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.

Insights on the Evolutionary Genomics of the Blautia Genus: Potential New Species and Genetic Content Among Lineages

“…Considering the aforementioned criterion, we found a set of 33 genomic species clusters from the Blautia dataset ( Table 1 and Supplementary Table 4 ); twelve of those genomic species groups include one sequenced type strain: B. argi , B. brookingsii , B. faecicola , B. hansenii , B. hominis , B. hydrogenotrophica , B. luti , B. massiliensis , B. obeum , B. faecis , B. caecimuris and B. wexlerae . Additionally, we could find that four previously proposed new members can be considered as new genomic species ( Liu et al, 2020 ): “ Blautia segnis ,” “ Blautia difficilis ,” “ Blautia intestinalis ” and “ Blautia celeris. ” These sequenced reference strains (from both official or proposed species) were useful to give a name to each group they represented ( Table 1 ).…”

“…Considering the aforementioned criterion, we found a set of 33 genomic species clusters from the Blautia dataset (Table 1 and Supplementary (Liu et al, 2020): "Blautia segnis, " "Blautia difficilis, " "Blautia intestinalis" and "Blautia celeris." These sequenced reference strains (from both official or proposed species) were useful to give a name to each group they represented (Table 1).…”

“…At this date, there are 17 officially accepted Blautia species, in addition to other 9 proposed so far, isolated from the GI tract from human and other mammals, including ruminants ( Supplementary Table 1 ): B. coccoides , B. hansenii , B. hydrogenotrophica , B. luti , B. producta , B. schinkii , B. wexlerae , B. glucerasei , B. stercoris , B. faecis , B. obeum , B. caecimuris , B. massiliensis , B. hominis , B. argi , B. brookingsii , and B. faecicola ( Liu et al, 2008 ; Furuya et al, 2010 ; Park et al, 2012 , 2013 ; Lawson and Finegold, 2015 ; Lagkouvardos et al, 2016 ; Durand et al, 2017 ; Shin et al, 2018 ; Paek et al, 2019 ; Ghimire et al, 2020 ; Kim et al, 2020 ). In addition, there are nine proposed species “ Blautia marasmi ,” “ B. phocaeensis ,” “ B. provencensis ,” “ B. intestinalis ,” “ B. segnis ,” “ B. tardus ,” “ B. celeris ,” “ B. lentus ” and “ B. difficilis ” ( Pham et al, 2017a , b ; Traore et al, 2017 ; Liu et al, 2020 ). Currently, there are 225 non-redundant genomes available in RefSeq associated with Blautia , mostly obtained from isolates found in human samples ( Supplementary Table 2 ); this dataset offers the opportunity to search for new previously undescribed species in this genus.…”

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“…As a final addendum, it was observed that the assembly of Blautia sp. M16 (GCF_014287855.1, See Supplementary Table 2), proposed in a preprint as another representative of a new species ("Blautia lentus") (Liu et al, 2020), was not included in the final list. A posterior BLAST-based analysis with the predicted proteome of M16 strain showed that 86% of the best hits for each protein was found from a member of the Clostridiaceae family, despite the fact that one of the copies of the 16S rRNA gene have a closer relationship with members of Blautia (data not shown).…”

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“…At this date, there are 17 officially accepted Blautia species, in addition to other 9 proposed so far, isolated from the GI tract from human and other mammals, including ruminants (Supplementary Table 1) (Liu et al, 2008;Furuya et al, 2010;Park et al, 2012Park et al, , 2013Lawson and Finegold, 2015;Lagkouvardos et al, 2016;Durand et al, 2017;Shin et al, 2018;Paek et al, 2019;Ghimire et al, 2020;Kim et al, 2020). In addition, there are nine proposed species "Blautia marasmi," "B. phocaeensis, " "B. provencensis, " "B. intestinalis, " "B. segnis, " "B. tardus, " "B. celeris, " "B. lentus" and "B. difficilis" (Pham et al, 2017a,b;Traore et al, 2017;Liu et al, 2020). Currently, there are 225 non-redundant genomes available in RefSeq associated with Blautia, mostly obtained from isolates found in human samples (Supplementary Table 2); this dataset offers the opportunity to search for new previously undescribed species in this genus.…”