Metagenome-Assembled Genomes Isolated from a Human Fecal Diarrhea Sample

ABSTRACT Few previous studies have assessed stability and “gold-standard” concordance of fecal sample collection methods for whole-genome shotgun metagenomic sequencing (WGSS), an increasingly popular method for studying the gut microbiome. We used WGSS data to investigate ambient temperature stability and putative gold-standard concordance of microbial profiles in fecal samples collected and stored using fecal occult blood test (FOBT) cards, fecal immunochemical test (FIT) tubes, 95% ethanol, or RNAlater. Among 15 Mayo Clinic employees, for each collection method, we calculated intraclass correlation coefficients (ICCs) to estimate stability of fecal microbial profiles after storage for 4 days at ambient temperature and concordance with immediately frozen, no-solution samples (i.e., the putative gold standard). ICCs were estimated for multiple metrics, including relative abundances of select phyla, species, KEGG k-genes (representing any coding sequence that had >70% identity and >70% query coverage with respect to a known KEGG ortholog), KEGG modules, and KEGG pathways; species and k-gene alpha diversity; and Bray-Curtis and Jaccard species beta diversity. ICCs for microbial profile stability were excellent (≥90%) for fecal samples collected via most of the collection methods, except those preserved in 95% ethanol. Concordance with the immediately frozen, no-solution samples varied for all collection methods, but the number of observed species and the beta diversity metrics tended to have higher concordance than other metrics. Our findings, taken together with previous studies and feasibility considerations, indicated that FOBT cards, FIT tubes, and RNAlater are acceptable choices for fecal sample collection methods in future WGSS studies. IMPORTANCE A major direction for future microbiome research is implementation of fecal sample collections in large-scale, prospective epidemiologic studies. Studying microbiome-disease associations likely requires microbial data to be pooled from multiple studies. Our findings suggest collection methods that are most optimal to be used standardly across future WGSS microbiome studies.

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Shotgun metagenomic sequencing from Manao-Pee cave, Thailand, reveals insight into the microbial community structure and its metabolic potential

BMC Microbiology ◽

10.1186/s12866-019-1521-8 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 8

Author(s):

Apirak Wiseschart ◽

Wuttichai Mhuantong ◽

Sithichoke Tangphatsornruang ◽

Duriya Chantasingh ◽

Kusol Pootanakit

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Metagenomic Sequencing ◽

Metabolic Potential ◽

Shotgun Metagenomic Sequencing ◽

Insight Into

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Multicenter assessment of microbial community profiling using 16S rRNA gene sequencing and shotgun metagenomic sequencing

Journal of Advanced Research ◽

10.1016/j.jare.2020.07.010 ◽

2020 ◽

Vol 26 ◽

pp. 111-121 ◽

Cited By ~ 1

Author(s):

Dongsheng Han ◽

Peng Gao ◽

Rui Li ◽

Ping Tan ◽

Jiehong Xie ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Community Profiling ◽

Shotgun Metagenomic Sequencing ◽

Rrna Gene Sequencing

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Shotgun metagenomic sequencing data of sunflower rhizosphere microbial community in South Africa

Data in Brief ◽

10.1016/j.dib.2020.105831 ◽

2020 ◽

Vol 31 ◽

pp. 105831

Author(s):

Olubukola Oluranti Babalola ◽

Temitayo Tosin Alawiye ◽

Carlos Rodriguez Lopez ◽

Ayansina Segun Ayangbenro

Keyword(s):

South Africa ◽

Microbial Community ◽

Metagenomic Sequencing ◽

Sequencing Data ◽

Shotgun Metagenomic Sequencing ◽

Rhizosphere Microbial Community

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Correction: Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing

PLoS ONE ◽

10.1371/journal.pone.0106124 ◽

2014 ◽

Vol 9 (8) ◽

pp. e106124 ◽

Cited By ~ 1

Author(s):

Keyword(s):

Microbial Community ◽

Human Saliva ◽

Metagenomic Sequencing ◽

Microbial Community Profiling ◽

Community Profiling ◽

Shotgun Metagenomic Sequencing

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Premature neonatal gut microbial community patterns supporting an epithelial TLR-mediated pathway for necrotizing enterocolitis

BMC Microbiology ◽

10.1186/s12866-021-02285-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Alexander G. Shaw ◽

Kathleen Sim ◽

Graham Rose ◽

David J. Wooldridge ◽

Ming-Shi Li ◽

...

Keyword(s):

Microbial Community ◽

Bayesian Regression ◽

Validation Dataset ◽

Metagenomic Sequencing ◽

Faecal Microbiota ◽

Community Patterns ◽

Cpg Dna ◽

Shotgun Metagenomic Sequencing ◽

Low Levels ◽

Stimulation Of

Abstract Background Necrotising enterocolitis (NEC) is a devastating bowel disease, primarily affecting premature infants, with a poorly understood aetiology. Prior studies have found associations in different cases with an overabundance of particular elements of the faecal microbiota (in particular Enterobacteriaceae or Clostridium perfringens), but there has been no explanation for the different results found in different cohorts. Immunological studies have indicated that stimulation of the TLR4 receptor is involved in development of NEC, with TLR4 signalling being antagonised by the activated TLR9 receptor. We speculated that differential stimulation of these two components of the signalling pathway by different microbiota might explain the dichotomous findings of microbiota-centered NEC studies. Here we used shotgun metagenomic sequencing and qPCR to characterise the faecal microbiota community of infants prior to NEC onset and in a set of matched controls. Bayesian regression was used to segregate cases from control samples using both microbial and clinical data. Results We found that the infants suffering from NEC fell into two groups based on their microbiota; one with low levels of CpG DNA in bacterial genomes and the other with high abundances of organisms expressing LPS. The identification of these characteristic communities was reproduced using an external metagenomic validation dataset. We propose that these two patterns represent the stimulation of a common pathway at extremes; the LPS-enriched microbiome suggesting overstimulation of TLR4, whilst a microbial community with low levels of CpG DNA suggests reduction of the counterbalance to TLR4 overstimulation. Conclusions The identified microbial community patterns support the concept of NEC resulting from TLR-mediated pathways. Identification of these signals suggests characteristics of the gastrointestinal microbial community to be avoided to prevent NEC. Potential pre- or pro-biotic treatments may be designed to optimise TLR signalling.

