocontrol strategy for this invasive insect pest as well as the ecological significance of some of the identified microbiota is discussed.},
}

Animals
*Moths/physiology
RNA, Ribosomal, 16S/genetics
Insecta
Larva/physiology
*Microbiota
*Solanum lycopersicum
Bacteria/genetics

@article {pmid38593340,
year = {2024},
author = {Suárez-Moo, P and Prieto-Davó, A},
title = {Biosynthetic potential of the sediment microbial subcommunities of an unexplored karst ecosystem and its ecological implications.},
journal = {MicrobiologyOpen},
volume = {13},
number = {2},
pages = {e1407},
pmid = {38593340},
issn = {2045-8827},
support = {//Consejo Nacional de Humanidades Ciencias y Tecnologías (CONAHCYT), México project A1-S-10785 (APD) and postdoctoral fellowship (362331) (PSM)/ ; },
mesh = {Bacteria/genetics ; Metagenome ; *Microbiota ; Multigene Family ; *Bacillaceae/genetics ; *Biological Products ; Biosynthetic Pathways/genetics ; },
abstract = {Microbial communities from various environments have been studied in the quest for new natural products with a broad range of applications in medicine and biotechnology. We employed an enrichment method and genome mining tools to examine the biosynthetic potential of microbial communities in the sediments of a coastal sinkhole within the karst ecosystem of the Yucatán Peninsula, Mexico. Our investigation led to the detection of 203 biosynthetic gene clusters (BGCs) and 55 secondary metabolites (SMs) within 35 high-quality metagenome-assembled genomes (MAGs) derived from these subcommunities. The most abundant types of BGCs were Terpene, Nonribosomal peptide-synthetase, and Type III polyketide synthase. Some of the in silico identified BGCs and SMs have been previously reported to exhibit biological activities against pathogenic bacteria and fungi. Others could play significant roles in the sinkhole ecosystem, such as iron solubilization and osmotic stress protection. Interestingly, 75% of the BGCs showed no sequence homology with bacterial BGCs previously reported in the MiBIG database. This suggests that the microbial communities in this environment could be an untapped source of genes encoding novel specialized compounds. The majority of the BGCs were identified in pathways found in the genus Virgibacillus, followed by Sporosarcina, Siminovitchia, Rhodococcus, and Halomonas. The latter, along with Paraclostridium and Lysinibacillus, had the highest number of identified BGC types. This study offers fresh insights into the potential ecological role of SMs from sediment microbial communities in an unexplored environment, underscoring their value as a source of novel natural products.},
}

Bacteria/genetics
Metagenome
*Microbiota
Multigene Family
*Bacillaceae/genetics
*Biological Products
Biosynthetic Pathways/genetics

@article {pmid38426620,
year = {2024},
author = {Zhang, L and Yuan, L and Wen, Y and Zhang, M and Huang, S and Wang, S and Zhao, Y and Hao, X and Li, L and Gao, Q and Wang, Y and Zhang, S and Huang, S and Liu, K and Yu, X and Li, D and Xu, J and Zhao, B and Zhang, L and Zhang, H and Zhou, W and Ai, C},
title = {Maize functional requirements drive the selection of rhizobacteria under long-term fertilization practices.},
journal = {The New phytologist},
volume = {242},
number = {3},
pages = {1275-1288},
doi = {10.1111/nph.19653},
pmid = {38426620},
issn = {1469-8137},
support = {2022YFD1900900//National Key Research and Development Program of China/ ; 32322076//National Natural Science Foundation of China/ ; 32272817//National Natural Science Foundation of China/ ; 05//Smart Fertilization Project/ ; BX20230425//Postdoctoral Innovation Talents Support Program/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; },
mesh = {Zea mays/microbiology ; Soil Microbiology ; Soil/chemistry ; *Microbiota ; *Alphaproteobacteria ; Rhizosphere ; Fertilization ; },
abstract = {Rhizosphere microbiomes are pivotal for crop fitness, but the principles underlying microbial assembly during root-soil interactions across soils with different nutrient statuses remain elusive. We examined the microbiomes in the rhizosphere and bulk soils of maize plants grown under six long-term (≥ 29 yr) fertilization experiments in three soil types across middle temperate to subtropical zones. The assembly of rhizosphere microbial communities was primarily driven by deterministic processes. Plant selection interacted with soil types and fertilization regimes to shape the structure and function of rhizosphere microbiomes. Predictive functional profiling showed that, to adapt to nutrient-deficient conditions, maize recruited more rhizobacteria involved in nutrient availability from bulk soil, although these functions were performed by different species. Metagenomic analyses confirmed that the number of significantly enriched Kyoto Encyclopedia of Genes and Genomes Orthology functional categories in the rhizosphere microbial community was significantly higher without fertilization than with fertilization. Notably, some key genes involved in carbon, nitrogen, and phosphorus cycling and purine metabolism were dominantly enriched in the rhizosphere soil without fertilizer input. In conclusion, our results show that maize selects microbes at the root-soil interface based on microbial functional traits beneficial to its own performance, rather than selecting particular species.},
}

Zea mays/microbiology
Soil Microbiology
Soil/chemistry
*Microbiota
*Alphaproteobacteria
Rhizosphere
Fertilization

@article {pmid37823484,
year = {2024},
author = {Straub, TJ and Lombardo, MJ and Bryant, JA and Diao, L and Lodise, TP and Freedberg, DE and Wortman, JR and Litcofsky, KD and Hasson, BR and McGovern, BH and Ford, CB and Henn, MR},
title = {Impact of a Purified Microbiome Therapeutic on Abundance of Antimicrobial Resistance Genes in Patients With Recurrent Clostridioides difficile Infection.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {78},
number = {4},
pages = {833-841},
pmid = {37823484},
issn = {1537-6591},
support = {//Seres Therapeutics/ ; },
mesh = {Adult ; Humans ; Female ; Aged ; Male ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Fecal Microbiota Transplantation ; *Clostridioides difficile/genetics ; Drug Resistance, Bacterial ; *Microbiota ; *Clostridium Infections/microbiology ; Bacteria ; Firmicutes ; },
abstract = {BACKGROUND: The gastrointestinal microbiota is an important line of defense against colonization with antimicrobial resistant (AR) bacteria. In this post hoc analysis of the phase 3 ECOSPOR III trial, we assessed impact of a microbiota-based oral therapeutic (fecal microbiota spores, live; VOWST Oral Spores [VOS], formerly SER-109]; Seres Therapeutics) compared with placebo, on AR gene (ARG) abundance in patients with recurrent Clostridioides difficile infection (rCDI).

METHODS: Adults with rCDI were randomized to receive VOS or placebo orally for 3 days following standard-of-care antibiotics. ARG and taxonomic profiles were generated using whole metagenomic sequencing of stool at baseline and weeks 1, 2, 8, and 24 posttreatment.

RESULTS: Baseline (n = 151) and serial posttreatment stool samples collected through 24 weeks (total N = 472) from 182 patients (59.9% female; mean age: 65.5 years) in ECOSPOR III as well as 68 stool samples obtained at a single time point from a healthy cohort were analyzed. Baseline ARG abundance was similar between arms and significantly elevated versus the healthy cohort. By week 1, there was a greater decline in ARG abundance in VOS versus placebo (P = .003) in association with marked decline of Proteobacteria and repletion of spore-forming Firmicutes, as compared with baseline. We observed abundance of Proteobacteria and non-spore-forming Firmicutes were associated with ARG abundance, while spore-forming Firmicutes abundance was negatively associated.

CONCLUSIONS: This proof-of-concept analysis suggests that microbiome remodeling with Firmicutes spores may be a potential novel approach to reduce ARG colonization in the gastrointestinal tract.},
}

Adult
Humans
Female
Aged
Male
Anti-Bacterial Agents/pharmacology/therapeutic use
Fecal Microbiota Transplantation
*Clostridioides difficile/genetics
Drug Resistance, Bacterial
*Microbiota
*Clostridium Infections/microbiology
Bacteria
Firmicutes

@article {pmid38589361,
year = {2024},
author = {Barker-Tejeda, TC and Zubeldia-Varela, E and Macías-Camero, A and Alonso, L and Martín-Antoniano, IA and Rey-Stolle, MF and Mera-Berriatua, L and Bazire, R and Cabrera-Freitag, P and Shanmuganathan, M and Britz-McKibbin, P and Ubeda, C and Francino, MP and Barber, D and Ibáñez-Sandín, MD and Barbas, C and Pérez-Gordo, M and Villaseñor, A},
title = {Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3004},
pmid = {38589361},
issn = {2041-1723},
support = {PI17/01087//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PI19/00044//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PI20/01366//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PCI2018-092930//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; },
mesh = {Infant ; Male ; Adult ; Female ; Humans ; Child ; Aged ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; Multiomics ; Metabolome ; Feces/microbiology ; Mothers ; },
abstract = {The human gut microbiome establishes and matures during infancy, and dysregulation at this stage may lead to pathologies later in life. We conducted a multi-omics study comprising three generations of family members to investigate the early development of the gut microbiota. Fecal samples from 200 individuals, including infants (0-12 months old; 55% females, 45% males) and their respective mothers and grandmothers, were analyzed using two independent metabolomics platforms and metagenomics. For metabolomics, gas chromatography and capillary electrophoresis coupled to mass spectrometry were applied. For metagenomics, both 16S rRNA gene and shotgun sequencing were performed. Here we show that infants greatly vary from their elders in fecal microbiota populations, function, and metabolome. Infants have a less diverse microbiota than adults and present differences in several metabolite classes, such as short- and branched-chain fatty acids, which are associated with shifts in bacterial populations. These findings provide innovative biochemical insights into the shaping of the gut microbiome within the same generational line that could be beneficial in improving childhood health outcomes.},
}

Infant
Male
Adult
Female
Humans
Child
Aged
Infant, Newborn
*Gastrointestinal Microbiome/genetics
RNA, Ribosomal, 16S/genetics/metabolism
Multiomics
Metabolome
Feces/microbiology
Mothers

@article {pmid38587642,
year = {2024},
author = {Srinivasan, S and Jnana, A and Murali, TS},
title = {Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {56},
pmid = {38587642},
issn = {1432-184X},
support = {CRG/2022/003227//Science and Engineering Research Board/ ; },
mesh = {Humans ; *Microbial Interactions ; *Microbiota ; Microbial Consortia ; Coculture Techniques ; Community Networks ; },
abstract = {Microbial interactions function as a fundamental unit in complex ecosystems. By characterizing the type of interaction (positive, negative, neutral) occurring in these dynamic systems, one can begin to unravel the role played by the microbial species. Towards this, various methods have been developed to decipher the function of the microbial communities. The current review focuses on the various qualitative and quantitative methods that currently exist to study microbial interactions. Qualitative methods such as co-culturing experiments are visualized using microscopy-based techniques and are combined with data obtained from multi-omics technologies (metagenomics, metabolomics, metatranscriptomics). Quantitative methods include the construction of networks and network inference, computational models, and development of synthetic microbial consortia. These methods provide a valuable clue on various roles played by interacting partners, as well as possible solutions to overcome pathogenic microbes that can cause life-threatening infections in susceptible hosts. Studying the microbial interactions will further our understanding of complex less-studied ecosystems and enable design of effective frameworks for treatment of infectious diseases.},
}

Humans
*Microbial Interactions
*Microbiota
Microbial Consortia
Coculture Techniques
Community Networks

@article {pmid38585649,
year = {2024},
author = {Yang, Y and Chen, J and Gao, H and Cui, M and Zhu, M and Xiang, X and Wang, Q},
title = {Characterization of the gut microbiota and fecal and blood metabolomes under various factors in urban children from Northwest China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1374544},
pmid = {38585649},
issn = {2235-2988},
mesh = {Pregnancy ; Child ; Humans ; Female ; *Gastrointestinal Microbiome ; Caffeine ; Cesarean Section ; Urban Population ; Metabolome ; Amino Acids ; },
abstract = {INTRODUCTION: Children have regional dynamics in the gut microbiota development trajectory. Hitherto, the features and influencing factors of the gut microbiota and fecal and plasma metabolites in children from Northwest China remain unclear.

METHODS: Shotgun metagenomic sequencing and untargeted metabolomics were performed on 100 healthy volunteers aged 2-12 years.

RESULTS: Age, body mass index (BMI), regular physical exercise (RPE), and delivery mode (DM) significantly affect gut microbiota and metabolites. Lactobacillus, Butyricimonas, Prevotella, Alistipes, and predicted pathway propanoate production were significantly increased with age while Bifidobacterium breve, B. animalis, B. pseudocatenulatum, Streptococcus infantis, and carbohydrate degradation were decreased. Fecal metabolome revealed that the metabolism of caffeine, amino acids, and lipid significantly increased with age while galactose metabolism decreased. Noticeably, BMI was positively associated with pathogens including Erysipelatoclostridium ramosum, Parabacteroides distasonis, Ruminococcus gnavus, and amino acid metabolism but negatively associated with beneficial Akkermansia muciniphila, Alistipes finegoldii, Eubacterium ramulus, and caffeine metabolism. RPE has increased probiotic Faecalibacterium prausnitzii and Anaerostipes hadrus, acetate and lactate production, and major nutrient metabolism in gut and plasma, but decreased pathobiont Bilophila wadsworthia, taurine degradation, and pentose phosphate pathway. Interestingly, DM affects the gut microbiota and metabolites throughout the whole childhood. Bifidobacterium animalis, Lactobacillus mucosae, L. ruminis, primary bile acid, and neomycin biosynthesis were enriched in eutocia, while anti-inflammatory Anaerofustis stercorihominis, Agathobaculum butyriciproducens, Collinsella intestinalis, and pathogenic Streptococcus salivarius, Catabacter hongkongensis, and amino acid metabolism were enriched in Cesarean section children.

DISCUSSION: Our results provided theoretical and data foundation for the gut microbiota and metabolites in preadolescent children's growth and development in Northwest China.},
}

Pregnancy
Child
Humans
Female
*Gastrointestinal Microbiome
Caffeine
Cesarean Section
Urban Population
Metabolome
Amino Acids

@article {pmid38584937,
year = {2024},
author = {Tang, H and Huang, Y and Yuan, D and Liu, J},
title = {Atherosclerosis, gut microbiome, and exercise in a meta-omics perspective: a literature review.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17185},
pmid = {38584937},
issn = {2167-8359},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Cardiovascular Diseases/metabolism ; Metabolomics/methods ; Metabolome ; *Atherosclerosis ; },
abstract = {BACKGROUND: Cardiovascular diseases are the leading cause of death worldwide, significantly impacting public health. Atherosclerotic cardiovascular diseases account for the majority of these deaths, with atherosclerosis marking the initial and most critical phase of their pathophysiological progression. There is a complex relationship between atherosclerosis, the gut microbiome's composition and function, and the potential mediating role of exercise. The adaptability of the gut microbiome and the feasibility of exercise interventions present novel opportunities for therapeutic and preventative approaches.

METHODOLOGY: We conducted a comprehensive literature review using professional databases such as PubMed and Web of Science. This review focuses on the application of meta-omics techniques, particularly metagenomics and metabolomics, in studying the effects of exercise interventions on the gut microbiome and atherosclerosis.

RESULTS: Meta-omics technologies offer unparalleled capabilities to explore the intricate connections between exercise, the microbiome, the metabolome, and cardiometabolic health. This review highlights the advancements in metagenomics and metabolomics, their applications in research, and examines how exercise influences the gut microbiome. We delve into the mechanisms connecting these elements from a metabolic perspective. Metagenomics provides insight into changes in microbial strains post-exercise, while metabolomics sheds light on the shifts in metabolites. Together, these approaches offer a comprehensive understanding of how exercise impacts atherosclerosis through specific mechanisms.

CONCLUSIONS: Exercise significantly influences atherosclerosis, with the gut microbiome serving as a critical intermediary. Meta-omics technology holds substantial promise for investigating the gut microbiome; however, its methodologies require further refinement. Additionally, there is a pressing need for more extensive cohort studies to enhance our comprehension of the connection among these element.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Cardiovascular Diseases/metabolism
Metabolomics/methods
Metabolome
*Atherosclerosis

@article {pmid38417116,
year = {2024},
author = {Zheng, R and Wang, C and Sun, C},
title = {Deep-sea in situ and laboratory multi-omics provide insights into the sulfur assimilation of a deep-sea Chloroflexota bacterium.},
journal = {mBio},
volume = {15},
number = {4},
pages = {e0000424},
pmid = {38417116},
issn = {2150-7511},
support = {LSKJ202203103//Science and Technology Innovation Project of Laoshan Laboratory/ ; },
mesh = {Proteomics ; Multiomics ; Thiosulfates/metabolism ; Oxidation-Reduction ; Bacteria/genetics ; *Chloroflexi/genetics ; *Microbiota ; Sulfur/metabolism ; Phylogeny ; },
abstract = {UNLABELLED: Chloroflexota bacteria are abundant and globally distributed in various deep-sea ecosystems. It has been reported based on metagenomics data that two deep-sea Chloroflexota lineages (the SAR202 group and Dehalococcoidia class) have the potential to drive sulfur cycling. However, the absence of cultured Chloroflexota representatives is a significant bottleneck toward understanding their contribution to the deep-sea sulfur cycling. In this study, we find that Phototrophicus methaneseepsis ZRK33 isolated from deep-sea sediment has a heterotrophic lifestyle and can assimilate sulfate and thiosulfate. Using combined physiological, genomic, proteomic, and in situ transcriptomic methods, we find that strain ZRK33 can perform assimilatory sulfate reduction in both laboratory and deep-sea conditions. Metabolism of sulfate or thiosulfate by strain ZRK33 significantly promotes the transport and degradation of various macromolecules and thereby stimulates the energy production. In addition, metagenomic results show that genes associated with assimilatory and dissimilatory sulfate reduction are ubiquitously distributed in the metagenome-assembled genomes of Chloroflexota members derived from deep-sea sediments. Metatranscriptomic results also show that the expression levels of related genes are upregulated, strongly suggesting that Chloroflexota bacteria may play undocumented roles in deep-sea sulfur cycling.

