mSystems, Год журнала: 2023, Номер 8(2)
Опубликована: Апрель 3, 2023
Comprehensive protein function annotation is essential for understanding microbiome-related disease mechanisms in the host organisms. However, a large portion of human gut microbial proteins lack functional annotation. Here, we have developed new metagenome analysis workflow integrating
Язык: Английский
Nucleic Acids Research, Год журнала: 2023, Номер 51(W1), С. W115 - W121
Опубликована: Май 1, 2023
Carbohydrate active enzymes (CAZymes) are made by various organisms for complex carbohydrate metabolism. Genome mining of CAZymes has become a routine data analysis in (meta-)genome projects, owing to the importance bioenergy, microbiome, nutrition, agriculture, and global carbon recycling. In 2012, dbCAN was provided as an online web server automated CAZyme annotation. dbCAN2 (https://bcb.unl.edu/dbCAN2) further developed 2018 meta combine multiple tools improved also included CGC-Finder, tool identifying gene clusters (CGCs) (meta-)genomes. We have updated dbCAN3 with following new functions components: (i) dbCAN-sub profile Hidden Markov Model database (HMMdb) substrate prediction at subfamily level; (ii) searching against experimentally characterized polysaccharide utilization loci (PULs) known glycan substates dbCAN-PUL CGC (iii) majority voting method consider all predicted from (iv) browsing visualization results on website. summary, not only inherits dbCAN2, but integrates three methods prediction.
Язык: Английский
Процитировано
378
iMeta, Год журнала: 2023, Номер 2(1)
Опубликована: Фев. 1, 2023
OmicStudio focuses on speed, quality together with flexibility. Generally, can not only meet the users' demand of ordinary bioinformatics data analysis, statistics, and visualization, but also provides them freedom mining beyond developer's framework. Additionally, unlimited to aesthetics, users get more elegant graphs through customizing. Available online https://www.omicstudio.cn.
Язык: Английский
Процитировано
165
Microbiome, Год журнала: 2022, Номер 10(1)
Опубликована: Апрель 19, 2022
Recent evidence implicates microbial sulfidogenesis as a potential trigger of colorectal cancer (CRC), highlighting the need for comprehensive knowledge sulfur metabolism within human gut. Microbial produces genotoxic hydrogen sulfide (H2S) in colon using inorganic (sulfate) and organic (taurine/cysteine/methionine) substrates; however, majority studies have focused on sulfate reduction dissimilatory sulfite reductases (Dsr).Here, we show that genes are more abundant diverse than previously observed statistically associated with CRC. Using ~ 17,000 bacterial genomes from publicly available stool metagenomes, studied diversity metabolic 667 participants across different health statuses: healthy, adenoma, carcinoma. Sulfidogenic were harbored by 142 genera both sulfidogenic Significantly, anaerobic reductase (asr) twice dsr, demonstrating Asr is likely important contributor to gut Dsr. We identified twelve pathways reductive taurine discovered novel harboring these pathways. Finally, prevalence indicates understudied substrates may be most source microbially derived H2S.Our findings significantly expand prevalent known, irrespective status (i.e., healthy diseased states). Our results increase bacteria Overall, our implications understanding role microbiome its contributions pathogenesis Video abstract.
Язык: Английский
Процитировано
85
Nature Microbiology, Год журнала: 2023, Номер 8(5), С. 946 - 957
Опубликована: Апрель 6, 2023
Abstract Many microbes in nature reside dense, metabolically interdependent communities. We investigated the and extent of microbe-virus interactions relation to microbial density syntrophy by examining a biomass deep-sea hydrothermal mat. Using metagenomic sequencing, we find numerous instances where phylogenetically distant (up domain level) encode CRISPR-based immunity against same viruses Evidence viral with hosts cross-cutting domains is particularly striking between known syntrophic partners, for example those engaged anaerobic methanotrophy. These patterns are corroborated proximity-ligation-based (Hi-C) inference. Surveys public datasets reveal additional interacting across diverse ecosystems harbour biofilms. propose that entry particles and/or DNA non-primary host cells may be common phenomenon densely populated ecosystems, eco-evolutionary implications CRISPR-mediated inter-population augmentation resilience viruses.
Язык: Английский
Процитировано
50
Microbiome, Год журнала: 2023, Номер 11(1)
Опубликована: Апрель 5, 2023
Abstract Background Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism microbially driven cycling along sediment depth mangrove wetlands remain elusive. Here we investigated vertical profile methane (CH 4 ), nitrogen (N) sulphur (S) genes/pathways their potential mechanisms using metagenome sequencing approaches. Results Our results showed that metabolic pathways involved in CH , N S were mainly shaped by pH acid volatile sulphide (AVS) a depth, AVS was critical electron donor impacting oxidation denitrification. Gene families denitrification significantly ( P < 0.05) decreased could be coupled S-driven denitrifiers, such Burkholderiaceae Sulfurifustis surface (0–15 cm). Interestingly, all denitrifier metagenome-assembled genomes (MAGs) appeared to incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous reductase (Nos), suggesting sulphide-utilizing groups might an important contributor 2 O production sediment. methanogenesis reduction increased depth. Based on both network MAG analyses, sulphate-reducing bacteria (SRB) develop syntrophic relationships anaerobic oxidizers (ANMEs) direct transfer or zero-valent sulphur, which would pull forward co-existence methanogens SRB middle deep layer sediments. Conclusions In addition offering perspective distribution genes/pathways, this study emphasizes role emissions various possible ANMEs The exploration provides novel insights into future synthetic microbial community construction analysis. This also has implications for predicting ecosystem functions within context environmental global change.
