Enlightening the Taxonomy Darkness of Human Gut Microbiomes With Cultured Biobank

Abstract Background The cultivated gut microbial resource plays essential role in gut microbiome studies such as gut microbial function and their interactions with host. Though several major studies had been performed to understand the cultured human gut microbiota, up to 70% of the Unified Human Gastrointestinal Genome species remain uncultivated and their taxonomy is not clear. Large-scale gut microbial isolation and identification and their access to pubic are imperative for gut microbial studies and for understanding of the human gut microbial functions.Results Here, we report the construction of an human Gut Microbial Biobank (hGMB) (homepage: hgmb.nmdc.cn) by large-scale cultivation of 10,558 isolates from 239 feces of healthy Chinese volunteers, and deposited 1,170 strains representing 404 different species in International Depository Authority for long-term preservation and public access worldwidely. We discovered and denominated 107 new species, and proposed 28 new genera and 3 new families. The new species and their newly sequenced genomes uncovered 16 “most-wanted” or “medium priority” taxa proposed by the Human Microbiome Project and 42 previously-uncultured MAGs in IGGdb, respectively. The hGMB represented over 80% of the common and dominant human gut microbial genera or species of global human gut 16S rRNA gene amplicon data (n=11,647), and covered 70% of the known genes (KEGG Orthologys) and 10% of the functionally-unknown genes in the global human gut gene catalogs. Conclusions A publically accessible human Gut Microbial Biobank (hGMB) that contains 1,170 strains and represents 404 human gut microbial speces is estabolished. The hGMB expands the currently known, taxonomically-characterized gut microbial resources and genomic repository by adding 107 new species and 115 new genomes of human gut microbes. Based on the newly discovered species in this study, 28 new genera and 3 new families of human gut microbes were identified and proposed.

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Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank

Microbiome ◽

10.1186/s40168-021-01064-3 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Chang Liu ◽

Meng-Xuan Du ◽

Rexiding Abuduaini ◽

Hai-Ying Yu ◽

Dan-Hua Li ◽

...

Keyword(s):

Large Scale ◽

Human Microbiome ◽

In Silico Analysis ◽

Human Microbiome Project ◽

Public Access ◽

Rrna Gene ◽

New Genera ◽

Human Gut ◽

Isolation And Identification ◽

Culture Collections

Abstract Background In gut microbiome studies, the cultured gut microbial resource plays essential roles, such as helping to unravel gut microbial functions and host-microbe interactions. Although several major studies have been performed to elucidate the cultured human gut microbiota, up to 70% of the Unified Human Gastrointestinal Genome species have not been cultured to date. Large-scale gut microbial isolation and identification as well as availability to the public are imperative for gut microbial studies and further characterizing human gut microbial functions. Results In this study, we constructed a human Gut Microbial Biobank (hGMB; homepage: hgmb.nmdc.cn) through the cultivation of 10,558 isolates from 31 sample mixtures of 239 fresh fecal samples from healthy Chinese volunteers, and deposited 1170 strains representing 400 different species in culture collections of the International Depository Authority for long-term preservation and public access worldwide. Following the rules of the International Code of Nomenclature of Prokaryotes, 102 new species were characterized and denominated, while 28 new genera and 3 new families were proposed. hGMB represented over 80% of the common and dominant human gut microbial genera and species characterized from global human gut 16S rRNA gene amplicon data (n = 11,647) and cultured 24 “most-wanted” and “medium priority” taxa proposed by the Human Microbiome Project. We in total sequenced 115 genomes representing 102 novel taxa and 13 previously known species. Further in silico analysis revealed that the newly sequenced hGMB genomes represented 22 previously uncultured species in the Unified Human Gastrointestinal Genome (UHGG) and contributed 24 representatives of potentially “dark taxa” that had not been discovered by UHGG. The nonredundant gene catalogs generated from the hGMB genomes covered over 50% of the functionally known genes (KEGG orthologs) in the largest global human gut gene catalogs and approximately 10% of the “most wanted” functionally unknown proteins in the FUnkFams database. Conclusions A publicly accessible human Gut Microbial Biobank (hGMB) was established that contained 1170 strains and represents 400 human gut microbial species. hGMB expands the gut microbial resources and genomic repository by adding 102 novel species, 28 new genera, 3 new families, and 115 new genomes of human gut microbes.