IMPORTANCE: The cycling of sulfur is one of Earth's major biogeochemical processes and is closely related to the energy metabolism of microorganisms living in the deep-sea cold seep and hydrothermal vents. To date, some of the members of Chloroflexota are proposed to play a previously unrecognized role in sulfur cycling. However, the sulfur metabolic characteristics of deep-sea Chloroflexota bacteria have never been reported, and remain to be verified in cultured deep-sea representatives. Here, we show that the deep-sea Chloroflexota bacterium ZRK33 can perform sulfate assimilation in both laboratory and deep-sea conditions, which expands our knowledge of the sulfur metabolic potential of deep-sea Chloroflexota bacteria. We also show that the genes associated with assimilatory and dissimilatory sulfate reduction ubiquitously distribute in the deep-sea Chloroflexota members, providing hints to the roles of Chloroflexota bacteria in deep-sea sulfur biogeochemical cycling.},
}

Proteomics
Multiomics
Thiosulfates/metabolism
Oxidation-Reduction
Bacteria/genetics
*Chloroflexi/genetics
*Microbiota
Sulfur/metabolism
Phylogeny

@article {pmid37344611,
year = {2024},
author = {Acar, C and Celik, SK and Ozdemirel, HO and Tuncdemir, BE and Alan, S and Mergen, H},
title = {Composition of the colon microbiota in the individuals with inflammatory bowel disease and colon cancer.},
journal = {Folia microbiologica},
volume = {69},
number = {2},
pages = {333-345},
pmid = {37344611},
issn = {1874-9356},
support = {FCD-2020-2065//Inönü Üniversitesi/ ; },
mesh = {Humans ; *Crohn Disease/microbiology ; *Inflammatory Bowel Diseases/microbiology ; *Microbiota ; *Colonic Neoplasms ; *Basidiomycota ; Intestinal Mucosa/microbiology ; },
abstract = {The human intestine is a habitat for microorganisms and, recently, the composition of the intestinal microbiota has been correlated with the etiology of diseases such as inflammations, sores, and tumors. Although many studies have been conducted to understand the composition of that microbiota, expanding these studies to more samples and different backgrounds will improve our knowledge. In this work, we showed the colon microbiota composition and diversity of healthy subjects, patients with inflammatory bowel disease (IBD), and colon cancer by metagenomic sequencing. Our results indicated that the relative abundance of prokaryotic and eukaryotic microbes differs between the healthy vs. tumor biopsies, tumor vs. IBD biopsies, and fresh vs. paraffin-embedded tumor biopsies. Fusobacterium, Escherichia-Shigella, and Streptococcus genera were relatively abundant in fresh tumor biopsies, while Pseudomonas was significantly elevated in IBD biopsies. Additionally, another opportunist pathogen Malasseziales was revealed as the most abundant fungal clade in IBD biopsies, especially in ulcerative colitis. We also found that, while the Basidiomycota:Ascomycota ratio was slightly lower in tumor biopsies compared to biopsies from healthy subjects, there was a significant increase in IBD biopsies. Our work will contribute to the known diversity of prokaryotic and eukaryotic microbes in the colon biopsies in patients with IBD and colon cancer.},
}

Humans
*Crohn Disease/microbiology
*Inflammatory Bowel Diseases/microbiology
*Microbiota
*Colonic Neoplasms
*Basidiomycota
Intestinal Mucosa/microbiology

@article {pmid38581039,
year = {2024},
author = {Li, Y and Liu, Y and Cui, J and Zhu, M and Wang, W and Chen, K and Huang, L and Liu, Y},
title = {Oral-gut microbial transmission promotes diabetic coronary heart disease.},
journal = {Cardiovascular diabetology},
volume = {23},
number = {1},
pages = {123},
pmid = {38581039},
issn = {1475-2840},
support = {82022076//National Outstanding Youth Foundation of China/ ; },
mesh = {Humans ; Animals ; Mice ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Fusobacterium nucleatum/physiology ; *Coronary Artery Disease/etiology ; *Diabetes Mellitus ; },
abstract = {BACKGROUND: Diabetes is a predominant driver of coronary artery disease worldwide. This study aims to unravel the distinct characteristics of oral and gut microbiota in diabetic coronary heart disease (DCHD). Simultaneously, we aim to establish a causal link between the diabetes-driven oral-gut microbiota axis and increased susceptibility to diabetic myocardial ischemia-reperfusion injury (MIRI).

METHODS: We comprehensively investigated the microbial landscape in the oral and gut microbiota in DCHD using a discovery cohort (n = 183) and a validation chohort (n = 68). Systematically obtained oral (tongue-coating) and fecal specimens were subjected to metagenomic sequencing and qPCR analysis, respectively, to holistically characterize the microbial consortia. Next, we induced diabetic MIRI by administering streptozotocin to C57BL/6 mice and subsequently investigated the potential mechanisms of the oral-gut microbiota axis through antibiotic pre-treatment followed by gavage with specific bacterial strains (Fusobacterium nucleatum or fecal microbiota from DCHD patients) to C57BL/6 mice.

RESULTS: Specific microbial signatures such as oral Fusobacterium nucleatum and gut Lactobacillus, Eubacterium, and Roseburia faecis, were identified as potential microbial biomarkers in DCHD. We further validated that oral Fusobacterium nucleatum and gut Lactobacillus are increased in DCHD patients, with a positive correlation between the two. Experimental evidence revealed that in hyperglycemic mice, augmented Fusobacterium nucleatum levels in the oral cavity were accompanied by an imbalance in the oral-gut axis, characterized by an increased coexistence of Fusobacterium nucleatum and Lactobacillus, along with elevated cardiac miRNA-21 and a greater extent of myocardial damage indicated by TTC, HE, TUNEL staining, all of which contributed to exacerbated MIRI.

CONCLUSION: Our findings not only uncover dysregulation of the oral-gut microbiota axis in diabetes patients but also highlight the pivotal intermediary role of the increased abundance of oral F. nucleatum and gut Lactobacillus in exacerbating MIRI. Targeting the oral-gut microbiota axis emerges as a potent strategy for preventing and treating DCHD. Oral-gut microbial transmission constitutes an intermediate mechanism by which diabetes influences myocardial injury, offering new insights into preventing acute events in diabetic patients with coronary heart disease.},
}

Humans
Animals
Mice
*Gastrointestinal Microbiome
Mice, Inbred C57BL
Fusobacterium nucleatum/physiology
*Coronary Artery Disease/etiology
*Diabetes Mellitus

@article {pmid38580930,
year = {2024},
author = {Hu, X and Yu, C and He, Y and Zhu, S and Wang, S and Xu, Z and You, S and Jiao, Y and Liu, SL and Bao, H},
title = {Integrative metagenomic analysis reveals distinct gut microbial signatures related to obesity.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {119},
pmid = {38580930},
issn = {1471-2180},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Obesity/microbiology ; Bacteria/genetics ; Feces/microbiology ; *Clostridiales ; Akkermansia ; },
abstract = {Obesity is a metabolic disorder closely associated with profound alterations in gut microbial composition. However, the dynamics of species composition and functional changes in the gut microbiome in obesity remain to be comprehensively investigated. In this study, we conducted a meta-analysis of metagenomic sequencing data from both obese and non-obese individuals across multiple cohorts, totaling 1351 fecal metagenomes. Our results demonstrate a significant decrease in both the richness and diversity of the gut bacteriome and virome in obese patients. We identified 38 bacterial species including Eubacterium sp. CAG:274, Ruminococcus gnavus, Eubacterium eligens and Akkermansia muciniphila, and 1 archaeal species, Methanobrevibacter smithii, that were significantly altered in obesity. Additionally, we observed altered abundance of five viral families: Mesyanzhinovviridae, Chaseviridae, Salasmaviridae, Drexlerviridae, and Casjensviridae. Functional analysis of the gut microbiome indicated distinct signatures associated to obesity and identified Ruminococcus gnavus as the primary driver for function enrichment in obesity, and Methanobrevibacter smithii, Akkermansia muciniphila, Ruminococcus bicirculans, and Eubacterium siraeum as functional drivers in the healthy control group. Additionally, our results suggest that antibiotic resistance genes and bacterial virulence factors may influence the development of obesity. Finally, we demonstrated that gut vOTUs achieved a diagnostic accuracy with an optimal area under the curve of 0.766 for distinguishing obesity from healthy controls. Our findings offer comprehensive and generalizable insights into the gut bacteriome and virome features associated with obesity, with the potential to guide the development of microbiome-based diagnostics.},
}

Humans
*Gastrointestinal Microbiome/genetics
Metagenome
Obesity/microbiology
Bacteria/genetics
Feces/microbiology
*Clostridiales
Akkermansia

@article {pmid38485093,
year = {2024},
author = {Riva, A and Sahin, E and Volpedo, G and Petretto, A and Lavarello, C and Di Sapia, R and Barbarossa, D and Zaniani, NR and Craparotta, I and Barbera, MC and Sezerman, U and Vezzani, A and Striano, P and Ravizza, T},
title = {Identification of an epilepsy-linked gut microbiota signature in a pediatric rat model of acquired epilepsy.},
journal = {Neurobiology of disease},
volume = {194},
number = {},
pages = {106469},
doi = {10.1016/j.nbd.2024.106469},
pmid = {38485093},
issn = {1095-953X},
mesh = {Humans ; Child ; Rats ; Animals ; *Gastrointestinal Microbiome ; *Epilepsy ; *Status Epilepticus ; Seizures ; Inflammation ; },
abstract = {A dysfunctional gut microbiota-brain axis is emerging as a potential pathogenic mechanism in epilepsy, particularly in pediatric forms of epilepsy. To add new insights into gut-related changes in acquired epilepsy that develops early in life, we used a multi-omics approach in a rat model with a 56% incidence of epilepsy. The presence of spontaneous seizures was assessed in adult rats (n = 46) 5 months after status epilepticus induced by intra-amygdala kainate at postnatal day 13, by 2 weeks (24/7) ECoG monitoring. Twenty-six rats developed epilepsy (Epi) while the remaining 20 rats (No-Epi) did not show spontaneous seizures. At the end of ECoG monitoring, all rats and their sham controls (n = 20) were sacrificed for quantitative histopathological and immunohistochemical analyses of the gut structure, glia and macrophages, as well as RTqPCR analysis of inflammation/oxidative stress markers. By comparing Epi, No-Epi rats, and sham controls, we found structural, cellular, and molecular alterations reflecting a dysfunctional gut, which were specifically associated with epilepsy. In particular, the villus height-to-crypt depth ratio and number of Goblet cells were reduced in the duodenum of Epi rats vs both No-Epi rats and sham controls (p < 0.01). Villus height and crypt depth in the duodenum and jejunum (p < 0.01) were increased in No-Epi vs both Epi and sham controls. We also detected enhanced Iba1-positive macrophages, together with increased IL1b and NFE2L2 transcripts and TNF protein, in the small intestine of Epi vs both No-Epi and sham control rats (p < 0.01), denoting the presence of inflammation and oxidative stress. Astroglial GFAP-immunostaining was similar in all experimental groups. Metagenomic analysis in the feces collected 5 months after status epilepticus showed that the ratio of two dominant phyla (Bacteroidota-to-Firmicutes) was similarly increased in Epi and No-Epi rats vs sham control rats. Notably, the relative abundance of families, genera, and species associated with SCFA production differed in Epi vs No-Epi rats, describing a bacterial imprint associated with epilepsy. Furthermore, Epi rats showed a blood metabolic signature characterized by changes in lipid metabolism compared to both No-Epi and sham control rats. Our study provides new evidence of long-term gut alterations, along with microbiota-related metabolic changes, occurring specifically in rats that develop epilepsy after brain injury early in life.},
}

Humans
Child
Rats
Animals
*Gastrointestinal Microbiome
*Epilepsy
*Status Epilepticus
Seizures
Inflammation

@article {pmid38246133,
year = {2024},
author = {Chulenbayeva, L and Ganzhula, Y and Kozhakhmetov, S and Jarmukhanov, Z and Nurgaziyev, M and Nurgozhina, A and Muhanbetzhanov, N and Sergazy, S and Zhetkenev, S and Borykbay, Z and Tkachev, V and Urazova, S and Vinogradova, E and Kushugulova, A},
title = {The Trajectory of Successful Aging: Insights from Metagenome and Cytokine Profiling.},
journal = {Gerontology},
volume = {70},
number = {4},
pages = {390-407},
doi = {10.1159/000536082},
pmid = {38246133},
issn = {1423-0003},
mesh = {Aged, 80 and over ; Humans ; *Metagenome ; Aging ; *Microbiota ; Longevity ; Cytokines ; },
abstract = {INTRODUCTION: The longevity is influenced by genetic, environmental, and lifestyle factors. The specific changes that occur in the gut microbiome during the aging process, and their relationship to longevity and immune function, have not yet been fully understood. The ongoing research of other microbiome based on longevity cohort in Kazakhstan provides preliminary information on longevity-related aging, where cytokine expression is associated with specific microbial communities and microbial functions.

METHODS: Metagenomic shotgun sequencing study of 40 long-lived individuals aged 90 years and over was carried out, who were conditionally healthy and active, able to serve themselves, without a history of serious infection and cancer, who had not taken any antimicrobials, including probiotics. Blood serum was analyzed for clinical and laboratory characteristics. The cytokine and chemokine profile in serum and stool samples was assessed using multiplex analysis.

RESULTS: We found a significant increase in the expression of pro-inflammatory cytokines IL-1a, IL-6, 12p70, IP-10, IFNα2, IL-15, TNFa, as well as chemokines MIP-1a/CCL3 and MIP-1b/CCL4, chemokine motif ligands MCP-3/CCL7 and MDC/CCL22(1c). Nonagenerians and centenarians demonstrated a greater diversity of core microbiota genera and showed an elevated prevalence of the genera Bacteroides, Clostridium, Escherichia, and Alistipes. Conversely, there was a decrease in the abundance of the genera Ruminococcus, Fusicatenibacter, Dorea, as well as the species Fusicatenibacter saccharivorans. Furthermore, functional analysis revealed that the microbiome in long-lived group has a high capacity for lipid metabolism, amino acid degradation, and potential signs of chronic inflammatory status.

CONCLUSION: Long-lived individuals exhibit an immune system imbalance and observed changes in the composition of the gut microbiota at the genus level between to the two age-groups. Age-related changes in the gut microbiome, metabolic functions of the microbial community, and chronic inflammation all contribute to immunosenescence. In turn, the inflammatory state and microbial composition of the gut is related to nutritional status.},
}

Aged, 80 and over
Humans
*Metagenome
Aging
*Microbiota
Longevity
Cytokines

@article {pmid37180436,
year = {2023},
author = {Che, Y and Wang, N and Ma, Q and Liu, J and Xu, Z and Li, Q and Wang, J and Sun, Y},
title = {Microbial characterization of the nasal cavity in patients with allergic rhinitis and non-allergic rhinitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1166389},
pmid = {37180436},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; Young Adult ; Adult ; *Rhinitis, Allergic/microbiology ; *Rhinitis/microbiology ; *Nasal Cavity/microbiology ; Metagenome ; Biodiversity ; *Microbiota ; RNA, Ribosomal, 16S/analysis ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {INTRODUCTION: Although recent studies have shown that the human microbiome is involved in the pathogenesis of allergic diseases, the impact of microbiota on allergic rhinitis (AR) and non-allergic rhinitis (nAR) has not been elucidated. The aim of this study was to investigate the differences in the composition of the nasal flora in patients with AR and nAR and their role in the pathogenesis.

METHOD: From February to September 2022, 35 AR patients and 35 nAR patients admitted to Harbin Medical University's Second Affiliated Hospital, as well as 20 healthy subjects who underwent physical examination during the same period, were subjected to 16SrDNA and metagenomic sequencing of nasal flora.

RESULTS: The microbiota composition of the three groups of study subjects differs significantly. The relative abundance of Vibrio vulnificus and Acinetobacter baumanni in the nasal cavity of AR patients was significantly higher when compared to nAR patients, while the relative abundance of Lactobacillus murinus, Lactobacillus iners, Proteobacteria, Pseudomonadales, and Escherichia coli was lower. In addition, Lactobacillus murinus and Lacttobacillus kunkeei were also negatively correlated with IgE, while Lacttobacillus kunkeei was positively correlated with age. The relative distribution of Faecalibacterium was higher in moderate than in severe AR patients. According to KEGG functional enrichment annotation, ICMT(protein-S-isoprenylcysteine O-methyltransferase,ICMT) is an AR microbiota-specific enzyme that plays a role, while glycan biosynthesis and metabolism are more active in AR microbiota. For AR, the model containing Parabacteroides goldstemii, Sutterella-SP-6FBBBBH3, Pseudoalteromonas luteoviolacea, Lachnospiraceae bacterium-615, and Bacteroides coprocola had the highest the area under the curve (AUC), which was 0.9733(95%CI:0.926-1.000) in the constructed random forest prediction model. The largest AUC for nAR is 0.984(95%CI:0.949-1.000) for the model containing Pseudomonas-SP-LTJR-52, Lachnospiraceae bacterium-615, Prevotella corporis, Anaerococcus vaginalis, and Roseburia inulinivorans.