Язык: Английский
Процитировано
49
Soil Biology and Biochemistry, Год журнала: 2024, Номер 192, С. 109369 - 109369
Опубликована: Фев. 23, 2024
Язык: Английский
Процитировано
46
Soil Biology and Biochemistry, Год журнала: 2024, Номер 193, С. 109382 - 109382
Опубликована: Март 12, 2024
Soil is an extremely complex and dynamic matrix, in part, due to the wide diversity of organisms living within it. organic matter (SOM) fundamental substrate on which delivery ecosystem services depends, providing metabolic fuel drive soil function. As such, studying metabolome (the concentration low molecular weight metabolites), as a subset SOM, holds potential greatly expand our understanding behaviour, fate, interaction functional significance small molecules soil. Encompassing range chemical classes (including amino acids, peptides, lipids carbohydrates) large number individual (ca. n = 105 106), resultant (indirect) output several layers biological hierarchy, namely metagenome, metatranscriptome metaproteome. it may also provide support validation for these "multi-omics" datasets. We present case increased use untargeted metabolomics biochemistry, particularly furthering functions driving SOM composition biogeochemical cycling. Further, we discuss scale challenge terms metabolite extraction, analysis interpretation plant-soil-microbial systems. Lastly, highlight key knowledge gaps currently limit metabolomic approaches better understand processes, including: (i) datasets; (ii) source, emission fate soil-derived volatile compounds (VOCs), (iii) assessing temporal fluxes metabolites, (iv) monitoring ecological interactions rhizosphere. While application science still its relative infancy, importance biochemical system relation regulation, management underpinning further elucidating links between organisms, well ability community process cycle nutrients.
Язык: Английский
Процитировано
20
Nature Communications, Год журнала: 2024, Номер 15(1)
Опубликована: Июль 14, 2024
Permafrost, characterized by its frozen soil, serves as a unique habitat for diverse microorganisms. Understanding these microbial communities is crucial predicting the response of permafrost ecosystems to climate change. However, large-scale evidence regarding stratigraphic variations in profiles remains limited. Here, we analyze community structure and functional potential based on 16S rRNA gene amplicon sequencing metagenomic data obtained from an ∼1000 km transect Tibetan Plateau. We find that alpha diversity declines but beta increases down soil profile. Microbial assemblages are primarily governed dispersal limitation drift, with importance drift decreasing increasing depth. Moreover, genes related reduction reactions (e.g., ferric iron reduction, dissimilatory nitrate denitrification) enriched subsurface layers. In addition, groups involved alternative electron accepting processes more contribute highly community-level metabolic layers, likely reflecting lower redox complicated trophic strategies microorganisms deeper soils. Overall, findings provide comprehensive insights into potentials regions.
Язык: Английский
Процитировано
18
iMeta, Год журнала: 2025, Номер unknown
Опубликована: Фев. 14, 2025
Abstract Shotgun metagenomics has become a pivotal technology in microbiome research, enabling in‐depth analysis of microbial communities at both the high‐resolution taxonomic and functional levels. This approach provides valuable insights diversity, interactions, their roles health disease. However, complexity data processing need for reproducibility pose significant challenges to researchers. To address these challenges, we developed EasyMetagenome, user‐friendly pipeline that supports multiple methods, including quality control host removal, read‐based, assembly‐based, binning, along with advanced genome analysis. The also features customizable settings, comprehensive visualizations, detailed parameter explanations, ensuring its adaptability across wide range scenarios. Looking forward, aim refine by addressing contamination issues, optimizing workflows third‐generation sequencing data, integrating emerging technologies like deep learning network analysis, further enhance accuracy. EasyMetageonome is freely available https://github.com/YongxinLiu/EasyMetagenome .
Язык: Английский
Процитировано
2
Frontiers in Cellular and Infection Microbiology, Год журнала: 2022, Номер 11
Опубликована: Янв. 4, 2022
Phages, short for bacteriophages, are viruses that specifically infect bacteria and the most abundant biological entities on earth found in every explored environment, from deep sea to Sahara Desert. Phages within human biome gaining increasing recognition as potential modulators of gut ecosystem. For example, they have been connected gastrointestinal diseases treatment efficacy Fecal Microbiota Transplant. The ability phages modulate microbiome has attributed predation or promotion bacterial survival by transfer genes enhance fitness upon infection. In addition, shown interact with immune system variable outcomes. Despite evidence supporting importance ecosystem, extent their influence shape ecosystem is yet be fully understood. Here, we discuss phage modulation microbiome, postulating pivotal contributors dynamics. We therefore propose novel research questions further elucidate role(s) its impact our health well-being.
Язык: Английский
Процитировано
59