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Enlightening the Taxonomy Darkness of Human Gut Microbiomes With a Cultured Biobank

10.21203/rs.3.rs-168279/v1 ◽

2021 ◽

Author(s):

Chang Liu ◽

Mengxuan Du ◽

Rexiding Abuduaini ◽

Hai-Ying Yu ◽

Dan-Hua Li ◽

...

Keyword(s):

Large Scale ◽

Human Microbiome ◽

Human Microbiome Project ◽

Public Access ◽

Rrna Gene ◽

New Genera ◽

Human Gut ◽

Isolation And Identification ◽

Culture Collections ◽

Host Microbe Interactions

Abstract BackgroundThe cultivated gut microbial resource plays essential roles in gut microbiome studies such as unraveling gut microbial functions and host-microbe interactions. Though several major studies have been performed to understand the cultured human gut microbiota, up to 70% of the Unified Human Gastrointestinal Genome species remain uncultivated. Large-scale gut microbial isolation and identification and their access to public are imperative for gut microbial studies and further understanding of the human gut microbial functions.ResultsHere, we report the construction of a human Gut Microbial Biobank (hGMB) (homepage: hgmb.nmdc.cn) by cultivation of 10,558 isolates from 239 feces samples of healthy Chinese volunteers, and deposited 1,170 strains representing 400 different species in culture collections of International Depository Authority for long-term preservation and public access worldwide. The hGMB enriched the existing cultivable gut microbial repository and represented over 80% of the common and dominant human gut microbial genera and species of global human gut 16S rRNA gene amplicon data (n=11,647).Moreover, 102 new species were characterized and denominated and 28 new genera and 3 new families were proposed, following the rules of International Code of Nomenclature of Prokaryotes. The hGMB uncovered 24 “most-wanted” and “medium priority” taxa proposed by the Human Microbiome Project, while the novel-taxon genomes represented 22 previously-uncultured species in Unified Human Gastrointestinal Genome (UHGG) and contributed 24 potentially “dark-taxon” representatives that were not discovered by UHGG. The 115 newly-sequenced hGMB genomes covered over 50% of the known genes (KEGG Orthologs) in the global human gut gene catalogs and over 10% of the “most-wanted” functionally unknown proteins in FUnkFams database.ConclusionsA publicly accessible human Gut Microbial Biobank (hGMB) is established and contains 1,170 strains and represents 400 human gut microbial species. The hGMB expands gut microbial resources and genomic repository by adding 102 novel species, 28 new genera and 3 new families, and 115 new genomes of human gut microbes.

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Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function

BMC Genomics ◽

10.1186/s12864-020-07307-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Gongchao Jing ◽

Yufeng Zhang ◽

Wenzhi Cui ◽

Lu Liu ◽

Jian Xu ◽

...

Keyword(s):