CONCLUSION: In conclusion, patients with AR and nAR had significantly different microbiota profiles compared to healthy controls. The results suggest that the nasal microbiota may play a key role in the pathogenesis and symptoms of AR and nAR, providing us with new ideas for the treatment of AR and nAR.},
}

Humans
Male
Female
Young Adult
Adult
*Rhinitis, Allergic/microbiology
*Rhinitis/microbiology
*Nasal Cavity/microbiology
Metagenome
Biodiversity
*Microbiota
RNA, Ribosomal, 16S/analysis
*Bacteria/classification/genetics/isolation & purification

@article {pmid38580669,
year = {2024},
author = {Schadt, C and Martin, S and Carrell, A and Fortner, A and Hopp, D and Jacobson, D and Klingeman, D and Kristy, B and Phillips, J and Piatkowski, B and Miller, MA and Smith, M and Patil, S and Flynn, M and Canon, S and Clum, A and Mungall, CJ and Pennacchio, C and Bowen, B and Louie, K and Northen, T and Eloe-Fadrosh, EA and Mayes, MA and Muchero, W and Weston, DJ and Mitchell, J and Doktycz, M},
title = {An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {339},
pmid = {38580669},
issn = {2052-4463},
mesh = {Fungi/genetics ; Gene Expression Profiling ; Genotype ; *Metagenome ; *Microbiota ; *Populus/genetics ; Soil ; *Transcriptome ; },
abstract = {Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa. Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences.},
}

Fungi/genetics
Gene Expression Profiling
Genotype
*Metagenome
*Microbiota
*Populus/genetics
Soil
*Transcriptome

@article {pmid38579579,
year = {2024},
author = {Lavilla-Lerma, ML and Aibar-Almazán, A and Martínez-Amat, A and Jiménez-García, JD and Hita-Contreras, F},
title = {Moderate-intensity continuous training and high-intensity interval training modulate the composition of the oral microbiota of elderly adults: Randomized controlled trial.},
journal = {Maturitas},
volume = {185},
number = {},
pages = {107973},
doi = {10.1016/j.maturitas.2024.107973},
pmid = {38579579},
issn = {1873-4111},
abstract = {OBJECTIVE: We investigates the effects of 16-week high-intensity interval training and moderate-intensity continuous training on the composition of the oral microbiota. To the best of our knowledge, at the time of writing this paper no other scholars had described the oral metagenomic changes associated with prescribed exercise in older adults.

METHODS: Forty-three participants aged 60-74 years were randomized 1:1:1 to a control group, high-intensity interval training or moderate-intensity continuous training twice weekly for 16 weeks. Saliva samples were sequenced at baseline, week 8 and week 16 of intervention.

RESULTS: High-intensity interval training produced significant differences over time in Richness and a clear trend to decreased Simpson and Shannon diversity indices. In contrast, Simpson and Shannon indices showed an upward trend over time with moderate-intensity continuous training, which also decreased Firmicutes and increased Bacteroidetes levels. Significant differences in the abundance of pathogenic species were also observed after the participants completed the exercise interventions of either type.

CONCLUSIONS: Both types of exercise promoted subtle changes in the oral microbiota, confirming the modulatory effect of high-intensity interval training and moderate-intensity continuous training on the oral microbiome. Clinical trial registration NCT05220670.},
}

@article {pmid38575861,
year = {2024},
author = {Murtaza, N and Nawaz, M and Yaqub, T and Mehmood, AK},
title = {Impact of Limosilactobacillus fermentum probiotic treatment on gut microbiota composition in sahiwal calves with rotavirus diarrhea: A 16S metagenomic analysis study".},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {114},
pmid = {38575861},
issn = {1471-2180},
mesh = {Animals ; Cattle ; *Rotavirus/genetics ; *Rotavirus Infections/drug therapy/veterinary ; *Gastrointestinal Microbiome/genetics ; *Limosilactobacillus fermentum ; Dysbiosis ; Diarrhea/drug therapy/veterinary ; Feces/microbiology ; *Probiotics/therapeutic use ; *Cattle Diseases/drug therapy/microbiology ; },
abstract = {BACKGROUND: Diarrhea poses a major threat to bovine calves leading to mortality and economic losses. Among the causes of calf diarrhea, bovine rotavirus is a major etiological agent and may result in dysbiosis of gut microbiota. The current study was designed to investigate the effect of probiotic Limosilactobacillus fermentum (Accession No.OR504458) on the microbial composition of rotavirus-infected calves using 16S metagenomic analysis technique. Screening of rotavirus infection in calves below one month of age was done through clinical signs and Reverse Transcriptase PCR. The healthy calves (n = 10) were taken as control while the infected calves (n = 10) before treatment was designated as diarrheal group were treated with Probiotic for 5 days. All the calves were screened for the presence of rotavirus infection on each day and fecal scoring was done to assess the fecal consistency. Infected calves after treatment were designated as recovered group. Fecal samples from healthy, recovered and diarrheal (infected calves before sampling) were processed for DNA extraction while four samples from each group were processed for 16S metagenomic analysis using Illumina sequencing technique and analyzed via QIIME 2.

RESULTS: The results show that Firmicutes were more abundant in the healthy and recovered group than in the diarrheal group. At the same time Proteobacteria was higher in abundance in the diarrheal group. Order Oscillospirales dominated healthy and recovered calves and Enterobacterials dominated the diarrheal group. Alpha diversity indices show that diversity indices based on richness were higher in the healthy group and lower in the diarrheal group while a mixed pattern of clustering between diarrheal and recovered groups samples in PCA plots based on beta diversity indices was observed.

CONCLUSION: It is concluded that probiotic Limosilactobacillus Fermentum N-30 ameliorate the dysbiosis caused by rotavirus diarrhea and may be used to prevent diarrhea in pre-weaned calves after further exploration.},
}

Animals
Cattle
*Rotavirus/genetics
*Rotavirus Infections/drug therapy/veterinary
*Gastrointestinal Microbiome/genetics
*Limosilactobacillus fermentum
Dysbiosis
Diarrhea/drug therapy/veterinary
Feces/microbiology
*Probiotics/therapeutic use
*Cattle Diseases/drug therapy/microbiology

@article {pmid38575625,
year = {2024},
author = {Flores, VS and Amgarten, DE and Iha, BKV and Ryon, KA and Danko, D and Tierney, BT and Mason, C and da Silva, AM and Setubal, JC},
title = {Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {7913},
pmid = {38575625},
issn = {2045-2322},
mesh = {*Bacteriophages/genetics ; *Railroads ; *Microbiota/genetics ; Metagenome/genetics ; Bacteria/genetics ; },
abstract = {Bacteriophages are recognized as the most abundant members of microbiomes and have therefore a profound impact on microbial communities through the interactions with their bacterial hosts. The International Metagenomics and Metadesign of Subways and Urban Biomes Consortium (MetaSUB) has sampled mass-transit systems in 60 cities over 3 years using metagenomics, throwing light into these hitherto largely unexplored urban environments. MetaSUB focused primarily on the bacterial community. In this work, we explored MetaSUB metagenomic data in order to recover and analyze bacteriophage genomes. We recovered and analyzed 1714 phage genomes with size at least 40 kbp, from the class Caudoviricetes, the vast majority of which (80%) are novel. The recovered genomes were predicted to belong to temperate (69%) and lytic (31%) phages. Thirty-three of these genomes have more than 200 kbp, and one of them reaches 572 kbp, placing it among the largest phage genomes ever found. In general, the phages tended to be site-specific or nearly so, but 194 genomes could be identified in every city from which phage genomes were retrieved. We predicted hosts for 48% of the phages and observed general agreement between phage abundance and the respective bacterial host abundance, which include the most common nosocomial multidrug-resistant pathogens. A small fraction of the phage genomes are carriers of antibiotic resistance genes, and such genomes tended to be particularly abundant in the sites where they were found. We also detected CRISPR-Cas systems in five phage genomes. This study expands the previously reported MetaSUB results and is a contribution to the knowledge about phage diversity, global distribution, and phage genome content.},
}

*Bacteriophages/genetics
*Railroads
*Microbiota/genetics
Metagenome/genetics
Bacteria/genetics

@article {pmid38575584,
year = {2024},
author = {Messer, LF and Bourne, DG and Robbins, SJ and Clay, M and Bell, SC and McIlroy, SJ and Tyson, GW},
title = {A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2902},
pmid = {38575584},
issn = {2041-1723},
mesh = {Animals ; *Anthozoa/genetics/microbiology ; *Resilience, Psychological ; *Microbiota/genetics ; Metagenome/genetics ; Nitrogen ; Coral Reefs ; Symbiosis/genetics ; },
abstract = {Microbial diversity has been extensively explored in reef-building corals. However, the functional roles of coral-associated microorganisms remain poorly elucidated. Here, we recover 191 bacterial and 10 archaeal metagenome-assembled genomes (MAGs) from the coral Acropora kenti (formerly A. tenuis) and adjacent seawater, to identify microbial functions and metabolic interactions within the holobiont. We show that 82 MAGs were specific to the A. kenti holobiont, including members of the Pseudomonadota, Bacteroidota, and Desulfobacterota. A. kenti-specific MAGs displayed significant differences in their genomic features and functional potential relative to seawater-specific MAGs, with a higher prevalence of genes involved in host immune system evasion, nitrogen and carbon fixation, and synthesis of five essential B-vitamins. We find a diversity of A. kenti-specific MAGs encode the biosynthesis of essential amino acids, such as tryptophan, histidine, and lysine, which cannot be de novo synthesised by the host or Symbiodiniaceae. Across a water quality gradient spanning 2° of latitude, A. kenti microbial community composition is correlated to increased temperature and dissolved inorganic nitrogen, with corresponding enrichment in molecular chaperones, nitrate reductases, and a heat-shock protein. We reveal mechanisms of A. kenti-microbiome-symbiosis on the Great Barrier Reef, highlighting the interactions underpinning the health of this keystone holobiont.},
}

Animals
*Anthozoa/genetics/microbiology
*Resilience, Psychological
*Microbiota/genetics
Metagenome/genetics
Nitrogen
Coral Reefs
Symbiosis/genetics

@article {pmid38568776,
year = {2024},
author = {Hu, ZQ and Hung, YM and Chen, LH and Lai, LC and Pan, MH and Chuang, EY and Tsai, MH},
title = {NURECON: A Novel Online System for Determining Nutrition Requirements Based on Microbial Composition.},
journal = {IEEE/ACM transactions on computational biology and bioinformatics},
volume = {21},
number = {2},
pages = {254-264},
doi = {10.1109/TCBB.2024.3349572},
pmid = {38568776},
issn = {1557-9964},
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Diet ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Nutritional Requirements ; },
abstract = {Dietary habits have been proven to have an impact on the microbial composition and health of the human gut. Over the past decade, researchers have discovered that gut microbiota can use nutrients to produce metabolites that have major implications for human physiology. However, there is no comprehensive system that specifically focuses on identifying nutrient deficiencies based on gut microbiota, making it difficult to interpret and compare gut microbiome data in the literature. This study proposes an analytical platform, NURECON, that can predict nutrient deficiency information in individuals by comparing their metagenomic information to a reference baseline. NURECON integrates a next-generation bacterial 16S rRNA analytical pipeline (QIIME2), metabolic pathway prediction tools (PICRUSt2 and KEGG), and a food compound database (FooDB) to enable the identification of missing nutrients and provide personalized dietary suggestions. Metagenomic information from total number of 287 healthy subjects was used to establish baseline microbial composition and metabolic profiles. The uploaded data is analyzed and compared to the baseline for nutrient deficiency assessment. Visualization results include gut microbial composition, related enzymes, pathways, and nutrient abundance. NURECON is a user-friendly online platform that provides nutritional advice to support dietitians' research or menu design.},
}

Humans
RNA, Ribosomal, 16S/genetics
*Diet
*Gastrointestinal Microbiome/genetics
Metagenome
Nutritional Requirements

@article {pmid38566975,
year = {2024},
author = {Moubset, O and Filloux, D and Fontes, H and Julian, C and Fernandez, E and Galzi, S and Blondin, L and Chehida, SB and Lett, JM and Mesléard, F and Kraberger, S and Custer, JM and Salywon, A and Makings, E and Marais, A and Chiroleu, F and Lefeuvre, P and Martin, DP and Candresse, T and Varsani, A and Ravigné, V and Roumagnac, P},
title = {Virome release of an invasive exotic plant species in southern France.},
journal = {Virus evolution},
volume = {10},
number = {1},
pages = {veae025},
pmid = {38566975},
issn = {2057-1577},
abstract = {The increase in human-mediated introduction of plant species to new regions has resulted in a rise of invasive exotic plant species (IEPS) that has had significant effects on biodiversity and ecosystem processes. One commonly accepted mechanism of invasions is that proposed by the enemy release hypothesis (ERH), which states that IEPS free from their native herbivores and natural enemies in new environments can outcompete indigenous species and become invasive. We here propose the virome release hypothesis (VRH) as a virus-centered variant of the conventional ERH that is only focused on enemies. The VRH predicts that vertically transmitted plant-associated viruses (PAV, encompassing phytoviruses and mycoviruses) should be co-introduced during the dissemination of the IEPS, while horizontally transmitted PAV of IEPS should be left behind or should not be locally transmitted in the introduced area due to a maladaptation of local vectors. To document the VRH, virome richness and composition as well as PAV prevalence, co-infection, host range, and transmission modes were compared between indigenous plant species and an invasive grass, cane bluestem (Bothriochloa barbinodis), in both its introduced range (southern France) and one area of its native range (Sonoran Desert, Arizona, USA). Contrary to the VRH, we show that invasive populations of B. barbinodis in France were not associated with a lower PAV prevalence or richness than native populations of B. barbinodis from the USA. However, comparison of virome compositions and network analyses further revealed more diverse and complex plant-virus interactions in the French ecosystem, with a significant richness of mycoviruses. Setting mycoviruses apart, only one putatively vertically transmitted phytovirus (belonging to the Amalgaviridae family) and one putatively horizontally transmitted phytovirus (belonging to the Geminiviridae family) were identified from B. barbinodis plants in the introduced area. Collectively, these characteristics of the B. barbinodis-associated PAV community in southern France suggest that a virome release phase may have immediately followed the introduction of B. barbinodis to France in the 1960s or 1970s, and that, since then, the invasive populations of this IEPS have already transitioned out of this virome release phase, and have started interacting with several local mycoviruses and a few local plant viruses.},
}

@article {pmid38566102,
year = {2024},
author = {Luo, WC and Mei, SQ and Huang, ZJ and Chen, ZH and Zhang, YC and Yang, MY and Liu, JQ and Xu, JY and Yang, XR and Zhong, RW and Tang, LB and Yin, LX and Deng, Y and Peng, YL and Lu, C and Chen, BL and Ke, DX and Tu, HY and Yang, JJ and Xu, CR and Wu, YL and Zhou, Q},
title = {Correlation of distribution characteristics and dynamic changes of gut microbiota with the efficacy of immunotherapy in EGFR-mutated non-small cell lung cancer.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {326},
pmid = {38566102},
issn = {1479-5876},
support = {82102808//National Natural Science Foundation of China/ ; 82373349//National Natural Science Foundation of China/ ; G623281109//The Southern Medical University's Young Talents Climbing Program for Science and Technology Development/ ; 2017B030314120//Guangdong Provincial Key Lab of Translational Medicine in Lung Cancer/ ; KY0120220136//Guangdong Provincial People's Hospital Young Talent Project/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/therapy/drug therapy ; *Lung Neoplasms/therapy/drug therapy ; *Gastrointestinal Microbiome ; Immunotherapy ; ErbB Receptors/genetics ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {BACKGROUND: The effects of gut microbiota and metabolites on the responses to immune checkpoint inhibitors (ICIs) in advanced epidermal growth factor receptor (EGFR) wild-type non-small cell lung cancer (NSCLC) have been studied. However, their effects on EGFR-mutated (EGFR +) NSCLC remain unknown.

METHODS: We prospectively recorded the clinicopathological characteristics of patients with advanced EGFR + NSCLC and assessed potential associations between the use of antibiotics or probiotics and immunotherapy efficacy. Fecal samples were collected at baseline, early on-treatment, response and progression status and were subjected to metagenomic next-generation sequencing and ultra-high-performance liquid chromatography-mass spectrometry analyses to assess the effects of gut microbiota and metabolites on immunotherapy efficacy.

RESULTS: The clinical data of 74 advanced EGFR + NSCLC patients were complete and 18 patients' fecal samples were dynamically collected. Patients that used antibiotics had shorter progression-free survival (PFS) (mPFS, 4.8 vs. 6.7 months; P = 0.037); probiotics had no impact on PFS. Two dynamic types of gut microbiota during immunotherapy were identified: one type showed the lowest relative abundance at the response time point, whereas the other type showed the highest abundance at the response time point. Metabolomics revealed significant differences in metabolites distribution between responders and non-responders. Deoxycholic acid, glycerol, and quinolinic acid were enriched in responders, whereas L-citrulline was enriched in non-responders. There was a significant correlation between gut microbiota and metabolites.

