Diversity of the Class Coriobacteriia Within Different Ecosystems Lesley Hoyles
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Diversity of the class Coriobacteriia within different ecosystems Lesley Hoyles Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, United Kingdom Within the human gut microbiota, the phylum Actinobacteria is represented The Integrated Microbial NGS (IMNGS) platform [12] systematically screens for, by obligate anaerobes belonging to the genus Bifidobacterium and the retrieves, processes and analyses all available prokaryotic 16S rRNA gene class Coriobacteriia. While bifidobacteria have been studied extensively, amplicon datasets and uses them to build sample-specific sequence databases the coriobacteria have received little attention, despite being more and OTU-based profiles. Its first release (June 2016) contained information for abundant than bifidobacteria in the faeces of healthy adults [1]. Collinsella 85,121 samples. Of these, 39,216 contained sequences annotated as belonging aerofaciens is a core member of the human gut microbiota, found in ~90 % to the class Coriobacteriia. 16S rRNA gene V region(s) covered by sequences in IMNGS are not recorded. To allow comparative analyses, V regions of 16S of people [2]. Eggerthella lenta is involved in drug and bile acid metabolism rRNA gene sequences of the Coriobacteriia type strains (Figure 1) were used (10 % of people) [3,4]. In between 30 and 60 % of people, equol (a as BLASTN databases for searches with the Coriobacteriia-positive IMNGS bioactive isoflavone) is produced by one or more Asaccharobacter, samples (Figure 3). In addition, the potential of the different 16S rRNA gene V Paraeggerthella and Slackia spp.; in mice, equol is produced by regions to discriminate members of the Coriobacteriia at different BLASTN Enterorhabdus spp. [5–8]. Gordonibacter and Ellagibacter spp. produce thresholds was determined (Figure 4). urolithin, which has anti-inflammatory activity in vivo [9]. In recent years, 33 novel species and 12 new genera within the class Coriobacteriia have been Figure 3. Breakdown of Coriobacteriia-positive IMNGS samples described (Figure 1). Most of these species have been recovered from based on V region(s) covered in each 16S rRNA gene amplicon sample. 38,874/39,216 of the Coriobacteriia-positive samples human intestinal samples. However, the prevalence of these bacteria in returned BLASTN hits (90 % sequence similarity threshold). mammalian (and environmental) samples is unknown. 17,238/38,874 of samples covered only the V4 region. Samples covering regions V1–V3 (5,400), V2 only (3,996) and V1–V2 (3,383) were also well represented in the dataset. Figure 1. Species of the Figure 4. Variable regions within complete 16S rRNA class Coriobacteriia gene sequences of the Coriobacteriia, based on a 20-bp belong to one of three sliding window. Hypervariable regions of the 16S rRNA families (Atopobiaceae, gene sequences of the Coriobacteriia were defined Coriobacteriaceae, using their flanking conserved sequences [13]. Only the Eggerthellaceae). V4 region and combined V1–V3 regions of the 16S *Type strains of species rRNA gene allow family (F) and genus (G) discrimination isolated from human of taxa within the Coriobacteriia at ≥ 92 % and ≥99 % or intestinal, faecal and ≥97 % sequence similarity, respectively. vaginal samples as a result of ‘culturomics’ studies (e.g. [11]). *Type strains of species Analyses of IMNGS samples covering the 16S rRNA gene V1–V3 and V4 isolated from faeces and regions showed the human gut microbiota to be predominated by taxa of the described outside the work of [11] and family Coriobacteriaceae, while the mouse gut is predominated by taxa of the colleagues. family Eggerthellaceae (and unknown Atopobiaceae, V4 region only) (Figure 5). Given the metabolic differences among the families of the Coriobacteriia, the human and mouse gut microbiotas will make very different contributions to mammalian microbiomes and host–microbiome co-metabolism. It is important to understand the diversity of Coriobacteriia in mammalian microbiotas as the three families currently recognized within the class have different metabolic capabilities (Figure 2). Figure 2. Metabolism of members of the class Coriobacteriia. Taxa of the families Atopobiaceae and Coriobacteriaceae are Figure 5. Summary of saccharolytic, while those IMNGS data based on belonging to family original and updated Eggerthellaceae are taxonomic information. asaccharolytic. proteomes from publicly available whole-genome sequence data were used to generate KEGG functional information for the Coriobacteriia using the online version of eggNOG-mapper v4.5.1. The data were visualized using the online tool FuncTree2. ACKNOWLEDGEMENTS REFERENCES This work used the computing resources of the UK MEDical [1] Thorasin et al. (2015). Microbiology 161, 565–579. [10] Beltrán et al. (2018). Int J Syst Evol Microbiol 68, 1707–1712. 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