16S Rrna ◽

Large Scale ◽

Low Cost ◽

Human Microbiome ◽

Amplicon Sequencing ◽

Training Sample ◽

Rrna Gene ◽

16S Amplicon Sequencing ◽

Cross Platform ◽

Functional Profiles

Abstract Background Due to their much lower costs in experiment and computation than metagenomic whole-genome sequencing (WGS), 16S rRNA gene amplicons have been widely used for predicting the functional profiles of microbiome, via software tools such as PICRUSt 2. However, due to the potential PCR bias and gene profile variation among phylogenetically related genomes, functional profiles predicted from 16S amplicons may deviate from WGS-derived ones, resulting in misleading results. Results Here we present Meta-Apo, which greatly reduces or even eliminates such deviation, thus deduces much more consistent diversity patterns between the two approaches. Tests of Meta-Apo on > 5000 16S-rRNA amplicon human microbiome samples from 4 body sites showed the deviation between the two strategies is significantly reduced by using only 15 WGS-amplicon training sample pairs. Moreover, Meta-Apo enables cross-platform functional comparison between WGS and amplicon samples, thus greatly improve 16S-based microbiome diagnosis, e.g. accuracy of gingivitis diagnosis via 16S-derived functional profiles was elevated from 65 to 95% by WGS-based classification. Therefore, with the low cost of 16S-amplicon sequencing, Meta-Apo can produce a reliable, high-resolution view of microbiome function equivalent to that offered by shotgun WGS. Conclusions This suggests that large-scale, function-oriented microbiome sequencing projects can probably benefit from the lower cost of 16S-amplicon strategy, without sacrificing the precision in functional reconstruction that otherwise requires WGS. An optimized C++ implementation of Meta-Apo is available on GitHub (https://github.com/qibebt-bioinfo/meta-apo) under a GNU GPL license. It takes the functional profiles of a few paired WGS:16S-amplicon samples as training, and outputs the calibrated functional profiles for the much larger number of 16S-amplicon samples.

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Computational Modeling of the Human Microbiome

Microorganisms ◽

10.3390/microorganisms8020197 ◽

2020 ◽

Vol 8 (2) ◽

pp. 197

Author(s):

Shomeek Chowdhury ◽

Stephen S. Fong

Keyword(s):

Computational Modeling ◽

Human Health ◽

Large Scale ◽

Human Microbiome ◽

Human Microbiome Project ◽

Microbial Composition ◽

Site Specific ◽

Microbiome Research ◽

High Level ◽

The Impact

The impact of microorganisms on human health has long been acknowledged and studied, but recent advances in research methodologies have enabled a new systems-level perspective on the collections of microorganisms associated with humans, the human microbiome. Large-scale collaborative efforts such as the NIH Human Microbiome Project have sought to kick-start research on the human microbiome by providing foundational information on microbial composition based upon specific sites across the human body. Here, we focus on the four main anatomical sites of the human microbiome: gut, oral, skin, and vaginal, and provide information on site-specific background, experimental data, and computational modeling. Each of the site-specific microbiomes has unique organisms and phenomena associated with them; there are also high-level commonalities. By providing an overview of different human microbiome sites, we hope to provide a perspective where detailed, site-specific research is needed to understand causal phenomena that impact human health, but there is equally a need for more generalized methodology improvements that would benefit all human microbiome research.

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Searching more genomic sequence with less memory for fast and accurate metagenomic profiling

10.1101/036681 ◽

2016 ◽

Author(s):

Shea N Gardner ◽

Sasha K Ames ◽

Maya B Gokhale ◽

Tom R Slezak ◽

Jonathan Allen

Keyword(s):

Large Scale ◽

Genomic Sequence ◽

Sequence Data ◽

Low Cost ◽

False Negative ◽

Human Microbiome ◽

Human Microbiome Project ◽

Metagenomic Data ◽

Reference Database ◽

Metagenomic Sequence

Software for rapid, accurate, and comprehensive microbial profiling of metagenomic sequence data on a desktop will play an important role in large scale clinical use of metagenomic data. Here we describe LMAT-ML (Livermore Metagenomics Analysis Toolkit-Marker Library) which can be run with 24 GB of DRAM memory, an amount available on many clusters, or with 16 GB DRAM plus a 24 GB low cost commodity flash drive (NVRAM), a cost effective alternative for desktop or laptop users. We compared results from LMAT with five other rapid, low-memory tools for metagenome analysis for 131 Human Microbiome Project samples, and assessed discordant calls with BLAST. All the tools except LMAT-ML reported overly specific or incorrect species and strain resolution of reads that were in fact much more widely conserved across species, genera, and even families. Several of the tools misclassified reads from synthetic or vector sequence as microbial or human reads as viral. We attribute the high numbers of false positive and false negative calls to a limited reference database with inadequate representation of known diversity. Our comparisons with real world samples show that LMAT-ML is the only tool tested that classifies the majority of reads, and does so with high accuracy.