CONCLUSIONS: The use of antibiotics weakens immunotherapy efficacy in patients with advanced EGFR + NSCLC. The distribution characteristics and dynamic changes of gut microbiota and metabolites may indicate the efficacy of immunotherapy in advanced EGFR + NSCLC.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/therapy/drug therapy
*Lung Neoplasms/therapy/drug therapy
*Gastrointestinal Microbiome
Immunotherapy
ErbB Receptors/genetics
Anti-Bacterial Agents/therapeutic use

@article {pmid38565843,
year = {2024},
author = {Brar, NK and Dhariwal, A and Åmdal, HA and Junges, R and Salvadori, G and Baker, JL and Edlund, A and Petersen, FC},
title = {Exploring ex vivo biofilm dynamics: consequences of low ampicillin concentrations on the human oral microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {37},
pmid = {38565843},
issn = {2055-5008},
support = {K99 DE029228/DE/NIDCR NIH HHS/United States ; R00 DE029228/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Ampicillin/pharmacology ; *Microbiota ; Bacteria/genetics ; Biofilms ; },
abstract = {Prolonged exposure to antibiotics at low concentration can promote processes associated with bacterial biofilm formation, virulence and antibiotic resistance. This can be of high relevance in microbial communities like the oral microbiome, where commensals and pathogens share a common habitat and where the total abundance of antibiotic resistance genes surpasses the abundance in the gut. Here, we used an ex vivo model of human oral biofilms to investigate the impact of ampicillin on biofilm viability. The ecological impact on the microbiome and resistome was investigated using shotgun metagenomics. The results showed that low concentrations promoted significant shifts in microbial taxonomic profile and could enhance biofilm viability by up to 1 to 2-log. For the resistome, low concentrations had no significant impact on antibiotic resistance gene (ARG) diversity, while ARG abundance decreased by up to 84%. A positive correlation was observed between reduced microbial diversity and reduced ARG abundance. The WHO priority pathogens Streptococcus pneumoniae and Staphylococcus aureus were identified in some of the samples, but their abundance was not significantly altered by ampicillin. Most of the antibiotic resistance genes that increased in abundance in the ampicillin group were associated with streptococci, including Streptococcus mitis, a well-known potential donor of ARGs to S. pneumoniae. Overall, the results highlight the potential of using the model to further our understanding of ecological and evolutionary forces driving antimicrobial resistance in oral microbiomes.},
}

Humans
*Anti-Bacterial Agents/pharmacology/therapeutic use
Ampicillin/pharmacology
*Microbiota
Bacteria/genetics
Biofilms

@article {pmid38503977,
year = {2024},
author = {Chang, HW and Lee, EM and Wang, Y and Zhou, C and Pruss, KM and Henrissat, S and Chen, RY and Kao, C and Hibberd, MC and Lynn, HM and Webber, DM and Crane, M and Cheng, J and Rodionov, DA and Arzamasov, AA and Castillo, JJ and Couture, G and Chen, Y and Balcazo, NP and Lebrilla, CB and Terrapon, N and Henrissat, B and Ilkayeva, O and Muehlbauer, MJ and Newgard, CB and Mostafa, I and Das, S and Mahfuz, M and Osterman, AL and Barratt, MJ and Ahmed, T and Gordon, JI},
title = {Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition.},
journal = {Nature microbiology},
volume = {9},
number = {4},
pages = {922-937},
pmid = {38503977},
issn = {2058-5276},
support = {F30 DK131866/DK/NIDDK NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; K01 DK134840/DK/NIDDK NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; INV-016367/GATES/Bill & Melinda Gates Foundation/United States ; F30 DK123838/DK/NIDDK NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; },
mesh = {Child ; Humans ; Animals ; Mice ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; *Malnutrition ; Weight Gain ; *Prevotella ; },
abstract = {Microbiota-directed complementary food (MDCF) formulations have been designed to repair the gut communities of malnourished children. A randomized controlled trial demonstrated that one formulation, MDCF-2, improved weight gain in malnourished Bangladeshi children compared to a more calorically dense standard nutritional intervention. Metagenome-assembled genomes from study participants revealed a correlation between ponderal growth and expression of MDCF-2 glycan utilization pathways by Prevotella copri strains. To test this correlation, here we use gnotobiotic mice colonized with defined consortia of age- and ponderal growth-associated gut bacterial strains, with or without P. copri isolates closely matching the metagenome-assembled genomes. Combining gut metagenomics and metatranscriptomics with host single-nucleus RNA sequencing and gut metabolomic analyses, we identify a key role of P. copri in metabolizing MDCF-2 glycans and uncover its interactions with other microbes including Bifidobacterium infantis. P. copri-containing consortia mediated weight gain and modulated energy metabolism within intestinal epithelial cells. Our results reveal structure-function relationships between MDCF-2 and members of the gut microbiota of malnourished children with potential implications for future therapies.},
}

Child
Humans
Animals
Mice
*Microbiota
*Gastrointestinal Microbiome/genetics
*Malnutrition
Weight Gain
*Prevotella

@article {pmid38485002,
year = {2024},
author = {Zhao, T and Huang, S and Zhang, Y and Chow, AT and Chen, P and Wang, Y and Lu, Y and Xiong, J},
title = {Removal of sulfur and nitrogen pollutants in a sediment microbial fuel cell coupled with Vallisneria natans: Efficiency, microbial community structure, and functional genes.},
journal = {Chemosphere},
volume = {354},
number = {},
pages = {141667},
doi = {10.1016/j.chemosphere.2024.141667},
pmid = {38485002},
issn = {1879-1298},
mesh = {*Bioelectric Energy Sources ; Nitrogen/metabolism ; Geologic Sediments/chemistry ; Water/chemistry ; *Microbiota ; Sulfur ; Denitrification ; },
abstract = {The rapid development of the economy has led to an increase in the sulfur and nitrogen load in surface water, which has the potential to cause river eutrophication and the emission of malodorous gases. A lab-scale sediment microbial fuel cell coupled with Vallisneria natans (P-SMFC) was designed for surface water remediation. The enhancement of pollutant removal performance of P-SMFC was evaluated in contrast to the SMFC system without plants (SMFC), the open-circuit control system with plants (C-P), and the open-circuit control system without plants (C-S), while illustrating the mechanisms of the sulfur and nitrogen transformation process. The results demonstrated that the effluent and sediment of P-SMFC had lower concentrations of sulfide compared to other systems. Furthermore, P-SMFC exhibited higher removal efficiency for COD (73.1 ± 8.7%), NH4[+]-N (80.5 ± 19.8%), and NO3[-]-N (88.5 ± 11.8%) compared to other systems. The closed-circuit conditions and growth of Vallisneria natans create a favorable ecological niche for functional microorganisms involved in power generation, sulfur oxidation, and nitrogen transformation. Additionally, metagenomic analysis revealed that multifunctional bacteria possessing both denitrification and sulfur oxidation genes, such as Thiobacillus, Dechloromonas, and Bacillus, may play simultaneous roles in metabolizing sulfur and nitrogen, thus serving as integral factors in maintaining the performance of P-SMFC. In summary, these findings provide a theoretical reference for the concurrent enhancement of sulfur and nitrogen pollutants removal in P-SMFC and will facilitate its practical application in the remediation of contaminated surface water.},
}

*Bioelectric Energy Sources
Nitrogen/metabolism
Geologic Sediments/chemistry
Water/chemistry
*Microbiota
Sulfur
Denitrification

@article {pmid38471380,
year = {2024},
author = {Meng, S and Peng, T and Liu, Y and Zhang, S and Qian, Z and Huang, T and Xie, Q and Gu, JD and Hu, Z},
title = {Novel insights into the synergetic degradation of pyrene by microbial communities from mangroves in China.},
journal = {Journal of hazardous materials},
volume = {469},
number = {},
pages = {133907},
doi = {10.1016/j.jhazmat.2024.133907},
pmid = {38471380},
issn = {1873-3336},
mesh = {Pyrenes/metabolism ; *Polycyclic Aromatic Hydrocarbons/analysis ; Bacteria/metabolism ; *Microbiota ; Biodegradation, Environmental ; },
abstract = {Pyrene is a high molecular weight polycyclic aromatic hydrocarbon (HMW-PAHs). It is a ubiquitous, persistent, and carcinogenic environmental contaminant that has raised concern worldwide. This research explored synergistic bacterial communities for efficient pyrene degradation in seven typical Southern China mangroves. The bacterial communities of seven typical mangroves were enriched by pyrene, and enriched bacterial communities showed an excellent pyrene degradation capacity of > 95% (except for HK mangrove and ZJ mangrove). Devosia, Hyphomicrobium, Flavobacterium, Marinobacter, Algoriphahus, and Youhaiella all have significant positive correlations with pyrene (R>0, p < 0.05) by 16SrRNA gene sequencing and metagenomics analysis, indicated that these genera play a vital role in pyrene metabolism. Meanwhile, the functional genes were involved in pyrene degradation that was enriched in the bacterial communities, including the genes of nagAa, ndoR, pcaG, etc. Furthermore, the analyses of functional genes and binning genomes demonstrated that some bacterial communities as a unique teamwork to cooperatively participate in pyrene degradation. Interestingly, the genes related to biogeochemical cycles were enriched, such as narG , soxA, and cyxJ, suggested that bacterial communities were also helpful in maintaining the stability of the ecological environment. In addition, some novel species with pyrene-degradation potential were identified in the pyrene-degrading bacterial communities, which can enrich the resource pool of pyrene-degrading strains. Overall, this study will help develop further research strategies for pollutant removal.},
}

Pyrenes/metabolism
*Polycyclic Aromatic Hydrocarbons/analysis
Bacteria/metabolism
*Microbiota
Biodegradation, Environmental

@article {pmid38471337,
year = {2024},
author = {Conco-Biyela, T and Malla, MA and Olatunji Awolusi, O and Allam, M and Ismail, A and Stenström, TA and Bux, F and Kumari, S},
title = {Metagenomics insights into microbiome and antibiotic resistance genes from free living amoeba in chlorinated wastewater effluents.},
journal = {International journal of hygiene and environmental health},
volume = {258},
number = {},
pages = {114345},
doi = {10.1016/j.ijheh.2024.114345},
pmid = {38471337},
issn = {1618-131X},
mesh = {Wastewater ; Anti-Bacterial Agents/pharmacology ; *Amoeba/microbiology ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; *Microbiota/genetics ; Bacteria ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Cephalosporins ; },
abstract = {Free living amoeba (FLA) are among the organisms commonly found in wastewater and are well-established hosts for diverse microbial communities. Despite its clinical significance, there is little knowledge on the FLA microbiome and resistome, with previous studies relying mostly on conventional approaches. In this study we comprehensively analyzed the microbiome, antibiotic resistome and virulence factors (VFs) within FLA isolated from final treated effluents of two wastewater treatment plants (WWTPs) using shotgun metagenomics. Acanthamoeba has been identified as the most common FLA, followed by Entamoeba. The bacterial diversity showed no significant difference (p > 0.05) in FLA microbiomes obtained from the two WWTPs. At phylum level, the most dominant taxa were Proteobacteria, followed by Firmicutes and Actinobacteria. The most abundant genera identified were Enterobacter followed by Citrobacter, Paenibacillus, and Cupriavidus. The latter three genera are reported here for the first time in Acanthamoeba. In total, we identified 43 types of ARG conferring resistance to cephalosporins, phenicol, streptomycin, trimethoprim, quinolones, cephalosporins, tigecycline, rifamycin, and kanamycin. Similarly, a variety of VFs in FLA metagenomes were detected which included flagellar proteins, Type IV pili twitching motility proteins (pilH and rpoN), alginate biosynthesis genes AlgI, AlgG, AlgD and AlgW and Type VI secretion system proteins and general secretion pathway proteins (tssM, tssA, tssL, tssK, tssJ, fha, tssG, tssF, tssC and tssB, gspC, gspE, gspD, gspF, gspG, gspH, gspI, gspJ, gspK, and gspM). To the best of our knowledge, this is the first study of its kind to examine both the microbiomes and resistome in FLA, as well as their potential pathogenicity in treated effluents. Additionally, this study showed that FLA can host a variety of potentially pathogenic bacteria including Paenibacillus, and Cupriavidus that had not previously been reported, indicating that their relationship may play a role in the spread and persistence of antibiotic resistant bacteria (ARBs) and antibiotic resistance genes (ARGs) as well as the evolution of novel pathogens.},
}

Wastewater
Anti-Bacterial Agents/pharmacology
*Amoeba/microbiology
Angiotensin Receptor Antagonists
Angiotensin-Converting Enzyme Inhibitors
*Microbiota/genetics
Bacteria
Genes, Bacterial
Drug Resistance, Microbial/genetics
Cephalosporins

@article {pmid38461607,
year = {2024},
author = {Wang, S and Zhang, C and Zhang, K and Zhang, L and Bi, R and Zhang, Y and Hu, Z},
title = {One-step bioremediation of hypersaline and nutrient-rich food industry process water with a domestic microbial community containing diatom Halamphora coffeaeformis.},
journal = {Water research},
volume = {254},
number = {},
pages = {121430},
doi = {10.1016/j.watres.2024.121430},
pmid = {38461607},
issn = {1879-2448},
mesh = {Wastewater ; Biodegradation, Environmental ; Water/analysis ; *Diatoms ; Phosphorus/analysis ; Bacteria/genetics/metabolism ; Food Industry ; Nutrients/analysis ; *Microbiota ; Biomass ; *Microalgae/metabolism ; Nitrogen/metabolism ; },
abstract = {Proper treatment of hypersaline and nutrient-rich food industry process water (FIPW) is challenging in conventional wastewater plants. Insufficient treatment leads to serious environmental hazards. However, bioremediation of FIPW with an indigenous microbial community can not only recover nutrients but generate biomass of diverse applications. In this study, monoculture of Halamphora coffeaeformis, together with synthetic bacteria isolated from a local wastewater plant, successfully recovered 91% of NH4[+]-N, 78% of total nitrogen, 95% of total phosphorus as well as 82% of total organic carbon from medium enriched with 10% FIPW. All identified organic acids and amino acids, except oxalic acid, were completely removed after 14 days treatment. A significantly higher biomass concentration (1.74 g L[-1]) was achieved after 14 days treatment in the medium with 10% FIPW than that in a nutrient-replete lab medium as control. The harvested biomass could be a potential feedstock for high-value biochemicals and fertilizer production, due to fucoxanthin accumulation (3 mg g[-1]) and a fantastic performance in P assimilation. Metagenomic analysis revealed that bacteria community in the algal system, dominated by Psychrobacter and Halomonas, also contributed to the biomass accumulation and uptake of nutrients. Transcriptomic analysis further disclosed that multiple pathways, involved in translation, folding, sorting and degradation as well as transport and catabolism, were depressed in H. coffeaeformis grown in FIPW-enriched medium, as compared to the control. Collectively, the proposed one-step strategy in this work offers an opportunity to achieve sustainable wastewater management and a way towards circular economy.},
}

Wastewater
Biodegradation, Environmental
Water/analysis
*Diatoms
Phosphorus/analysis
Bacteria/genetics/metabolism
Food Industry
Nutrients/analysis
*Microbiota
Biomass
*Microalgae/metabolism
Nitrogen/metabolism

@article {pmid38451230,
year = {2024},
author = {Eisenhofer, R and Nesme, J and Santos-Bay, L and Koziol, A and Sørensen, SJ and Alberdi, A and Aizpurua, O},
title = {A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics.},
journal = {Microbiology spectrum},
volume = {12},
number = {4},
pages = {e0359023},
doi = {10.1128/spectrum.03590-23},
pmid = {38451230},
issn = {2165-0497},
support = {DNRF143//Danish National Research Foundation award/ ; CF20-0460//The Carlsberg Foundation/ ; },
mesh = {Animals ; Mice ; Sequence Analysis, DNA/methods ; *Genome, Bacterial ; *Microbiota/genetics ; Metagenomics/methods ; DNA ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both. To assess the pros and cons of these different approaches, we used 22 fecal DNA extracts collected weekly for 11 weeks from two respective lab mice to study seven performance metrics over four combinations of sequencing depth and technology: (i) 20 Gbp of Illumina short-read data, (ii) 40 Gbp of short-read data, (iii) 20 Gbp of PacBio HiFi long-read data, and (iv) 40 Gbp of hybrid (20 Gbp of short-read +20 Gbp of long-read) data. No strategy was best for all metrics; instead, each one excelled across different metrics. The long-read approach yielded the best assembly statistics, with the highest N50 and lowest number of contigs. The 40 Gbp short-read approach yielded the highest number of refined bins. Finally, the hybrid approach yielded the longest assemblies and the highest mapping rate to the bacterial genomes. Our results suggest that while long-read sequencing significantly improves the quality of reconstructed bacterial genomes, it is more expensive and requires deeper sequencing than short-read approaches to recover a comparable amount of reconstructed genomes. The most optimal strategy is study-specific and depends on how researchers assess the trade-off between the quantity and quality of recovered genomes.IMPORTANCEMice are an important model organism for understanding the gut microbiome. When studying these gut microbiomes using DNA techniques, researchers can choose from technologies that use short or long DNA reads. In this study, we perform an extensive benchmark between short- and long-read DNA sequencing for studying mice gut microbiomes. We find that no one approach was best for all metrics and provide information that can help guide researchers in planning their experiments.},
}

Animals
Mice
Sequence Analysis, DNA/methods
*Genome, Bacterial
*Microbiota/genetics
Metagenomics/methods
DNA
High-Throughput Nucleotide Sequencing/methods

@article {pmid38441977,
year = {2024},
author = {Chen, H and Huang, S and Zhao, Y and Sun, R and Wang, J and Yao, S and Huang, J and Yu, Z},
title = {Metagenomic analysis of the intestinal microbiome reveals the potential mechanism involved in Bacillus amyloliquefaciens in treating schistosomiasis japonica in mice.},
journal = {Microbiology spectrum},
volume = {12},
number = {4},
pages = {e0373523},
doi = {10.1128/spectrum.03735-23},
pmid = {38441977},
issn = {2165-0497},
support = {32300051//MOST | National Natural Science Foundation of China (NSFC)/ ; 32170071//MOST | National Natural Science Foundation of China (NSFC)/ ; 82102428//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022JJ40663//HSTD | Natural Science Foundation of Hunan Province ()/ ; },
mesh = {Animals ; Mice ; *Schistosomiasis japonica/drug therapy ; *Gastrointestinal Microbiome ; *Bacillus amyloliquefaciens ; Urease ; *Schistosoma japonicum/genetics ; Bacteria/genetics ; },
abstract = {UNLABELLED: Schistosomiasis japonica is one of the neglected tropical diseases characterized by chronic hepatic, intestinal granulomatous inflammation and fibrosis, as well as dysbiosis of intestinal microbiome. Previously, the probiotic Bacillus amyloliquefaciens has been shown to alleviate the pathological injuries in mice infected with Schistosoma japonicum by improving the disturbance of the intestinal microbiota. However, the underlying mechanisms involved in this process remain unclear. In this study, metagenomics sequencing and functional analysis were employed to investigate the differential changes in taxonomic composition and functional genes of the intestinal microbiome in S. japonicum-infected mice treated with B. amyloliquefaciens. The results revealed that intervention with B. amyloliquefaciens altered the taxonomic composition of the intestinal microbiota at the species level in infected mice and significantly increased the abundance of beneficial bacteria. Moreover, the abundance of predicted genes in the intestinal microbiome was also significantly changed, and the abundance of xfp/xpk and genes translated to urease was significantly restored. Further analysis showed that Limosilactobacillus reuteri was positively correlated with several KEGG Orthology (KO) genes and metabolic reactions, which might play important roles in alleviating the pathological symptoms caused by S. japonicum infection, indicating that it has the potential to function as another effective therapeutic agent for schistosomiasis. These data suggested that treatment of murine schistosomiasis japonica by B. amyloliquefaciens might be induced by alterations in the taxonomic composition and functional gene of the intestinal microbiome in mice. We hope this study will provide adjuvant strategies and methods for the early prevention and treatment of schistosomiasis japonica.

