scholarly journals MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome

2021 ◽  
Vol 17 (1) ◽  
pp. e1008487
Author(s):  
Preecha Patumcharoenpol ◽  
Massalin Nakphaichit ◽  
Gianni Panagiotou ◽  
Anchalee Senavonge ◽  
Narissara Suratannon ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gut Microbiome ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Functional Capability ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Metabolic Functions ◽  
Scale Models

Investigating metabolic functional capability of a human gut microbiome enables the quantification of microbiome changes, which can cause a phenotypic change of host physiology and disease. One possible way to estimate the functional capability of a microbial community is through inferring metagenomic content from 16S rRNA gene sequences. Genome-scale models (GEMs) can be used as scaffold for functional estimation analysis at a systematic level, however up to date, there is no integrative toolbox based on GEMs for uncovering metabolic functions. Here, we developed the MetGEMs (metagenome-scale models) toolbox, an open-source application for inferring metabolic functions from 16S rRNA gene sequences to facilitate the study of the human gut microbiome by the wider scientific community. The developed toolbox was validated using shotgun metagenomic data and shown to be superior in predicting functional composition in human clinical samples compared to existing state-of-the-art tools. Therefore, the MetGEMs toolbox was subsequently applied for annotating putative enzyme functions and metabolic routes related in human disease using atopic dermatitis as a case study.

scholarly journals Correction: 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome

PLoS ONE ◽  
2019 ◽  
Vol 14 (2) ◽  
pp. e0212474 ◽  
Author(s):  
Daniel E. Almonacid ◽  
Laurens Kraal ◽  
Francisco J. Ossandon ◽  
Yelena V. Budovskaya ◽  
Juan Pablo Cardenas ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gut Microbiome ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Reference Ranges ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Rrna Gene Sequencing

scholarly journals 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome

PLoS ONE ◽  
2017 ◽  
Vol 12 (5) ◽  
pp. e0176555 ◽  
Author(s):  
Daniel E. Almonacid ◽  
Laurens Kraal ◽  
Francisco J. Ossandon ◽  
Yelena V. Budovskaya ◽  
Juan Pablo Cardenas ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gut Microbiome ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Reference Ranges ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Rrna Gene Sequencing

scholarly journals A unique and reliable fecal DNA extraction method for 16S rRNA gene and shotgun metagenomic sequencing in the analysis of the human gut microbiome

2020 ◽  
Author(s):  
Céline Elie ◽  
Magali Perret ◽  
Karen Louis ◽  
Asmaà Fritah-Lafont ◽  
Philippe Leissner ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Extraction ◽  
Gut Microbiome ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Shotgun Metagenomic Sequencing

Abstract Background: The gut microbiome is widely analyzed using high-throughput sequencing, such as 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing (SMS). DNA extraction is known to have a large impact on the metagenomic analyses. The aim of this study was to select a unique and best performing DNA extraction protocol for both metagenomic sequencing methods. In that context, four commonly used DNA extraction methods were compared for the analysis of the gut microbiota. Commercial versions were evaluated against modified protocols using a stool preprocessing device (SPD, bioMérieux) in order to facilitate DNA extraction. Stool samples from nine healthy volunteers and nine patients with a Clostridium difficile infection were extracted with all protocols and sequenced with both metagenomic methods. Protocols were ranked using wet- and dry-lab criteria, including quality controls of the extracted genomic DNA, alpha-diversity, accuracy using a mock community of known composition and repeatability across technical replicates.Results: Independently of the sequencing methods used, SPD significantly improved efficiency of the four tested protocols compared with their commercial version, in terms of extracted DNA quality, accuracy of the predicted composition of the microbiota (notably for Gram-positive bacteria), sample alpha-diversity, and experimental repeatability. The best overall performance was obtained for the S-DQ protocol, SPD combined to the DNeasy PowerLyser PowerSoil protocol from QIAGEN.Conclusion: Based on this evaluation, we recommend to use the S-DQ protocol, to obtain standardized and high quality extracted DNA in the human gut microbiome studies.

scholarly journals Analysis of Human Gut Microbiome: Taxonomy and Metabolic Functions in Thai Adults

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 331
Author(s):  
Nachon Raethong ◽  
Massalin Nakphaichit ◽  
Narissara Suratannon ◽  
Witida Sathitkowitchai ◽  
Wanlapa Weerapakorn ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Asian Country ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Thai Population ◽  
Shotgun Metagenomics ◽  
Human Gut Microbiome ◽  
Metabolic Functions

The gut microbiome plays a major role in the maintenance of human health. Characterizing the taxonomy and metabolic functions of the human gut microbiome is necessary for enhancing health. Here, we analyzed the metagenomic sequencing, assembly and construction of a meta-gene catalogue of the human gut microbiome with the overall aim of investigating the taxonomy and metabolic functions of the gut microbiome in Thai adults. As a result, the integrative analysis of 16S rRNA gene and whole metagenome shotgun (WMGS) sequencing data revealed that the dominant gut bacterial families were Lachnospiraceae and Ruminococcaceae of the Firmicutes phylum. Consistently, across 3.8 million (M) genes annotated from 163.5 gigabases (Gb) of WMGS sequencing data, a significant number of genes associated with carbohydrate metabolism of the dominant bacterial families were identified. Further identification of bacterial community-wide metabolic functions promisingly highlighted the importance of Roseburia and Faecalibacterium involvement in central carbon metabolism, sugar utilization and metabolism towards butyrate biosynthesis. This work presents an initial study of shotgun metagenomics in a Thai population-based cohort in a developing Southeast Asian country.

Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces.

2020 ◽  
Author(s):  
CC Kim ◽  
WJ Kelly ◽  
ML Patchett ◽  
GW Tannock ◽  
Z Jordens ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Middle Lamella ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Citrus Peel ◽  
Human Faeces ◽  
The Family

© 2017 IUMS. A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7% sequence similarity). Strain 14T shared ~99% sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6μm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae. The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).

scholarly journals The Termite Group I Phylum Is Highly Diverse and Widespread in the Environment

2007 ◽  
Vol 73 (20) ◽  
pp. 6682-6685 ◽  
Author(s):  
Daniel P. R. Herlemann ◽  
Oliver Geissinger ◽  
Andreas Brune
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Specific Primers ◽  
Environmental Distribution ◽  
Data Set ◽  
Group I

ABSTRACT The bacterial candidate phylum Termite Group I (TG-1) presently consists mostly of “Endomicrobia,” which are endosymbionts of flagellate protists occurring exclusively in the hindguts of termites and wood-feeding cockroaches. Here, we show that public databases contain many, mostly undocumented 16S rRNA gene sequences from other habitats that are affiliated with the TG-1 phylum but are only distantly related to “Endomicrobia.” Phylogenetic analysis of the expanded data set revealed several diverse and deeply branching lineages comprising clones from many different habitats. In addition, we designed specific primers to explore the diversity and environmental distribution of bacteria in the TG-1 phylum.

scholarly journals Microbiological and Geochemical Heterogeneity in an In Situ Uranium Bioremediation Field Site

2005 ◽  
Vol 71 (10) ◽  
pp. 6308-6318 ◽  
Author(s):  
Helen A. Vrionis ◽  
Robert T. Anderson ◽  
Irene Ortiz-Bernad ◽  
Kathleen R. O'Neill ◽  
Charles T. Resch ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Acid Volatile Sulfide ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Geochemical Heterogeneity

ABSTRACT The geochemistry and microbiology of a uranium-contaminated subsurface environment that had undergone two seasons of acetate addition to stimulate microbial U(VI) reduction was examined. There were distinct horizontal and vertical geochemical gradients that could be attributed in large part to the manner in which acetate was distributed in the aquifer, with more reduction of Fe(III) and sulfate occurring at greater depths and closer to the point of acetate injection. Clone libraries of 16S rRNA genes derived from sediments and groundwater indicated an enrichment of sulfate-reducing bacteria in the order Desulfobacterales in sediment and groundwater samples. These samples were collected nearest the injection gallery where microbially reducible Fe(III) oxides were highly depleted, groundwater sulfate concentrations were low, and increases in acid volatile sulfide were observed in the sediment. Further down-gradient, metal-reducing conditions were present as indicated by intermediate Fe(II)/Fe(total) ratios, lower acid volatile sulfide values, and increased abundance of 16S rRNA gene sequences belonging to the dissimilatory Fe(III)- and U(VI)-reducing family Geobacteraceae. Maximal Fe(III) and U(VI) reduction correlated with maximal recovery of Geobacteraceae 16S rRNA gene sequences in both groundwater and sediment; however, the sites at which these maxima occurred were spatially separated within the aquifer. The substantial microbial and geochemical heterogeneity at this site demonstrates that attempts should be made to deliver acetate in a more uniform manner and that closely spaced sampling intervals, horizontally and vertically, in both sediment and groundwater are necessary in order to obtain a more in-depth understanding of microbial processes and the relative contribution of attached and planktonic populations to in situ uranium bioremediation.

scholarly journals Paenibacillus xinjiangensis sp. nov., isolated from Xinjiang province in China

2006 ◽  
Vol 56 (11) ◽  
pp. 2579-2582 ◽  
Author(s):  
Jee-Min Lim ◽  
Che Ok Jeon ◽  
Dong-Jin Park ◽  
Li-Hua Xu ◽  
Cheng-Lin Jiang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Sequence Similarities

Strain B538T is a Gram-positive, motile, rod-shaped bacterium, which was isolated from Xinjiang province in China. This organism grew optimally at 30–35 °C and pH 8.0–8.5. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B538T belonged to the genus Paenibacillus and chemotaxonomic data (DNA G+C content, 47.0 mol%; major isoprenoid quinone, MK-7; cell wall type, A1γ meso-diaminopimelic acid; major fatty acids, anteiso-C15 : 0 and C16 : 0) supported affiliation of the isolate with the genus Paenibacillus. Comparative 16S rRNA gene sequence analyses showed that the isolate was most closely related to Paenibacillus glycanilyticus DS-1T, with 16S rRNA gene sequence similarity of 98.1 %; sequence similarities to other members of the genus Paenibacillus used in the phylogenetic tree were less than 96.5 %. The DNA–DNA relatedness between strain B538T and P. glycanilyticus DS-1T was about 8.0 %. On the basis of physiological and molecular properties, strain B538T (=KCTC 3952T=DSM 16970T) is proposed as the type strain of a novel species within the genus Paenibacillus, for which the name Paenibacillus xinjiangensis sp. nov. is proposed.

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