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Bacterial communities associated with cell phones and shoes

PeerJ ◽

10.7717/peerj.9235 ◽

2020 ◽

Vol 8 ◽

pp. e9235

Author(s):

David A. Coil ◽

Russell Y. Neches ◽

Jenna M. Lang ◽

Guillaume Jospin ◽

Wendy E. Brown ◽

...

Keyword(s):

Large Scale ◽

Cell Phones ◽

Human Microbiome ◽

16S Rrna Gene Sequencing ◽

The United States ◽

Oral Microbiome ◽

Rrna Gene ◽

Sporting Events ◽

Rrna Gene Sequencing ◽

Source And Sink

Background Every human being carries with them a collection of microbes, a collection that is likely both unique to that person, but also dynamic as a result of significant flux with the surrounding environment. The interaction of the human microbiome (i.e., the microbes that are found directly in contact with a person in places such as the gut, mouth, and skin) and the microbiome of accessory objects (e.g., shoes, clothing, phones, jewelry) is of potential interest to both epidemiology and the developing field of microbial forensics. Therefore, the microbiome of personal accessories are of interest because they serve as both a microbial source and sink for an individual, they may provide information about the microbial exposure experienced by an individual, and they can be sampled non-invasively. Findings We report here a large-scale study of the microbiome found on cell phones and shoes. Cell phones serve as a potential source and sink for skin and oral microbiome, while shoes can act as sampling devices for microbial environmental experience. Using 16S rRNA gene sequencing, we characterized the microbiome of thousands of paired sets of cell phones and shoes from individuals at sporting events, museums, and other venues around the United States. Conclusions We place this data in the context of previous studies and demonstrate that the microbiome of phones and shoes are different. This difference is driven largely by the presence of “environmental” taxa (taxa from groups that tend to be found in places like soil) on shoes and human-associated taxa (taxa from groups that are abundant in the human microbiome) on phones. This large dataset also contains many novel taxa, highlighting the fact that much of microbial diversity remains uncharacterized, even on commonplace objects.

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Altered Bacterial-Fungal Interkingdom Networks in the Guts of Ankylosing Spondylitis Patients

mSystems ◽

10.1128/msystems.00176-18 ◽

2019 ◽

Vol 4 (2) ◽

Cited By ~ 8

Author(s):

Ming Li ◽

Bingbing Dai ◽

Yawei Tang ◽

Lei Lei ◽

Ningning Li ◽

...

Keyword(s):