IMPORTANCE: Targeted interventions of probiotics on gut microbiome were used to explore the mechanism of alleviating schistosomiasis japonica. Through metagenomic analysis, there were significant changes in the composition of gut microbiota in mice infected with Schistosoma japonicum and significant increase in the abundance of beneficial bacteria after the intervention of Bacillus amyloliquefaciens. At the same time, the abundance of functional genes was found to change significantly. The abundance of genes related to urease metabolism and xfp/xpk related to D-erythrose 4-phosphate production was significantly restored, highlighting the importance of Limosilactobacillus reuteri in the recovery and abundance of predicted genes of the gut microbiome. These results indicated potential regulatory mechanism between the gene function of gut microbiome and host immune response. Our research lays the foundation for elucidating the regulatory mechanism of probiotic intervention in alleviating schistosomiasis japonica, and provides potential adjuvant treatment strategies for early prevention and treatment of schistosomiasis japonica.},
}

Animals
Mice
*Schistosomiasis japonica/drug therapy
*Gastrointestinal Microbiome
*Bacillus amyloliquefaciens
Urease
*Schistosoma japonicum/genetics
Bacteria/genetics

@article {pmid38441468,
year = {2024},
author = {Xiao, Y and Wang, Y and Tong, B and Gu, Y and Zhou, X and Zhu, N and Xu, X and Yin, X and Kou, Y and Tan, Y and Wang, J and Li, W},
title = {Eubacterium rectale is a potential marker of altered gut microbiota in psoriasis and psoriatic arthritis.},
journal = {Microbiology spectrum},
volume = {12},
number = {4},
pages = {e0115423},
doi = {10.1128/spectrum.01154-23},
pmid = {38441468},
issn = {2165-0497},
support = {ZYJC21050//The 1.3.5 project for disciplines of excellence, West China Hospital, Sichuan University/ ; },
mesh = {Humans ; *Arthritis, Psoriatic/diagnosis/drug therapy/metabolism ; Eubacterium ; *Gastrointestinal Microbiome ; *Psoriasis/diagnosis/drug therapy/metabolism ; Feces ; },
abstract = {UNLABELLED: Previous studies have profiled the gut microbiota among psoriatic patients compared to that among healthy individuals. However, a comprehensive understanding of the magnitude, direction, and detailed compositional and functional profiles remains limited. Additionally, research exploring the gut microbiota in the context of both plaque psoriasis (PsO) and psoriatic arthritis (PsA) is lacking. To assess the taxonomic and functional characteristics of the gut microbiota in PsO and PsA patients and investigate potential links between the gut microbiota and disease pathogenesis. We collected fecal samples from 70 psoriatic patients (44 PsO and 26 PsA) and 25 age- and gender-matched healthy controls (HC) and employed deep metagenomic sequencing to characterize their gut microbiota. We noted significant alternations in the gut microbiota compositions of both PsO and PsA patients compared to those of HC. Despite limited effect sizes in alpha diversity (12.3% reduction of microbial richness but unchanged evenness in psoriatic patients) and beta diversity (disease accounts for 3.5% of total variations), we consistently observed substantial reductions of Eubacterium rectale in both PsO and PsA patients, with PsA patients exhibiting even lower levels of E. rectale than PsO patients. Additionally, two Alistipes species were also depleted in psoriatic patients. These microorganisms are known to play crucial roles in carbohydrate metabolism pathways, mainly producing short-chain fatty acids with anti-inflammatory effects. Overall, our observations supplemented the profiling of altered gut microbiota in patients with PsO and PsA at the species level and described a link between the dominant short-chain fatty acid-producing bacterial species and systemic immunity in psoriatic patients.

IMPORTANCE: In this observational clinical study with sufficient sample size and metagenomic sequencing to profile the gut microbiota, we identified consistent signals of the depleted abundance of Eubacterium rectale and related functional genes among psoriatic patients, including those with psoriatic arthritis. E. rectale may serve as an ecologically important functional unit in the gut microbiota, holding potential as a diagnostic marker and target for therapeutic interventions to achieve lasting effects. Our findings provide comprehensive gut microbiota profiling in psoriasis, resolving previous contradictions and generating new hypotheses for further investigation. These insights may significantly impact psoriasis management and related conditions.},
}

Humans
*Arthritis, Psoriatic/diagnosis/drug therapy/metabolism
Eubacterium
*Gastrointestinal Microbiome
*Psoriasis/diagnosis/drug therapy/metabolism
Feces

@article {pmid38421192,
year = {2024},
author = {Zhang, N and Gao, X and Li, D and Xu, L and Zhou, G and Xu, M and Peng, L and Sun, G and Pan, F and Li, Y and Ren, R and Huang, R and Yang, Y and Wang, Z},
title = {Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites.},
journal = {Microbiology spectrum},
volume = {12},
number = {4},
pages = {e0143723},
doi = {10.1128/spectrum.01437-23},
pmid = {38421192},
issn = {2165-0497},
mesh = {Rats ; Animals ; *Gastrointestinal Microbiome/physiology ; Sleep Deprivation/complications ; Lipopolysaccharides ; Anxiety/metabolism ; Inflammation/metabolism ; },
abstract = {UNLABELLED: The present study aimed to characterize the gut microbiota and serum metabolome changes associated with sleep deprivation (SD) as well as to explore the potential benefits of multi-probiotic supplementation in alleviating SD-related mental health disorders. Rats were subjected to 7 days of SD, followed by 14 days of multi-probiotics or saline administration. Open-field tests were conducted at baseline, end of SD (day 7), and after 14 days of saline or multi-probiotic gavage (day 21). Metagenomic sequencing was conducted on fecal samples, and serum metabolites were measured by untargeted liquid chromatography tandem-mass spectrometry. At day 7, anxiety-like behaviors, including significant decreases in total movement distance (P = 0.0002) and staying time in the central zone (P = 0.021), were observed. In addition, increased levels of lipopolysaccharide (LPS; P = 0.028) and decreased levels of uridine (P = 0.018) and tryptophan (P = 0.01) were detected in rats after 7 days of SD. After SD, the richness of the gut bacterial community increased, and the levels of Akkermansia muciniphila, Muribaculum intestinale, and Bacteroides caecimuris decreased. The changes in the host metabolism and gut microbiota composition were strongly associated with the anxiety-like behaviors caused by SD. In addition, multi-probiotic supplementation for 14 days modestly improved the anxiety-like behaviors in SD rats but significantly reduced the serum level of LPS (P = 0.045). In conclusion, SD induces changes in the gut microbiota and serum metabolites, which may contribute to the development of chronic inflammatory responses and affect the gut-brain axis, causing anxiety-like behaviors. Probiotic supplementation significantly reduces serum LPS, which may alleviate the influence of chronic inflammation.

IMPORTANCE: The disturbance in the gut microbiome and serum metabolome induced by SD may be involved in anxiety-like behaviors. Probiotic supplementation decreases serum levels of LPS, but this reduction may be insufficient for alleviating SD-induced anxiety-like behaviors.},
}

Rats
Animals
*Gastrointestinal Microbiome/physiology
Sleep Deprivation/complications
Lipopolysaccharides
Anxiety/metabolism
Inflammation/metabolism

@article {pmid38385739,
year = {2024},
author = {Hong, J-C and Chen, J-S and Jiang, Z-J and Chen, Z-C and Ruan, N and Yao, X-P},
title = {Microbiota in adult perianal abscess revealed by metagenomic next-generation sequencing.},
journal = {Microbiology spectrum},
volume = {12},
number = {4},
pages = {e0347423},
doi = {10.1128/spectrum.03474-23},
pmid = {38385739},
issn = {2165-0497},
support = {2019QH1079//Startup Fund for Scientific Research, Fujian Medical University/ ; 82171841//MOST | National Natural Science Foundation of China (NSFC)/ ; 2020Y9118//Joint Funds for the Innovation of Science and Technology, Fujian Province/ ; },
mesh = {Adult ; Humans ; Abscess/diagnosis ; Escherichia coli/genetics ; Retrospective Studies ; *Microbiota ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents ; Bacteroides fragilis/genetics ; Metagenomics ; *Skin Diseases ; Biomarkers ; },
abstract = {The microbiota of perianal abscesses is scarcely investigated. Identifying causative bacteria is essential to develop antibiotic therapy. However, culture-based methods and molecular diagnostics through 16S PCR technology are often hampered by the polymicrobial nature of perianal abscesses. We sought to characterize the microbiota composition of perianal abscesses via metagenomic next-generation sequencing (mNGS). Fourteen patients suffering from perianal abscesses between March 2023 and August 2023 underwent retrospective assessment. Information from medical records was used, including clinical information, laboratory data, and culture and mNGS results. Forty bacterial taxa were identified from perianal abscesses through mNGS, with Bilophila wadsworthia (71.4%), Bacteroides fragilis (57.1%), and Escherichia coli (50.0%) representing the most prevalent species. mNGS identified an increased number of bacterial taxa, with an average of 6.1 compared to a traditional culture-based method which only detected an average of 1.1 in culture-positive perianal abscess patients, predominantly E. coli (75.0%), revealing the polymicrobial nature of perianal abscesses. Our study demonstrates that a more diverse bacterial profile is detected by mNGS in perianal abscesses, and that Bilophila wadsworthia is the most prevalent microorganism, potentially serving as a potential biomarker for perianal abscess.IMPORTANCEAccurately, identifying the bacteria causing perianal abscesses is crucial for effective antibiotic therapy. However, traditional culture-based methods and 16S PCR technology often struggle with the polymicrobial nature of these abscesses. This study employed metagenomic next-generation sequencing (mNGS) to comprehensively analyze the microbiota composition. Results revealed 40 bacterial taxa, with Bilophila wadsworthia (71.4%), Bacteroides fragilis (57.1%), and Escherichia coli (50.0%) being the most prevalent species. Compared to the culture-based approach, mNGS detected a significantly higher number of bacterial taxa (average 6.1 vs 1.1), highlighting the complex nature of perianal abscesses. Notably, Bilophila wadsworthia emerged as a potential biomarker for these abscesses. This research emphasizes the importance of mNGS in understanding perianal abscesses and suggests its potential for improving diagnostic accuracy and guiding targeted antibiotic therapy in the future.},
}

Adult
Humans
Abscess/diagnosis
Escherichia coli/genetics
Retrospective Studies
*Microbiota
High-Throughput Nucleotide Sequencing
Anti-Bacterial Agents
Bacteroides fragilis/genetics
Metagenomics
*Skin Diseases
Biomarkers

@article {pmid38385646,
year = {2024},
author = {Hou, Z and Zhang, T and Ding, Z and Qian, T and Wang, P and Wu, B and Pan, X and Li, X},
title = {Analysis on the change of gut microbiota and metabolome in lung transplant patients.},
journal = {Microbiology spectrum},
volume = {12},
number = {4},
pages = {e0314223},
doi = {10.1128/spectrum.03142-23},
pmid = {38385646},
issn = {2165-0497},
support = {32070623//MOST | National Natural Science Foundation of China (NSFC)/ ; LHGJ20190027 and LHGJ20190109//Henan Province medical science and technology research plan joint construction projects/ ; SBGJ202002015 Wjlx2020080//Joint construction by provinces and the Ministry of Education/ ; 20211013//Engineering Laboratory of Henan Province/ ; XKZDQY202006//The advanced medical research center of Zhengzhou University/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Metabolome ; Enterococcus ; *Lung Transplantation ; Tretinoin ; Immunoglobulin A ; RNA, Ribosomal, 16S ; },
abstract = {UNLABELLED: Previous studies have shown that the gut microbiota and its metabolites are associated with the success of organ transplantation. However, the specific changes in the gut microbiota of lung transplant patients remain unclear. Hence, this study aimed to elucidate the interplay between the gut microbiota, metabolome, and lung transplantation outcomes. Using 16S metagenomics sequencing and untargeted metabolic profiling, we conducted a comprehensive analysis of gut microbial and metabolic alterations in lung transplant recipients relative to non-transplant group. Our findings revealed the predominance of Enterococcus and Streptococcus genera within the lung transplant cohort, accompanied by the significant reduction in Bacteroides, Epulopiscium, Faecalibacterium, and Prevotella abundance. In addition, a significant reduction in ATRA (all-trans retinoic acid) levels and suppression of IgA production were observed in lung transplant recipients, which were found to be closely associated with the Enterococcus genus. It was speculated that the association might have implications for the prognosis of lung transplant patients. Notably, the differences in gut microbial composition and metabolomic profiles between successful transplant recipients and those experiencing chronic rejection were not statistically significant. These novel insights shed light on the putative implications of the gut microbiota and metabolome in shaping lung transplantation outcomes, and provide a foundation for future investigations and targeted therapeutic interventions.

IMPORTANCE: This study has profound implications for lung transplantation as it uncovers the important role of gut microbiota and metabolome in shaping transplantation outcomes. The identification of dominant bacterial genera, such as Enterococcus and Streptococcus, within the lung transplant cohort, along with the significant decrease in Bacteroides, Epulopiscium, Faecalibacterium, and Prevotella abundance, reveals potential microbial imbalances associated with lung transplantation. In addition, a significant reduction in ATRA (all-trans retinoic acid) levels and suppression of IgA production were observed in lung transplant recipients, which were found to be closely associated with the Enterococcus genus. It was speculated that the association might have implications for the prognosis of lung transplant patients. These findings hold immense clinical significance as they lay the groundwork for future research and targeted therapeutic interventions. Understanding the impact of the gut microbiota and metabolome on lung transplantation outcomes offers promising avenues for improving transplantation patient prognosis.},
}

Humans
*Gastrointestinal Microbiome
Metabolome
Enterococcus
*Lung Transplantation
Tretinoin
Immunoglobulin A
RNA, Ribosomal, 16S

@article {pmid38302666,
year = {2024},
author = {Gose, MA and Humble, E and Brownlow, A and Wall, D and Rogan, E and Sigurðsson, GM and Kiszka, JJ and Thøstesen, CB and IJsseldijk, LL and Ten Doeschate, M and Davison, NJ and Øien, N and Deaville, R and Siebert, U and Ogden, R},
title = {Population genomics of the white-beaked dolphin (Lagenorhynchus albirostris): Implications for conservation amid climate-driven range shifts.},
journal = {Heredity},
volume = {132},
number = {4},
pages = {192-201},
pmid = {38302666},
issn = {1365-2540},
mesh = {Animals ; *Dolphins/genetics ; Metagenomics ; Climate Change ; Temperature ; },
abstract = {Climate change is rapidly affecting species distributions across the globe, particularly in the North Atlantic. For highly mobile and elusive cetaceans, the genetic data needed to understand population dynamics are often scarce. Cold-water obligate species such as the white-beaked dolphin (Lagenorhynchus albirostris) face pressures from habitat shifts due to rising sea surface temperatures in addition to other direct anthropogenic threats. Unravelling the genetic connectivity between white-beaked dolphins across their range is needed to understand the extent to which climate change and anthropogenic pressures may impact species-wide genetic diversity and identify ways to protect remaining habitat. We address this by performing a population genomic assessment of white-beaked dolphins using samples from much of their contemporary range. We show that the species displays significant population structure across the North Atlantic at multiple scales. Analysis of contemporary migration rates suggests a remarkably high connectivity between populations in the western North Atlantic, Iceland and the Barents Sea, while two regional populations in the North Sea and adjacent UK and Irish waters are highly differentiated from all other clades. Our results have important implications for the conservation of white-beaked dolphins by providing guidance for the delineation of more appropriate management units and highlighting the risk that local extirpation may have on species-wide genetic diversity. In a broader context, this study highlights the importance of understanding genetic structure of all species threatened with climate change-driven range shifts to assess the risk of loss of species-wide genetic diversity.},
}

Animals
*Dolphins/genetics
Metagenomics
Climate Change
Temperature

@article {pmid38565528,
year = {2024},
author = {Liang, JL and Feng, SW and Lu, JL and Wang, XN and Li, FL and Guo, YQ and Liu, SY and Zhuang, YY and Zhong, SJ and Zheng, J and Wen, P and Yi, X and Jia, P and Liao, B and Shu, WS and Li, JT},
title = {Hidden diversity and potential ecological function of phosphorus acquisition genes in widespread terrestrial bacteriophages.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2827},
pmid = {38565528},
issn = {2041-1723},
support = {41622106//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42177009//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Bacteriophages/genetics ; Ecosystem ; Phosphorus ; Metagenome/genetics ; Soil ; },
abstract = {Phosphorus (P) limitation of ecosystem processes is widespread in terrestrial habitats. While a few auxiliary metabolic genes (AMGs) in bacteriophages from aquatic habitats are reported to have the potential to enhance P-acquisition ability of their hosts, little is known about the diversity and potential ecological function of P-acquisition genes encoded by terrestrial bacteriophages. Here, we analyze 333 soil metagenomes from five terrestrial habitat types across China and identify 75 viral operational taxonomic units (vOTUs) that encode 105 P-acquisition AMGs. These AMGs span 17 distinct functional genes involved in four primary processes of microbial P-acquisition. Among them, over 60% (11/17) have not been reported previously. We experimentally verify in-vitro enzymatic activities of two pyrophosphatases and one alkaline phosphatase encoded by P-acquisition vOTUs. Thirty-six percent of the 75 P-acquisition vOTUs are detectable in a published global topsoil metagenome dataset. Further analyses reveal that, under certain circumstances, the identified P-acquisition AMGs have a greater influence on soil P availability and are more dominant in soil metatranscriptomes than their corresponding bacterial genes. Overall, our results reinforce the necessity of incorporating viral contributions into biogeochemical P cycling.},
}