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Metagenome Analysis of Surface Waters of the Shardara Reservoir, the Largest Artificial Reservoir in Southern Kazakhstan

Microbiology Resource Announcements ◽

10.1128/mra.00053-20 ◽

2020 ◽

Vol 9 (11) ◽

Author(s):

Madina S. Alexyuk ◽

Andrey P. Bogoyavlenskiy ◽

Pavel G. Alexyuk ◽

Yergali S. Moldakhanov ◽

Vladimir E. Berezin

Keyword(s):

Microbial Community ◽

Surface Waters ◽

Metagenomic Analysis ◽

Metagenomic Sequencing ◽

Metagenome Analysis ◽

Artificial Reservoir ◽

Shotgun Metagenomic Sequencing ◽

Hydropower Engineering

Here, we present a metagenomic analysis of the microflora of the surface waters of the Shardara reservoir, the largest artificial reservoir in Southern Kazakhstan, created to meet irrigation and hydropower engineering needs. In this case, shotgun metagenomic sequencing of the microbial community DNA was used.

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Premature Neonatal Gut Microbial Community Patterns Supporting An Epithelial TLR-Mediated Pathway For Necrotizing Enterocolitis

10.21203/rs.3.rs-147550/v1 ◽

2021 ◽

Author(s):

Alexander G Shaw ◽

Kathleen Sim ◽

Graham Rose ◽

David J. Wooldridge ◽

Ming-Shi Li ◽

...

Keyword(s):

Microbial Community ◽

Validation Dataset ◽

Metagenomic Sequencing ◽

Faecal Microbiota ◽

Community Patterns ◽

Cpg Dna ◽

Shotgun Metagenomic Sequencing ◽

Low Levels ◽

Gut Microbial Community ◽

Stimulation Of

Abstract Background: Necrotising enterocolitis (NEC) is a devastating bowel disease, primarily affecting premature infants, with a poorly understood aetiology. Prior studies have found associations in different cases with an overabundance of particular elements of the faecal microbiota (in particular Enterobacteriaceae or Clostridium perfringens), but there has been no explanation for the different results found in different cohorts. Immunological studies have indicated that stimulation of the TLR4 receptor is involved in development of NEC, with TLR4 signalling being antagonised by the activated TLR9 receptor. We speculated that differential stimulation of these two components of the signalling pathway by different microbiota might explain the dichotomous findings of microbiota-centered NEC studies. Here we used shotgun metagenomic sequencing and qPCR to characterise the faecal microbiota community of infants prior to NEC onset and in a set of matched controls. Logistic regression was used to segregate cases from control samples using both microbial and clinical data.Results: We found that the infants suffering from NEC fell into two groups based on their microbiota; one with relatively low levels of CpG DNA in bacterial genomes and the other with high abundances of organisms expressing LPS. The identification of these characteristic communities was reproduced using an external metagenomic validation dataset. We suggest that these two patterns represent the stimulation of a common pathway at extremes; the LPS leading to overstimulation of TLR4, whilst low levels of CpG fail to sufficiently stimulate TLR9. Conclusions: The identified microbial community patterns support the concept of NEC resulting from TLR-mediated pathways. Identification of these signals suggests characteristics of the gastrointestinal microbial community to be avoided to prevent NEC. Potential pre- or pro-biotic treatments may be designed to optimise TLR signalling.

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Phyllosphere Microbiome in Response to Citrus Melanose

10.21203/rs.3.rs-51076/v1 ◽

2020 ◽

Author(s):

Pudong Li ◽

Jianping Xu ◽

Zhengyi Wang ◽

Hongye Li

Keyword(s):

Microbial Community ◽

Community Response ◽

Microbial Interactions ◽

Metagenomic Sequencing ◽

Fungal Cell ◽

Pathogen Invasion ◽

Shotgun Metagenomic Sequencing ◽

Dna Metabarcoding ◽

Functional Features ◽

Microbial Community Assembly

Abstract Background: Like microbiomes in the rhizosphere, phyllosphere microbiomes can have an important role in plant growth and health. However, whether and how the phyllosphere microbiomes respond to the invasion of pathogens is not well understood. In this study, we address this question using the citrus phyllosphere-associated microbiome as a model.Results: Through DNA metabarcoding (16S for bacteria and ITS for fungi) and shotgun metagenomic sequencing, we found that phyllosphere microbiomes in different ecological habitats (epiphytes and endophytes) responded differently to melanose disease caused by the fungal pathogen Diaporthe citri on citrus (Citrus unshiu) leaves. We observed that citrus phyllosphere-associated microbiome responded to the melanose disease in five ways: (1) increasing microbial richness; (2) reducing community evenness; (3) enriching selected microbes; (4) enhancing microbial interactions; and (5) enriching functional features involved in metabolism and fungal cell wall degrading.Conclusions: Our study revealed how phyllosphere microbiomes in the epiphytic and endophytic habitats differ between diseased and healthy leaves. Based on the differences at both the taxonomic and functional levels, we propose a general conceptual paradigm to describe the different microbial community assembly processes for the phyllosphere microbiome in response to leaf disease and how such processes impact plant health. Our results provide novel insights for understanding the contributions of the phyllosphere microbial community response during pathogen invasion.

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