Ankylosing Spondylitis ◽

Disease Activity ◽

Large Scale ◽

Activity Index ◽

Disease Activity Index ◽

Rrna Gene ◽

Human Gut ◽

Reactive Protein ◽

Inflammatory Drugs ◽

Bacteria And Fungi

ABSTRACT Intestinal bacterial dysbiosis has been increasingly linked to ankylosing spondylitis (AS), which is a prototypic and best studied subtype of spondyloarthritis (SpA). Fungi and bacteria coexist in the human gut and interact with each other. Although they have been shown to contribute actively to health or disease, no studies have investigated whether the fungal microbiota in AS patients is perturbed. In this study, fecal samples from 22 AS patients, with clinical and radiographic assessments, and 16 healthy controls (HCs) were collected to systematically characterize the gut microbiota and mycobiota in AS patients by 16S rRNA gene- and ITS2-based DNA sequencing. Our results showed that the microbiota of AS patients was characterized by increased abundance of Proteobacteria and decreased Bacteroidetes, which was contributed by enrichment of Escherichia-Shigella, Veillonella, Lachnospiraceae NK4A136 group, and reduction of Prevotella strain 9, Megamona, and Fusobacterium. The gut mycobiota of AS patients was characterized by higher levels of Ascomycota, especially the class of Dothideomycetes, and decreased abundance of Basidiomycota, which was mainly contributed by the decease of Agaricales. Compared to HCs, decreased ITS2/16S biodiversity ratios and altered bacterial-fungal interkingdom networks were observed in AS patients. Compared with nonsteroidal anti-inflammatory drugs (NSAIDs), treating AS patients with biological agents induced obvious changes in the gut mycobiota, and this result was highly associated with disease activity indexes, including AS disease activity index (ASDAS) C-reactive protein (asCRP), erythrocyte sedimentation rate (ESR), and Bath AS disease activity index (BASDAI). In addition, altered mycobiota in AS patients was also found associated with the degree of radiographic damage. IMPORTANCE The human gut is colonized by diverse fungi (mycobiota), and fungi have long been suspected in the pathogenesis of SpA. Our study unraveled a disease-specific interkingdom network alteration in AS, suggesting that fungi, or the interkingdom interactions between bacteria and fungi, may play an essential role in AS development. However, our study is limited by sample size, and in-depth mechanism studies and additional large-scale investigations characterizing the gut mycobiome in AS patients are needed to form a foundation for research into the relationship between mycobiota dysbiosis and AS development.

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Biodiversity, systematics, and new taxa of cladid crinoids from the Ordovician Brechin Lagerstätte

Journal of Paleontology ◽

10.1017/jpa.2019.81 ◽

2019 ◽

Vol 94 (2) ◽

pp. 334-357 ◽

Cited By ~ 2

Author(s):

David F. Wright ◽

Selina R. Cole ◽

William I. Ausich

Keyword(s):

New Species ◽

New Taxa ◽

Large Scale ◽

Unexpected Result ◽

Taxonomic Study ◽

New Genera ◽

Early Paleozoic ◽

Upper Ordovician ◽

Major Lineage ◽

Lake Simcoe

AbstractUpper Ordovician (Katian) strata of the Lake Simcoe region of Ontario record a spectacularly diverse and abundant echinoderm fauna known as the Brechin Lagerstätte. Despite recognition as the most taxonomically diverse Katian crinoid paleocommunity, the Brechin Lagerstätte has received relatively little taxonomic study since Frank Springer published his classic monograph on the “Kirkfield fauna” in 1911.Using a new collection of exceptionally preserved material, we evaluate all dicyclic inadunate crinoids occurring in the Brechin Lagerstätte, which is predominantly comprised of cladids (Eucladida and Flexibilia). We document 15 species across 11 genera, including descriptions of two new genera and four new species. New taxa include Konieckicrinus brechinensis n. gen. n. sp., K. josephi n. gen. n. sp., Simcoecrinus mahalaki n. gen. n. sp., and Dendrocrinus simcoensis n. sp.Although cladids are not commonly considered major components of the Early Paleozoic Crinoid Macroevolutionary Fauna, which is traditionally conceived as dominated by disparids and diplobathrid camerates, they are the most diverse major lineage of crinoids occurring in the Brechin Lagerstätte. This unexpected result highlights the important roles of specimen-based taxonomy and systematic revisions in the study of large-scale diversity patterns.UUID: http://zoobank.org/09dda7c2-f2c5-4411-93be-3587ab1652ab

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Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome

mBio ◽

10.1128/mbio.01343-17 ◽

2017 ◽

Vol 8 (5) ◽

Cited By ~ 89

Author(s):

Tanja V. Maier ◽

Marianna Lucio ◽

Lang Ho Lee ◽

Nathan C. VerBerkmoes ◽

Colin J. Brislawn ◽

...