*Bacteriophages/genetics
Ecosystem
Phosphorus
Metagenome/genetics
Soil

@article {pmid38563656,
year = {2024},
author = {Zhu, J and Yin, J and Chen, J and Hu, M and Lu, W and Wang, H and Zhang, H and Chen, W},
title = {Integrative analysis with microbial modelling and machine learning uncovers potential alleviators for ulcerative colitis.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2336877},
pmid = {38563656},
issn = {1949-0984},
mesh = {Animals ; Mice ; Humans ; *Colitis, Ulcerative ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases ; *Colitis ; Machine Learning ; },
abstract = {Ulcerative colitis (UC) is a challenging form of inflammatory bowel disease, and its etiology is intricately linked to disturbances in the gut microbiome. To identify the potential alleviators of UC, we employed an integrative analysis combining microbial community modeling with advanced machine learning techniques. Using metagenomics data sourced from the Integrated Human Microbiome Project, we constructed individualized microbiome community models for each participant. Our analysis highlighted a significant decline in both α and β-diversity of strain-level microbial populations in UC subjects compared to controls. Distinct differences were also observed in the predicted fecal metabolite profiles and strain-to-metabolite contributions between the two groups. Using tree-based machine learning models, we successfully identified specific microbial strains and their associated metabolites as potential alleviators of UC. Notably, our experimental validation using a dextran sulfate sodium-induced UC mouse model demonstrated that the administration of Parabacteroides merdae ATCC 43,184 and N-acetyl-D-mannosamine provided notable relief from colitis symptoms. In summary, our study underscores the potential of an integrative approach to identify novel therapeutic avenues for UC, paving the way for future targeted interventions.},
}

Animals
Mice
Humans
*Colitis, Ulcerative
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases
*Colitis
Machine Learning

@article {pmid38253195,
year = {2024},
author = {Wang, H and Wang, Z and Yu, J and Ma, C and Liu, L and Xu, D and Zhang, J},
title = {The function and keystone microbiota in typical habitats under the influence of anthropogenic activities in Baiyangdian Lake.},
journal = {Environmental research},
volume = {247},
number = {},
pages = {118196},
doi = {10.1016/j.envres.2024.118196},
pmid = {38253195},
issn = {1096-0953},
mesh = {Animals ; Humans ; *Lakes/chemistry ; Anthropogenic Effects ; *Microbiota ; Oxidation-Reduction ; Fishes ; Water ; },
abstract = {Microbe is an essential driver in regulating the biochemical cycles of carbon, nitrogen, and sulfur. In freshwater lake, microbial communities and functions are influenced by multiple factors, especially anthropogenic activities. Baiyangdian Lake consisted of various habitats, and was frequently interfered with human activities. In this study, 16 S rRNA sequencing and metagenomic sequencing were performed to characterize the microbial communities, determine keystone taxa and reveal dominated metabolic functions in typical habitats in Baiyangdian Lake. The results showed that the diversity of microbial community was significantly higher in sediment compared with corresponding water sample. Microbial community showed strong spatial heterogeneity in sediment, and temporal heterogeneity in water. As for different habitats, significantly higher alpha diversity was observed in ecotone, where the interference of human activities was relatively weak. The shared OTUs were distinguished from the keystone taxa, which indicated the uniqueness of microbiota in different ecological habitat. Moreover, the interactions of microbial in ecological restoration area (abandoned fish pond) were relatively simple, suggesting that this ecosystem was relatively fragile compared with others. Based on the metagenomic sequencing, we recognized that the canal, open water, and abandoned fish pond were beneficial for methanogenic and the ecotone might be a hot zone for the oxidation of methane. Notably, most of the microbes that participated in these predominant metabolisms were unclassified, which indicated the hug potential for exploring functional microorganisms in Baiyangdian Lake. This study provided a comprehensive understanding of the ecology characteristics of microbiota in habitats undergoing various human interference in Baiyangdian Lake.},
}

Animals
Humans
*Lakes/chemistry
Anthropogenic Effects
*Microbiota
Oxidation-Reduction
Fishes
Water

@article {pmid38150226,
year = {2024},
author = {Li, S and Fan, Y and Han, J and Liu, F and Ding, Y and Li, X and Yu, E and Wang, S and Wang, F and Wang, C},
title = {Foodborne Pathogen and Microbial Community Differences in Fresh Processing Tomatoes in Xinjiang, China.},
journal = {Foodborne pathogens and disease},
volume = {21},
number = {4},
pages = {236-247},
doi = {10.1089/fpd.2023.0014},
pmid = {38150226},
issn = {1556-7125},
mesh = {*Solanum lycopersicum ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Fungi/genetics ; Bacteria/genetics ; },
abstract = {The microbes on fresh processing tomatoes correlate closely with diseases, preservation, and quality control. Investigation of the microbial communities on processing tomatoes from different production regions may help define microbial specificity, inform disease prevention methods, and improve quality. In this study, surface microbes on processing tomatoes from 10 samples in two primary production areas of southern and northern Xinjiang were investigated by sequencing fungal internal transcribed spacer and bacterial 16S rRNA hypervariable sequences. A total of 133 different fungal and bacterial taxonomies were obtained from processing tomatoes in the two regions, of which 63 genera were predominant. Bacterial and fungal communities differed significantly between southern and northern Xinjiang, and fungal diversity was higher in southern Xinjiang. Alternaria and Cladosporium on processing tomatoes in southern Xinjiang were associated with plant pathogenic risk. The plant pathogenic fungi of processing tomatoes in northern Xinjiang were more abundant in Alternaria and Fusarium. The abundance of Alternaria on processing tomatoes was higher in four regions of northern Xinjiang, indicating that there is a greater risk of plant pathogenicity in these areas. Processing tomatoes in northern and southern Xinjiang contained bacterial genera identified as gut microbes, such as Pantoea, Erwinia, Enterobacter, Enterococcus, and Serratia, indicating the potential risk of contamination of processing tomatoes with foodborne pathogens. This study highlighted the microbial specificity of processing tomatoes in two tomato production regions, providing a basis for further investigation and screening for foodborne pathogenic microorganisms.},
}

*Solanum lycopersicum
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Fungi/genetics
Bacteria/genetics

@article {pmid38562473,
year = {2024},
author = {Seth, N and Vats, S and Lakhanpaul, S and Arafat, Y and Mazumdar-Leighton, S and Bansal, M and Babu, CR},
title = {Microbial community diversity of an integrated constructed wetland used for treatment of sewage.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1355718},
pmid = {38562473},
issn = {1664-302X},
abstract = {The microbial community diversity in Constructed Wetland System (CWS) plays a key role in the removal of pollutants from waste water. An integrated functional CWS developed at Neela Hauz Biodiversity Park, Delhi was selected to assess the diversity in composition and structure of microbial community diversity of sludge and sediment of CWS, based on metagenomic approach using 16S rRNA genes. The sediment showed higher diversity than sludge and both formed distinct clusters. The taxonomic structure of the microbial community of CWS is represented by 6,731 OTUs distributed among 2 kingdoms, 103 phyla, 227 classes, 337 orders, 320 families, 295 identified genera, and 84 identified species. The relative abundance of top 5 dominant phyla of sludge and sediment varied from 3.77% (Acidobacteria) to 35.33% (Proteobacteria) and 4.07% (Firmicutes) to 28.20% (Proteobacteria), respectively. The range of variation in relative abundance of top 5 dominant genera of sludge and sediment was 2.58% (Hyphomicrobium) to 6.61% (Planctomyces) and 2.47% (Clostridium) to 4.22% (Syntrophobacter), respectively. The rich microbial diversity of CWS makes it perform better in pollutants removal (59.91-95.76%) than other CWs. Based on the abundance values of taxa, the taxa are grouped under four frequency distribution classes-abundant (>20), common (10-19), rare (5-9), and very rare (1-4). The unique structure of microbial communities of integrated CWS is that the number of abundant taxa decreases in descending order of taxonomic hierarchy, while the number of rare and very rare taxa increases. For example, the number of abundant phyla was 14 and 21 in sludge and sediment, respectively and both communities have only 3 abundant genera each. This is in contrast to 4 and 17 very rare phyla in sludge and sediment, respectively and both the communities have 114 and 91 very rare genera, respectively. The outcomes of the study is that the integrated CWS has much higher microbial community diversity than the diversity reported for other CWs, and the rich diversity can be used for optimizing the performance efficiency of CWS in the removal of pollutants from waste water. Such structural diversity might be an adaptation to heterogeneous environment of CWS.},
}

@article {pmid38561814,
year = {2024},
author = {Logares, R},
title = {Decoding populations in the ocean microbiome.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {67},
pmid = {38561814},
issn = {2049-2618},
support = {PID2019-105775RB-I00//Agencia Estatal de Investigación/ ; },
mesh = {Animals ; *Ecosystem ; *Microbiota/genetics ; Oceans and Seas ; Metagenomics ; },
abstract = {Understanding the characteristics and structure of populations is fundamental to comprehending ecosystem processes and evolutionary adaptations. While the study of animal and plant populations has spanned a few centuries, microbial populations have been under scientific scrutiny for a considerably shorter period. In the ocean, analyzing the genetic composition of microbial populations and their adaptations to multiple niches can yield important insights into ecosystem function and the microbiome's response to global change. However, microbial populations have remained elusive to the scientific community due to the challenges associated with isolating microorganisms in the laboratory. Today, advancements in large-scale metagenomics and metatranscriptomics facilitate the investigation of populations from many uncultured microbial species directly from their habitats. The knowledge acquired thus far reveals substantial genetic diversity among various microbial species, showcasing distinct patterns of population differentiation and adaptations, and highlighting the significant role of selection in structuring populations. In the coming years, population genomics is expected to significantly increase our understanding of the architecture and functioning of the ocean microbiome, providing insights into its vulnerability or resilience in the face of ongoing global change. Video Abstract.},
}

Animals
*Ecosystem
*Microbiota/genetics
Oceans and Seas
Metagenomics

@article {pmid38470313,
year = {2024},
author = {Yu, J and Lee, JYY and Tang, SN and Lee, PKH},
title = {Niche differentiation in microbial communities with stable genomic traits over time in engineered systems.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38470313},
issn = {1751-7370},
support = {9231297//TAL Apparel Limited to the City University of Hong Kong/ ; },
mesh = {*Sewage ; Bacteria/genetics ; *Microbiota/genetics ; Metagenome ; Genomics ; },
abstract = {Microbial communities in full-scale engineered systems undergo dynamic compositional changes. However, mechanisms governing assembly of such microbes and succession of their functioning and genomic traits under various environmental conditions are unclear. In this study, we used the activated sludge and anaerobic treatment systems of four full-scale industrial wastewater treatment plants as models to investigate the niches of microbes in communities and the temporal succession patterns of community compositions. High-quality representative metagenome-assembled genomes revealed that taxonomic, functional, and trait-based compositions were strongly shaped by environmental selection, with replacement processes primarily driving variations in taxonomic and functional compositions. Plant-specific indicators were associated with system environmental conditions and exhibited strong determinism and trajectory directionality over time. The partitioning of microbes in a co-abundance network according to groups of plant-specific indicators, together with significant between-group differences in genomic traits, indicated the occurrence of niche differentiation. The indicators of the treatment plant with rich nutrient input and high substrate removal efficiency exhibited a faster predicted growth rate, lower guanine-cytosine content, smaller genome size, and higher codon usage bias than the indicators of the other plants. In individual plants, taxonomic composition displayed a more rapid temporal succession than functional and trait-based compositions. The succession of taxonomic, functional, and trait-based compositions was correlated with the kinetics of treatment processes in the activated sludge systems. This study provides insights into ecological niches of microbes in engineered systems and succession patterns of their functions and traits, which will aid microbial community management to improve treatment performance.},
}

*Sewage
Bacteria/genetics
*Microbiota/genetics
Metagenome
Genomics

@article {pmid38193195,
year = {2024},
author = {Abdulnour-Nakhoul, SM and Kolls, JK and Flemington, EK and Ungerleider, NA and Nakhoul, HN and Song, K and Nakhoul, NL},
title = {Alterations in gene expression and microbiome composition upon calcium-sensing receptor deletion in the mouse esophagus.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {326},
number = {4},
pages = {G438-G459},
doi = {10.1152/ajpgi.00066.2023},
pmid = {38193195},
issn = {1522-1547},
support = {U54 GM104940/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Mice ; *Calcium/metabolism ; Receptors, Calcium-Sensing/genetics/metabolism ; Esophagus/metabolism ; *Microbiota ; Inflammation ; Gene Expression ; },
abstract = {The calcium-sensing receptor (CaSR), a G protein-coupled receptor, regulates Ca[2+] concentration in plasma by regulating parathyroid hormone secretion. In other tissues, it is reported to play roles in cellular differentiation and migration and in secretion and absorption. We reported previously that CaSR can be conditionally deleted in the mouse esophagus. This conditional knockout (KO) ([Eso]CaSR[-/-]) model showed a significant reduction in the levels of adherens and tight junction proteins and had a marked buildup of bacteria on the luminal esophageal surface. To further examine the role of CaSR, we used RNA sequencing to determine gene expression profiles in esophageal epithelia of control and [Eso]CaSR[-/-]mice RNA Seq data indicated upregulation of gene sets involved in DNA replication and cell cycle in [Eso]CaSR[-/-]. This is accompanied by the downregulation of gene sets involved in the innate immune response and protein homeostasis including peptide elongation and protein trafficking. Ingenuity pathway analysis (IPA) demonstrated that these genes are mapped to important biological networks including calcium and Ras homologus A (RhoA) signaling pathways. To further explore the bacterial buildup in [Eso]CaSR[-/-] esophageal tissue, 16S sequencing of the mucosal-associated bacterial microbiome was performed. Three bacterial species, g_Rodentibacter, s_Rodentibacter_unclassified, and s_Lactobacillus_hilgardi were significantly increased in [Eso]CaSR[-/-]. Furthermore, metagenomic analysis of 16S sequences indicated that pathways related to oxidative phosphorylation and metabolism were downregulated in [Eso]CaSR[-/-] tissues. These data demonstrate that CaSR impacts major pathways of cell proliferation, differentiation, cell cycle, and innate immune response in esophageal epithelium. The disruption of these pathways causes inflammation and significant modifications of the microbiome.NEW & NOTEWORTHY Calcium-sensing receptor (CaSR) plays a significant role in maintaining the barrier function of esophageal epithelium. Using RNA sequencing, we show that conditional deletion of CaSR from mouse esophagus causes upregulation of genes involved in DNA replication and cell cycle and downregulation of genes involved in the innate immune response, protein translation, and cellular protein synthesis. Pathway analysis shows disruption of signaling pathways of calcium and actin cytoskeleton. These changes caused inflammation and esophageal dysbiosis.},
}

Animals
Mice
*Calcium/metabolism
Receptors, Calcium-Sensing/genetics/metabolism
Esophagus/metabolism
*Microbiota
Inflammation
Gene Expression

@article {pmid37696680,
year = {2024},
author = {Del Chierico, F and Cardile, S and Baldelli, V and Alterio, T and Reddel, S and Bramuzzo, M and Knafelz, D and Lega, S and Bracci, F and Torre, G and Maggiore, G and Putignani, L},
title = {Characterization of the Gut Microbiota and Mycobiota in Italian Pediatric Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis.},
journal = {Inflammatory bowel diseases},
volume = {30},
number = {4},
pages = {529-537},
pmid = {37696680},
issn = {1536-4844},
support = {//Italian Ministry of Health/ ; },
mesh = {Humans ; Child ; *Colitis, Ulcerative/complications ; *Gastrointestinal Microbiome ; *Cholangitis, Sclerosing/complications ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Bacteroidetes ; Italy ; },
abstract = {BACKGROUND: Primary sclerosing cholangitis (PSC) is a chronic, fibroinflammatory, cholestatic liver disease of unknown etiopathogenesis, often associated with inflammatory bowel diseases. Recent evidence ascribes, together with immunologic and environmental components, a significant role to the intestinal microbiota or its molecules in the PSC pathogenesis.

METHODS: By metagenomic sequencing of 16S rRNA and ITS2 loci, we describe the fecal microbiota and mycobiota of 26 pediatric patients affected by PSC and concomitant ulcerative colitis (PSC-UC), 27 patients without PSC but with UC (UC), and 26 healthy subjects (CTRLs).

RESULTS: Compared with CTRL, the bacterial and fungal gut dysbiosis was evident for both PSC-UC and UC groups; in particular, Streptococcus, Saccharomyces, Sporobolomyces, Tilletiopsis, and Debaryomyces appeared increased in PSC-UC, whereas Klebsiella, Haemophilus, Enterococcus Collinsella, Piptoporus, Candida, and Hyphodontia in UC. In both patient groups, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma and Malassezia were decreased. Co-occurrence analysis evidenced the lowest number of nodes and edges for fungi networks compared with bacteria. Finally, we identified a specific patient profile, based on liver function tests, bacterial and fungal signatures, that is able to distinguish PSC-UC from UC patients.