Keyword(s):

Lipid Metabolism ◽

Gut Microbiome ◽

Resistant Starch ◽

Metabolic Pathways ◽

Bacterial Species ◽

Human Microbiome ◽

Rrna Gene ◽

Gut Microbes ◽

Mechanistic Understanding ◽

The Impact

ABSTRACT Diet can influence the composition of the human microbiome, and yet relatively few dietary ingredients have been systematically investigated with respect to their impact on the functional potential of the microbiome. Dietary resistant starch (RS) has been shown to have health benefits, but we lack a mechanistic understanding of the metabolic processes that occur in the gut during digestion of RS. Here, we collected samples during a dietary crossover study with diets containing large or small amounts of RS. We determined the impact of RS on the gut microbiome and metabolic pathways in the gut, using a combination of “omics” approaches, including 16S rRNA gene sequencing, metaproteomics, and metabolomics. This multiomics approach captured changes in the abundance of specific bacterial species, proteins, and metabolites after a diet high in resistant starch (HRS), providing key insights into the influence of dietary interventions on the gut microbiome. The combined data showed that a high-RS diet caused an increase in the ratio of Firmicutes to Bacteroidetes , including increases in relative abundances of some specific members of the Firmicutes and concurrent increases in enzymatic pathways and metabolites involved in lipid metabolism in the gut. IMPORTANCE This work was undertaken to obtain a mechanistic understanding of the complex interplay between diet and the microorganisms residing in the intestine. Although it is known that gut microbes play a key role in digestion of the food that we consume, the specific contributions of different microorganisms are not well understood. In addition, the metabolic pathways and resultant products of metabolism during digestion are highly complex. To address these knowledge gaps, we used a combination of molecular approaches to determine the identities of the microorganisms in the gut during digestion of dietary starch as well as the metabolic pathways that they carry out. Together, these data provide a more complete picture of the function of the gut microbiome in digestion, including links between an RS diet and lipid metabolism and novel linkages between specific gut microbes and their metabolites and proteins produced in the gut.

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Captivity humanizes the primate microbiome

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1521835113 ◽

2016 ◽

Vol 113 (37) ◽

pp. 10376-10381 ◽

Cited By ~ 168

Author(s):

Jonathan B. Clayton ◽

Pajau Vangay ◽

Hu Huang ◽

Tonya Ward ◽

Benjamin M. Hillmann ◽

...

Keyword(s):

Gut Microbiome ◽

Meta Analysis ◽

Human Microbiome ◽

16S Rrna Gene Sequencing ◽

Modern Human ◽

Primate Species ◽

Rrna Gene ◽

Human Gut ◽

Dietary Analysis ◽

Human Gut Microbiome

The primate gastrointestinal tract is home to trillions of bacteria, whose composition is associated with numerous metabolic, autoimmune, and infectious human diseases. Although there is increasing evidence that modern and Westernized societies are associated with dramatic loss of natural human gut microbiome diversity, the causes and consequences of such loss are challenging to study. Here we use nonhuman primates (NHPs) as a model system for studying the effects of emigration and lifestyle disruption on the human gut microbiome. Using 16S rRNA gene sequencing in two model NHP species, we show that although different primate species have distinctive signature microbiota in the wild, in captivity they lose their native microbes and become colonized with Prevotella and Bacteroides, the dominant genera in the modern human gut microbiome. We confirm that captive individuals from eight other NHP species in a different zoo show the same pattern of convergence, and that semicaptive primates housed in a sanctuary represent an intermediate microbiome state between wild and captive. Using deep shotgun sequencing, chemical dietary analysis, and chloroplast relative abundance, we show that decreasing dietary fiber and plant content are associated with the captive primate microbiome. Finally, in a meta-analysis including published human data, we show that captivity has a parallel effect on the NHP gut microbiome to that of Westernization in humans. These results demonstrate that captivity and lifestyle disruption cause primates to lose native microbiota and converge along an axis toward the modern human microbiome.

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