CONCLUSIONS: We describe the gut microbiota and mycobiota dysbiosis associated to PSC-UC disease. Our results evidenced a gut imbalance, with the reduction of gut commensal microorganisms with stated anti-inflammatory properties (ie, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma, and Malassezia) and the increase of pathobionts (ie, Streptococcus, Saccharomyces, and Debaryomyces) that could be involved in PSC progression. Altogether, these events may concur in the pathophysiology of PSC in the framework of UC.},
}

Humans
Child
*Colitis, Ulcerative/complications
*Gastrointestinal Microbiome
*Cholangitis, Sclerosing/complications
Dysbiosis/microbiology
RNA, Ribosomal, 16S/genetics
Bacteria/genetics
Bacteroidetes
Italy

@article {pmid38561312,
year = {2024},
author = {Hong, L and Huang, Y and Han, J and Li, S and Zhang, L and Zhou, Q and Cao, X and Yu, W and Guo, X and Yang, Y and Zhou, Y and Yan, W and Hong, S and Jiang, S and Cao, Y},
title = {Pathogen-specific alterations in intestinal microbiota precede urinary tract infections in preterm infants: a longitudinal case-control study.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2333413},
pmid = {38561312},
issn = {1949-0984},
mesh = {Infant ; Child ; Humans ; Infant, Newborn ; Adolescent ; Case-Control Studies ; *Gastrointestinal Microbiome ; Escherichia coli ; Infant, Premature ; Anti-Bacterial Agents/therapeutic use ; *Urinary Tract Infections ; Enterobacteriaceae ; Leukocyte L1 Antigen Complex ; },
abstract = {Urinary tract infections (UTIs) are among the most common late-onset infections in preterm infants, characterized by nonspecific symptoms and a pathogenic spectrum that diverges from that of term infants and older children, which present unique diagnostic and therapeutic challenges. Existing data on the role of gut microbiota in UTI pathogenesis in this demographic are limited. This study aims to investigate alterations in gut microbiota and fecal calprotectin levels and their association with the development of UTIs in hospitalized preterm infants. A longitudinal case-control study was conducted involving preterm infants admitted between January 2018 and October 2020. Fecal samples were collected weekly and analyzed for microbial profiles and calprotectin levels. Propensity score matching, accounting for key perinatal factors including age and antibiotic use, was utilized to match samples from UTI-diagnosed infants to those from non-UTI counterparts. Among the 151 preterm infants studied, 53 were diagnosed with a UTI, predominantly caused by Enterobacteriaceae (79.3%) and Enterococcaceae (19.0%). Infants with UTIs showed a significantly higher abundance of these families compared to non-UTI infants, for both Gram-negative and positive pathogens, respectively. Notably, there was a significant pre-UTI increase in the abundance of pathogen-specific taxa in infants later diagnosed with UTIs, offering high predictive value for early detection. Shotgun metagenomic sequencing further confirmed the dominance of specific pathogenic species pre-UTI and revealed altered virulence factor profiles associated with Klebsiella aerogenes and Escherichia coli infections. Additionally, a decline in fecal calprotectin levels was observed preceding UTI onset, particularly in cases involving Enterobacteriaceae. The observed pathogen-specific alterations in the gut microbiota preceding UTI onset offer novel insight into the UTI pathogenesis and promising early biomarkers for UTIs in preterm infants, potentially enhancing the timely management of this common infection. However, further validation in larger cohorts is essential to confirm these findings.},
}

Infant
Child
Humans
Infant, Newborn
Adolescent
Case-Control Studies
*Gastrointestinal Microbiome
Escherichia coli
Infant, Premature
Anti-Bacterial Agents/therapeutic use
*Urinary Tract Infections
Enterobacteriaceae
Leukocyte L1 Antigen Complex

@article {pmid38558277,
year = {2024},
author = {Ye, S and Lu, Y and Li, G and Li, D and Wu, Y and Yao, Y},
title = {Stenotrophomonas maltophilia Isolated from the Gut Symbiotic Community of the Plastic-Eating Tenebrio molitor.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {38558277},
issn = {1559-0291},
support = {02020200-K02013008//Zhejiang University/ ; },
abstract = {Polyvinyl chloride (PVC) waste is a major environmental challenge. In this study, we found that a PVC-eating insect, Tenebrio molitor, could survive by consuming PVC as a dietary supplement. To understand the gut symbiotic community, metagenomic analysis was performed to reveal the biodiversity of a symbiotic community in the midgut of Tenebrio molitor. Among them, seven genera were enriched from the midgut of the insect under culture conditions with PVC as carbon source. A strain of Stenotrophomonas maltophilia was isolated from the midgut symbiotic community of the plastic-eating Tenebrio molitor. To unravel the functional gene for the biodegradation enzyme, we sequenced the whole genome of Stenotrophomonas maltophilia and found that orf00390, annotated as a hydrolase, was highly expressed in the PVC culture niche.},
}

@article {pmid38558266,
year = {2024},
author = {Rassner, SME and Cook, JM and Mitchell, AC and Stevens, IT and Irvine-Fynn, TDL and Hodson, AJ and Edwards, A},
title = {The distinctive weathering crust habitat of a High Arctic glacier comprises discrete microbial micro-habitats.},
journal = {Environmental microbiology},
volume = {26},
number = {4},
pages = {e16617},
doi = {10.1111/1462-2920.16617},
pmid = {38558266},
issn = {1462-2920},
support = {//The Rolex Foundation/ ; NE/S001034/1//Natural Environment Research Council/ ; NE/V012991/1//Natural Environment Research Council/ ; RF-2018-584/4//Leverhulme Trust/ ; 288402//Norges Forskningsråd/ ; },
mesh = {*Ice Cover/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Arctic Regions ; },
abstract = {Sunlight penetrates the ice surfaces of glaciers and ice sheets, forming a water-bearing porous ice matrix known as the weathering crust. This crust is home to a significant microbial community. Despite the potential implications of microbial processes in the weathering crust for glacial melting, biogeochemical cycles, and downstream ecosystems, there have been few explorations of its microbial communities. In our study, we used 16S rRNA gene sequencing and shotgun metagenomics of a Svalbard glacier surface catchment to characterise the microbial communities within the weathering crust, their origins and destinies, and the functional potential of the weathering crust metagenome. Our findings reveal that the bacterial community in the weathering crust is distinct from those in upstream and downstream habitats. However, it comprises two separate micro-habitats, each with different taxa and functional categories. The interstitial porewater is dominated by Polaromonas, influenced by the transfer of snowmelt, and exported via meltwater channels. In contrast, the ice matrix is dominated by Hymenobacter, and its metagenome exhibits a diverse range of functional adaptations. Given that the global weathering crust area and the subsequent release of microbes from it are strongly responsive to climate projections for the rest of the century, our results underscore the pressing need to integrate the microbiome of the weathering crust with other communities and processes in glacial ecosystems.},
}

*Ice Cover/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Bacteria/genetics
Arctic Regions

@article {pmid38555499,
year = {2024},
author = {Heston, SM and Young, RR and Jenkins, K and Martin, PL and Stokhuyzen, A and Ward, DV and Bhattarai, SK and Bucci, V and Arshad, M and Chao, NJ and Seed, PC and Kelly, MS},
title = {The effects of antibiotic exposures on the gut resistome during hematopoietic cell transplantation in children.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2333748},
pmid = {38555499},
issn = {1949-0984},
mesh = {Child ; Humans ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; Fluoroquinolones/pharmacology ; *Hematopoietic Stem Cell Transplantation ; },
abstract = {Antibiotic resistance is a global threat driven primarily by antibiotic use. We evaluated the effects of antibiotic exposures on the gut microbiomes and resistomes of children at high risk of colonization by antibiotic-resistant bacteria. We performed shotgun metagenomic sequencing of 691 serially collected fecal samples from 80 children (<18 years) undergoing hematopoietic cell transplantation. We evaluated the effects of aerobic (cefepime, vancomycin, fluoroquinolones, aminoglycosides, macrolides, and trimethoprim-sulfamethoxazole) and anaerobic (piperacillin-tazobactam, carbapenems, metronidazole, and clindamycin) antibiotic exposures on the diversity and composition of the gut microbiome and resistome. We identified 372 unique antibiotic resistance genes (ARGs); the most frequent ARGs identified encode resistance to tetracyclines (n = 88), beta-lactams (n = 84), and fluoroquinolones (n = 79). Both aerobic and anaerobic antibiotic exposures were associated with a decrease in the number of bacterial species (aerobic, β = 0.71, 95% CI: 0.64, 0.79; anaerobic, β = 0.66, 95% CI: 0.53, 0.82) and the number of unique ARGs (aerobic, β = 0.81, 95% CI: 0.74, 0.90; anaerobic, β = 0.73, 95% CI: 0.61, 0.88) within the gut metagenome. However, only antibiotic regimens that included anaerobic activity were associated with an increase in acquisition of new ARGs (anaerobic, β = 1.50; 95% CI: 1.12, 2.01) and an increase in the relative abundance of ARGs in the gut resistome (anaerobic, β = 1.62; 95% CI: 1.15, 2.27). Specific antibiotic exposures were associated with distinct changes in the number and abundance of ARGs for individual antibiotic classes. Our findings detail the impact of antibiotics on the gut microbiome and resistome and demonstrate that anaerobic antibiotics are particularly likely to promote acquisition and expansion of antibiotic-resistant bacteria.},
}

Child
Humans
Anti-Bacterial Agents/pharmacology/therapeutic use
*Gastrointestinal Microbiome/genetics
Bacteria/genetics
Fluoroquinolones/pharmacology
*Hematopoietic Stem Cell Transplantation

@article {pmid38555322,
year = {2024},
author = {Nagy, NA and Tóth, GE and Kurucz, K and Kemenesi, G and Laczkó, L},
title = {The updated genome of the Hungarian population of Aedes koreicus.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {7545},
pmid = {38555322},
issn = {2045-2322},
support = {OTKA PD142602//National Research, Development and Innovation Office/ ; FK-138563//National Research, Development and Innovation Office/ ; },
mesh = {Animals ; Humans ; *Aedes/genetics ; Mosquito Vectors/genetics ; Hungary ; Europe/epidemiology ; Introduced Species ; },
abstract = {Vector-borne diseases pose a potential risk to human and animal welfare, and understanding their spread requires genomic resources. The mosquito Aedes koreicus is an emerging vector that has been introduced into Europe more than 15 years ago but only a low quality, fragmented genome was available. In this study, we carried out additional sequencing and assembled and characterized the genome of the species to provide a background for understanding its evolution and biology. The updated genome was 1.1 Gbp long and consisted of 6099 contigs with an N50 value of 329,610 bp and a BUSCO score of 84%. We identified 22,580 genes that could be functionally annotated and paid particular attention to the identification of potential insecticide resistance genes. The assessment of the orthology of the genes indicates a high turnover at the terminal branches of the species tree of mosquitoes with complete genomes, which could contribute to the adaptation and evolutionary success of the species. These results could form the basis for numerous downstream analyzes to develop targets for the control of mosquito populations.},
}

Animals
Humans
*Aedes/genetics
Mosquito Vectors/genetics
Hungary
Europe/epidemiology
Introduced Species

@article {pmid38502869,
year = {2024},
author = {Nelson, AR and Fegel, TS and Danczak, RE and Caiafa, MV and Roth, HK and Dunn, OI and Turvold, CA and Borch, T and Glassman, SI and Barnes, RT and Rhoades, CC and Wilkins, MJ},
title = {Soil microbiome feedbacks during disturbance-driven forest ecosystem conversion.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrae047},
pmid = {38502869},
issn = {1751-7370},
support = {DEB-2114868//National Science Foundation/ ; 2021-67019-34608//US Department of Agriculture National Institute of Food and Agriculture/ ; 21-1-01-49//US Bureau of Land Management Joint Fire Science Program Graduate Research Innovation/ ; //CSU Agricultural Experiment Station/ ; //Facilities Integrating Collaborations for User Science/ ; 504279//Joint Genome Institute/ ; //US Department of Energy Office of Science User Facility/ ; DE-AC02-05CH11231//Office of Biological and Environmental Research/ ; },
mesh = {Humans ; Ecosystem ; Soil/chemistry ; Cicatrix ; Feedback ; Forests ; *Microbiota ; *Burns ; },
abstract = {Disturbances cause rapid changes to forests, with different disturbance types and severities creating unique ecosystem trajectories that can impact the underlying soil microbiome. Pile burning-the combustion of logging residue on the forest floor-is a common fuel reduction practice that can have impacts on forest soils analogous to those following high-severity wildfire. Further, pile burning following clear-cut harvesting can create persistent openings dominated by nonwoody plants surrounded by dense regenerating conifer forest. A paired 60-year chronosequence of burn scar openings and surrounding regenerating forest after clear-cut harvesting provides a unique opportunity to assess whether belowground microbial processes mirror aboveground vegetation during disturbance-induced ecosystem shifts. Soil ectomycorrhizal fungal diversity was reduced the first decade after pile burning, which could explain poor tree seedling establishment and subsequent persistence of herbaceous species within the openings. Fine-scale changes in the soil microbiome mirrored aboveground shifts in vegetation, with short-term changes to microbial carbon cycling functions resembling a postfire microbiome (e.g. enrichment of aromatic degradation genes) and respiration in burn scars decoupled from substrate quantity and quality. Broadly, however, soil microbiome composition and function within burn scar soils converged with that of the surrounding regenerating forest six decades after the disturbances, indicating potential microbial resilience that was disconnected from aboveground vegetation shifts. This work begins to unravel the belowground microbial processes that underlie disturbance-induced ecosystem changes, which are increasing in frequency tied to climate change.},
}

Humans
Ecosystem
Soil/chemistry
Cicatrix
Feedback
Forests
*Microbiota
*Burns

@article {pmid38423316,
year = {2024},
author = {Xiang, Y and Yu, Y and Wang, J and Li, W and Rong, Y and Ling, H and Chen, Z and Qian, Y and Han, X and Sun, J and Yang, Y and Chen, L and Zhao, C and Li, J and Chen, K},
title = {Neural network establishes co-occurrence links between transformation products of the contaminant and the soil microbiome.},
journal = {The Science of the total environment},
volume = {924},
number = {},
pages = {171287},
doi = {10.1016/j.scitotenv.2024.171287},
pmid = {38423316},
issn = {1879-1026},
mesh = {*Soil/chemistry ; RNA, Ribosomal, 16S ; *Microbiota ; Isotopes/analysis ; DNA ; Pyrenes ; Neural Networks, Computer ; Soil Microbiology ; },
abstract = {It remains challenging to establish reliable links between transformation products (TPs) of contaminants and corresponding microbes. This challenge arises due to the sophisticated experimental regime required for TP discovery and the compositional nature of 16S rRNA gene amplicon sequencing and mass spectrometry datasets, which can potentially confound statistical inference. In this study, we present a new strategy by combining the use of [2]H-labeled Stable Isotope-Assisted Metabolomics ([2]H-SIAM) with a neural network-based algorithm (i.e., MMvec) to explore links between TPs of pyrene and the soil microbiome. The links established by this novel strategy were further validated using different approaches. Briefly, a metagenomic study provided indirect evidence for the established links, while the identification of pyrene degraders from soils, and a DNA-based stable isotope probing (DNA-SIP) study offered direct evidence. The comparison among different approaches, including Pearson's and Spearman's correlations, further confirmed the superior performance of our strategy. In conclusion, we summarize the unique features of the combined use of [2]H-SIAM and MMvec. This study not only addresses the challenges in linking TPs to microbes but also introduces an innovative and effective approach for such investigations. Environmental Implication: Taxonomically diverse bacteria performing successive metabolic steps of the contaminant were firstly depicted in the environmental matrix.},
}

*Soil/chemistry
RNA, Ribosomal, 16S
*Microbiota
Isotopes/analysis
DNA
Pyrenes
Neural Networks, Computer
Soil Microbiology

@article {pmid38316105,
year = {2024},
author = {Benvenuti, E and Ferriani, R and Gianella, P and Ruggiero, P and Cagnasso, F and Borrelli, A and Benvenuto, G and Bertoldi, L and Bottero, E},
title = {The fecal bacterial microbiota is not useful for discriminating between lymphoplasmacytic enteritis and low-grade intestinal T-cell lymphoma in cats nor for predicting therapeutic response.},
journal = {American journal of veterinary research},
volume = {85},
number = {4},
pages = {},
doi = {10.2460/ajvr.23.11.0251},
pmid = {38316105},
issn = {1943-5681},
mesh = {Humans ; Cats ; Animals ; RNA, Ribosomal, 16S/genetics ; *Enteritis/diagnosis/veterinary ; Feces/microbiology ; Bacteria ; *Microbiota ; *Lymphoma, T-Cell/veterinary ; *Cat Diseases/diagnosis ; },
abstract = {OBJECTIVE: To evaluate the fecal bacterial microbiota at the time of diagnosis (T0) and after 1 month of therapy (T1) in cats diagnosed with lymphoplasmacytic enteritis (LPE) or cats with low-grade intestinal T-cell lymphoma (LGITL) and to compare these findings with those of healthy cats.

ANIMALS: 5 healthy cats, 13 cats with LPE, and 7 cats with LGITL were prospectively enrolled between June 2020 and June 2021.

METHODS: Fecal samples were collected at T0 and T1, and DNA was extracted for 16S ribosomal amplicon sequencing. Alpha diversity and beta diversity were computed. The taxonomic assignment was performed using sequences from the Silva v138 formatted reference database. Differential abundant taxa were selected in each taxonomic level, with the P value adjusted < .05, as the cut-off.

RESULTS: No significant differences in alpha and beta diversity were found either at T0 or T1 between healthy and diseased cats or between cats with LPE and LGITL. Beta-diversity analysis showed an increase in the Fusobacteriaceae family in cats with LGITL at T0, compared to cats with LPE. Regardless of histological diagnosis, several microbiota differences were found at T0 based on serum cobalamin levels.

CLINICAL RELEVANCE: Fecal samples were successfully used to characterize the bacteriome of the intestinal tract in cats by 16S rRNA gene sequencing. However, results highlighted that the metagenomic evaluation was not useful to discriminate between LPE and LGITL nor to predict the therapeutic response in this study population.},
}

Humans
Cats
Animals
RNA, Ribosomal, 16S/genetics
*Enteritis/diagnosis/veterinary
Feces/microbiology
Bacteria
*Microbiota
*Lymphoma, T-Cell/veterinary
*Cat Diseases/diagnosis

@article {pmid37665015,
year = {2024},
author = {Sinjab, K and Sawant, S and Ou, A and Fenno, JC and Wang, HL and Kumar, P},
title = {Impact of surface characteristics on the peri-implant microbiome in health and disease.},
journal = {Journal of periodontology},
volume = {95},
number = {3},
pages = {244-255},
pmid = {37665015},
issn = {1943-3670},
support = {R01 DE022579/DE/NIDCR NIH HHS/United States ; R01 DE027857/DE/NIDCR NIH HHS/United States ; R01DE027857/NH/NIH HHS/United States ; },
mesh = {Humans ; *Peri-Implantitis/microbiology ; *Dental Implants/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria ; *Microbiota/genetics ; },
abstract = {BACKGROUND: Because little is known about the impact of implant surface modifications on the peri-implant microbiome, we aimed to examine peri-implant communities in various surface types in order to better understand the impact of these surfaces on the development of peri-implantitis (PI).

METHODS: One hundred and six systemically healthy individuals with anodized (AN), hydroxyapatite-coated (HA), or sandblasted acid-etched (SLA) implants that were >6 months in function were recruited and categorized into health (H) or PI. Peri-implant biofilm was analyzed using 16S rRNA gene sequencing and compared between health/disease and HA/SLA/AN using community-level and taxa-level metrics.

RESULTS: Healthy implants did not demonstrate significant differences in clustering, alpha- or beta-diversity based on surface modification. AN and HA surfaces displayed significant differences between health and PI (p < 0.05); however, such a clustering was not evident with SLA (p > 0.05). AN and HA surfaces also differed in the magnitude and diversity of differences between health and PI. Six species belonging to the genera Shuttleworthia, Scardovia, and Prevotella demonstrated lower abundances in AN implants with PI, and 18 species belonging to the genera Fretibacterium, Tannerella, Treponema, and Fusobacterium were elevated, while in HA implants with PI, 20 species belonging to the genera Streptococcus, Lactobacillus, Veillonella, Rothia, and family Ruminococcaceae were depleted and Peptostreptococcaceae, Atopobiaceae, Veillonellaceae, Porphyromonadaceae, Desulfobulbaceae, and order Synergistales were enriched.

CONCLUSIONS: Within the limitations of this study, we demonstrate that implant surface can differentially modify the disease-associated microbiome, suggesting that surface topography must be considered in the multi-factorial etiology of peri-implant diseases.},
}

Humans
*Peri-Implantitis/microbiology
*Dental Implants/microbiology
RNA, Ribosomal, 16S/genetics
Bacteria
*Microbiota/genetics

@article {pmid36782070,
year = {2023},
author = {Pascal Andreu, V and Augustijn, HE and Chen, L and Zhernakova, A and Fu, J and Fischbach, MA and Dodd, D and Medema, MH},
title = {gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota.},
journal = {Nature biotechnology},
volume = {41},
number = {10},
pages = {1416-1423},
pmid = {36782070},
issn = {1546-1696},
support = {R01 DK101674/DK/NIDDK NIH HHS/United States ; K08 DK110335/DK/NIDDK NIH HHS/United States ; R35 GM142873/GM/NIGMS NIH HHS/United States ; R01 AT011396/AT/NCCIH NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; DP1 DK113598/DK/NIDDK NIH HHS/United States ; DP1 DK113598/DK/NIDDK NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; K08 DK110335/DK/NIDDK NIH HHS/United States ; R35 GM142873/GM/NIGMS NIH HHS/United States ; R01 AT011396/AT/NCCIH NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Feces/microbiology ; Bacteria ; Metabolic Networks and Pathways/genetics ; },
abstract = {The gut microbiota produce hundreds of small molecules, many of which modulate host physiology. Although efforts have been made to identify biosynthetic genes for secondary metabolites, the chemical output of the gut microbiome consists predominantly of primary metabolites. Here we introduce the gutSMASH algorithm for identification of primary metabolic gene clusters, and we used it to systematically profile gut microbiome metabolism, identifying 19,890 gene clusters in 4,240 high-quality microbial genomes. We found marked differences in pathway distribution among phyla, reflecting distinct strategies for energy capture. These data explain taxonomic differences in short-chain fatty acid production and suggest a characteristic metabolic niche for each taxon. Analysis of 1,135 individuals from a Dutch population-based cohort shows that the level of microbiome-derived metabolites in plasma and feces is almost completely uncorrelated with the metagenomic abundance of corresponding metabolic genes, indicating a crucial role for pathway-specific gene regulation and metabolite flux. This work is a starting point for understanding differences in how bacterial taxa contribute to the chemistry of the microbiome.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Microbiota
Feces/microbiology
Bacteria
Metabolic Networks and Pathways/genetics

@article {pmid36715883,
year = {2024},
author = {Song, Y and Sun, M and Ma, F and Xu, D and Mu, G and Jiao, Y and Yu, P and Tuo, Y},
title = {Lactiplantibacillus plantarum DLPT4 Protects Against Cyclophosphamide-Induced Immunosuppression in Mice by Regulating Immune Response and Intestinal Flora.},
journal = {Probiotics and antimicrobial proteins},
volume = {16},
number = {2},
pages = {321-333},
pmid = {36715883},
issn = {1867-1314},
support = {31571813//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Mice ; Cytokines/metabolism ; *Gastrointestinal Microbiome ; Immunosuppression Therapy ; Cyclophosphamide/adverse effects/analysis ; Tumor Necrosis Factor-alpha/genetics ; Immunity ; *Lactobacillus plantarum/metabolism ; *Probiotics ; },
abstract = {In this study, the strain Lactiplantibacillus plantarum DLPT4 was investigated for the immunostimulatory activity in cyclophosphamide (CTX)-induced immunosuppressed BALB/c mice. L. plantarum DLPT4 was administered to BALB/c mice by oral gavage for 30 days, and CTX was injected intraperitoneally from the 25th to the 27th days. Intraperitoneal injection of CTX caused damage to the thymic cortex and intestines, and the immune dysfunction of the BALB/c mice. L. plantarum DLPT4 oral administration exerted immunoregulating effects evidenced by increasing serum immunoglobulin (IgA, IgG, and IgM) levels and reducing the genes expression of pro-inflammatory factors (IL-6, IL-1β, and TNF-α) of the CTX-induced immunosuppressed mice. The results of the metagenome-sequencing analysis showed that oral administration of L. plantarum DLPT4 could regulate the intestinal microbial community of the immunosuppressed mice by changing the ratio of Lactiplantibacillus and Bifidobacterium. Meanwhile, the abundance of carbohydrate enzyme (CAZyme), immune diseases metabolic pathways, and AP-1/MAPK signaling pathways were enriched in the mice administrated with L. plantarum DLPT4. In conclusion, oral administration of L. plantarum DLPT4 ameliorated symptoms of CTX-induced immunosuppressed mice by regulating gut microbiota, influencing the abundance of carbohydrate esterase in the intestinal flora, and enhancing immune metabolic activity. L. plantarum DLPT4 could be a potential probiotic to regulate the immune response.},
}

Animals
Mice
Cytokines/metabolism
*Gastrointestinal Microbiome
Immunosuppression Therapy
Cyclophosphamide/adverse effects/analysis
Tumor Necrosis Factor-alpha/genetics
Immunity
*Lactobacillus plantarum/metabolism
*Probiotics

@article {pmid38553666,
year = {2024},
author = {Ma, ZS},
title = {Towards a unified medical microbiome ecology of the OMU for metagenomes and the OTU for microbes.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {137},
pmid = {38553666},
issn = {1471-2105},
mesh = {Animals ; Humans ; Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome ; Biodiversity ; Sequence Analysis, DNA ; Metagenomics/methods ; },
abstract = {BACKGROUND: Metagenomic sequencing technologies offered unprecedented opportunities and also challenges to microbiology and microbial ecology particularly. The technology has revolutionized the studies of microbes and enabled the high-profile human microbiome and earth microbiome projects. The terminology-change from microbes to microbiomes signals that our capability to count and classify microbes (microbiomes) has achieved the same or similar level as we can for the biomes (macrobiomes) of plants and animals (macrobes). While the traditional investigations of macrobiomes have usually been conducted through naturalists' (Linnaeus & Darwin) naked eyes, and aerial and satellite images (remote-sensing), the large-scale investigations of microbiomes have been made possible by DNA-sequencing-based metagenomic technologies. Two major types of metagenomic sequencing technologies-amplicon sequencing and whole-genome (shotgun sequencing)-respectively generate two contrastingly different categories of metagenomic reads (data)-OTU (operational taxonomic unit) tables representing microorganisms and OMU (operational metagenomic unit), a new term coined in this article to represent various cluster units of metagenomic genes.

RESULTS: The ecological science of microbiomes based on the OTU representing microbes has been unified with the classic ecology of macrobes (macrobiomes), but the unification based on OMU representing metagenomes has been rather limited. In a previous series of studies, we have demonstrated the applications of several classic ecological theories (diversity, composition, heterogeneity, and biogeography) to the studies of metagenomes. Here I push the envelope for the unification of OTU and OMU again by demonstrating the applications of metacommunity assembly and ecological networks to the metagenomes of human gut microbiomes. Specifically, the neutral theory of biodiversity (Sloan's near neutral model), Ning et al.stochasticity framework, core-periphery network, high-salience skeleton network, special trio-motif, and positive-to-negative ratio are applied to analyze the OMU tables from whole-genome sequencing technologies, and demonstrated with seven human gut metagenome datasets from the human microbiome project.

CONCLUSIONS: All of the ecological theories demonstrated previously and in this article, including diversity, composition, heterogeneity, stochasticity, and complex network analyses, are equally applicable to OMU metagenomic analyses, just as to OTU analyses. Consequently, I strongly advocate the unification of OTU/OMU (microbiomes) with classic ecology of plants and animals (macrobiomes) in the context of medical ecology.},
}

Animals
Humans
Metagenome
*Microbiota/genetics
*Gastrointestinal Microbiome
Biodiversity
Sequence Analysis, DNA
Metagenomics/methods

@article {pmid38553222,
year = {2024},
author = {Hafeez, R and Guo, J and Ahmed, T and Jiang, H and Raza, M and Shahid, M and Ibrahim, E and Wang, Y and Wang, J and Yan, C and An, Q and White, JC and Li, B},
title = {Bio-formulated chitosan nanoparticles enhance disease resistance against rice blast by physiomorphic, transcriptional, and microbiome modulation of rice (Oryza sativa L.).},
journal = {Carbohydrate polymers},
volume = {334},
number = {},
pages = {122023},
doi = {10.1016/j.carbpol.2024.122023},
pmid = {38553222},
issn = {1879-1344},
mesh = {Disease Resistance ; *Oryza/genetics ; *Chitosan/pharmacology ; Bacteria ; *Microbiota ; Plant Diseases/prevention & control ; },
abstract = {Rice blast disease (RBD) caused by Magnaporthe oryzae, threaten food security by cutting agricultural output. Nano agrochemicals are now perceived as sustainable, cost-effective alternatives to traditional pesticides. This study investigated bioformulation of moringa chitosan nanoparticles (M-CsNPs) and their mechanisms for suppressing RBD while minimizing toxic effects on the microenvironment. M-CsNPs, sized 46 nm with semi-spherical morphology, significantly suppressed pathogen growth, integrity, and colonization at 200 mg L[-1]in vitro. Greenhouse tests with foliar exposure to the same concentration resulted in a substantial 77.7 % reduction in RBD, enhancing antioxidant enzyme activity and plant health. Furthermore, M-CsNPs improved photosynthesis, gas exchange, and the nutritional profile of diseased rice plants. RNA-seq analysis highlighted upregulated defense-related genes in treated rice plants. Metagenomic study showcased reshaping of the rice microbiome, reducing Magnaporthe abundance by 93.5 %. Both healthy and diseased rice plants showed increased microbial diversity, particularly favoring specific beneficial species Thiobacillus, Nitrospira, Nocardioides, and Sphingomicrobium in the rhizosphere and Azonexus, Agarivorans, and Bradyrhizobium in the phyllosphere. This comprehensive study unravels the diverse mechanisms by which M-CsNPs interact with plants and pathogens, curbing M. oryzae damage, promoting plant growth, and modulating the rice microbiome. It underscores the significant potential for effective plant disease management.},
}

Disease Resistance
*Oryza/genetics
*Chitosan/pharmacology
Bacteria
*Microbiota
Plant Diseases/prevention & control

@article {pmid38548676,
year = {2024},
author = {Jiao, B and Ouyang, Z and Liu, Q and Xu, T and Wan, M and Ma, G and Zhou, L and Guo, J and Wang, J and Tang, B and Zhao, Z and Shen, L},
title = {Integrated analysis of gut metabolome, microbiome, and brain function reveal the role of gut-brain axis in longevity.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2331434},
doi = {10.1080/19490976.2024.2331434},
pmid = {38548676},
issn = {1949-0984},
mesh = {Aged, 80 and over ; Humans ; Brain-Gut Axis ; *Gastrointestinal Microbiome ; Metabolome ; *Microbiota ; Brain ; },
abstract = {The role of microbiota-gut-brain axis in modulating longevity remains undetermined. Here, we performed a multiomics analysis of gut metagenomics, gut metabolomics, and brain functional near-infrared spectroscopy (fNIRS) in a cohort of 164 participants, including 83 nonagenarians (NAs) and 81 non-nonagenarians (NNAs) matched with their spouses and offspring. We found that 438 metabolites were significantly different between the two groups; among them, neuroactive compounds and anti-inflammatory substances were enriched in NAs. In addition, increased levels of neuroactive metabolites in NAs were significantly associated with NA-enriched species that had three corresponding biosynthetic potentials: Enterocloster asparagiformis, Hungatella hathewayi and Oxalobacter formigenes. Further analysis showed that the altered gut microbes and metabolites were linked to the enhanced brain connectivity in NAs, including the left dorsolateral prefrontal cortex (DLPFC)-left premotor cortex (PMC), left DLPFC-right primary motor area (M1), and right inferior frontal gyrus (IFG)-right M1. Finally, we found that neuroactive metabolites, altered microbe and enhanced brain connectivity contributed to the cognitive preservation in NAs. Our findings provide a comprehensive understanding of the microbiota-gut-brain axis in a long-lived population and insights into the establishment of a microbiome and metabolite homeostasis that can benefit human longevity and cognition by enhancing functional brain connectivity.},
}

Aged, 80 and over
Humans
Brain-Gut Axis
*Gastrointestinal Microbiome
Metabolome
*Microbiota
Brain

@article {pmid38547246,
year = {2024},
author = {Wang, Z and Peters, BA and Yu, B and Grove, ML and Wang, T and Xue, X and Thyagarajan, B and Daviglus, ML and Boerwinkle, E and Hu, G and Mossavar-Rahmani, Y and Isasi, CR and Knight, R and Burk, RD and Kaplan, RC and Qi, Q},
title = {Gut Microbiota and Blood Metabolites Related to Fiber Intake and Type 2 Diabetes.},
journal = {Circulation research},
volume = {134},
number = {7},
pages = {842-854},
doi = {10.1161/CIRCRESAHA.123.323634},
pmid = {38547246},
issn = {1524-4571},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2/diagnosis/microbiology ; Diet ; Bacteria ; Dietary Fiber ; },
abstract = {BACKGROUND: Consistent evidence suggests diabetes-protective effects of dietary fiber intake. However, the underlying mechanisms, particularly the role of gut microbiota and host circulating metabolites, are not fully understood. We aimed to investigate gut microbiota and circulating metabolites associated with dietary fiber intake and their relationships with type 2 diabetes (T2D).

METHODS: This study included up to 11 394 participants from the HCHS/SOL (Hispanic Community Health Study/Study of Latinos). Diet was assessed with two 24-hour dietary recalls at baseline. We examined associations of dietary fiber intake with gut microbiome measured by shotgun metagenomics (350 species/85 genera and 1958 enzymes; n=2992 at visit 2), serum metabolome measured by untargeted metabolomics (624 metabolites; n=6198 at baseline), and associations between fiber-related gut bacteria and metabolites (n=804 at visit 2). We examined prospective associations of serum microbial-associated metabolites (n=3579 at baseline) with incident T2D over 6 years.

RESULTS: We identified multiple bacterial genera, species, and related enzymes associated with fiber intake. Several bacteria (eg, Butyrivibrio, Faecalibacterium) and enzymes involved in fiber degradation (eg, xylanase EC3.2.1.156) were positively associated with fiber intake, inversely associated with prevalent T2D, and favorably associated with T2D-related metabolic traits. We identified 159 metabolites associated with fiber intake, 47 of which were associated with incident T2D. We identified 18 of these 47 metabolites associated with the identified fiber-related bacteria, including several microbial metabolites (eg, indolepropionate and 3-phenylpropionate) inversely associated with the risk of T2D. Both Butyrivibrio and Faecalibacterium were associated with these favorable metabolites. The associations of fiber-related bacteria, especially Faecalibacterium and Butyrivibrio, with T2D were attenuated after further adjustment for these microbial metabolites.

CONCLUSIONS: Among United States Hispanics/Latinos, dietary fiber intake was associated with favorable profiles of gut microbiota and circulating metabolites for T2D. These findings advance our understanding of the role of gut microbiota and microbial metabolites in the relationship between diet and T2D.},
}

Humans
*Gastrointestinal Microbiome
*Diabetes Mellitus, Type 2/diagnosis/microbiology
Diet
Bacteria
Dietary Fiber