Reclassification of the Clostridium clostridioforme and Clostridium sphenoides clades as Enterocloster gen. nov. and Lacrimispora gen. nov., including reclassification of 15 taxa

Haas, Kelly; Blanchard, Jeffrey L.

doi:10.1099/ijsem.0.003698

Cited by 142 publications

(75 citation statements)

References 78 publications

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“…Phylofactorization of microbiome data from PKU and control samples revealed three factors to be influential at the genus level ( Figure 3): Romboutsia, two unknown Lachnospiraceae genera, and Enterocloster. Currently, the specific roles of Romboutsia and Enterocloster are largely unknown due to recent isolations and classifications; however, further studies of the bacteria may expose the importance of their presence [39,49]. Potentially relevant to PKU is that isolated Romboutsia genera lack a catalytic enzyme for the biosynthesis of phenylalanine and tyrosine [50].…”

Section: Discussionmentioning

confidence: 99%

“…F-statistics identified "bioindicator" clades between conditions ( Figure 3A). Clades of interest for PKU in comparison to control samples included: Romboutsia (green; W = 19, p = 3.049 × 10 −5 ) was lower in PKU samples ( Figure 3B), Lachnospiraceae (purple; W = 47, p = 0.005567) was lower in PKU samples ( Figure 3C), and Enterocloster (formerly classified as Clostridium in EZBioCloud database [39]) (orange; W = 192, p = 0.001691) was higher in PKU samples compared to control samples ( Figure 3D). Enterocloster (formerly classified as Clostridium in EZBioCloud database [39]) (orange; W = 192, p = 0.001691) was higher in PKU samples compared to control samples (Figure 3d).…”

Section: Gut Microbial Composition Of Pku Patients Diverges From Contmentioning

confidence: 99%

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The Adult Phenylketonuria (PKU) Gut Microbiome

et al. 2021

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Phenylketonuria (PKU) is an inborn error of phenylalanine metabolism primarily treated through a phenylalanine-restrictive diet that is frequently supplemented with an amino acid formula to maintain proper nutrition. Little is known of the effects of these dietary interventions on the gut microbiome of PKU patients, particularly in adults. In this study, we sequenced the V4 region of the 16S rRNA gene from stool samples collected from adults with PKU (n = 11) and non-PKU controls (n = 21). Gut bacterial communities were characterized through measurements of diversity and taxa abundance. Additionally, metabolic imputation was performed based on detected bacteria. Gut community diversity was lower in PKU individuals, though this effect was only statistically suggestive. A total of 65 genera across 5 phyla were statistically differentially abundant between PKU and control samples (p < 0.001). Additionally, we identified six metabolic pathways that differed between groups (p < 0.05), with four enriched in PKU samples and two in controls. While the child PKU gut microbiome has been previously investigated, this is the first study to explore the gut microbiome of adult PKU patients. We find that microbial diversity in PKU children differs from PKU adults and highlights the need for further studies to understand the effects of dietary restrictions.

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Section: Discussionmentioning

confidence: 99%

Section: Gut Microbial Composition Of Pku Patients Diverges From Contmentioning

confidence: 99%

The Adult Phenylketonuria (PKU) Gut Microbiome

et al. 2021

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“…At the bottom of each Genome page, the classification of the genome is provided for each GTDB release (Figure 2D ). For example, GCF_002234575.2 was reclassified from Clostridium_M bolteae to E. bolteae in GTDB R95 in accordance with a new taxonomic opinion ( 17 ). Changes in GTDB classifications and their relationship to the NCBI taxonomy can also be explored at the taxon level using the GTDB Taxon History tool (Figure 2E ).…”

Section: Resource Contentmentioning

confidence: 99%

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

Parks

Chuvochina

Rinke

et al. 2021

Nucleic Acids Research

984

832

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The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy for prokaryotic genomes sourced from the NCBI Assembly database. GTDB R06-RS202 spans 254 090 bacterial and 4316 archaeal genomes, a 270% increase since the introduction of the GTDB in November, 2017. These genomes are organized into 45 555 bacterial and 2339 archaeal species clusters which is a 200% increase since the integration of species clusters into the GTDB in June, 2019. Here, we explore prokaryotic diversity from the perspective of the GTDB and highlight the importance of metagenome-assembled genomes in expanding available genomic representation. We also discuss improvements to the GTDB website which allow tracking of taxonomic changes, easy assessment of genome assembly quality, and identification of genomes assembled from type material or used as species representatives. Methodological updates and policy changes made since the inception of the GTDB are then described along with the procedure used to update species clusters in the GTDB. We conclude with a discussion on the use of average nucleotide identities as a pragmatic approach for delineating prokaryotic species.

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“…For instance, the family Lachnospiraceae contains diverse intestinal bacteria belonging to the Clostridium cluster XIVa (or Clostridium coccoides ), such as Acetitomaculum , Butyrivibrio , Catonella , Coprococcus , Dorea , Lachnobacterium , Lachnospira and Roseburia [12]. Recently, to place them in the order of the clostridial taxonomy, 15 taxa related to the Clostridium clostridioforme and Clostridium sphenoides clades within the family Lachnospiraceae were validly reclassified as Enterocloster gen. nov. and Lacrimispora gen. nov., respectively [9]. In this study, we isolated strain SNUG30386 T , which belongs to the family Lachnospiraceae , and described its distinct phylogenetic relationships as well as phenotypic biochemical activities.…”

Section: Full-textmentioning

confidence: 99%

“…The establishment of culturomics is one of the efforts to overcome the limitations of traditional culture techniques [6, 7]. At the same time, collective efforts to reclassify Clostridium species are in progress to reflect their exclusive characteristics [8, 9]. In contrast to the simple rules in the past that the genus Clostridium within the family Clostridiaceae shows Gram-positive, spore-forming characteristics, gut microbiome research has supported the heterogeneous properties of the Clostridium , which includes influential gut commensals within other families [10, 11].…”

Section: Full-textmentioning

confidence: 99%

Clostridium fessum sp. nov., isolated from human faeces

Seo

Jeon

Baek

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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An obligately anaerobic, Gram-stain-positive and spore-forming strain, SNUG30386T was isolated from a faecal sample of a healthy Korean subject. The strain formed a round ivory-coloured colony and cells were chained rods with tapered ends, approximately 2.0–2.5×0.6–0.8 μm in size. The taxonomic analysis indicated that strain SNUG30386T was within the family Lachnospiraceae . According to the 16S rRNA gene sequence similarity, the closest species to strain SNUG30386T was Clostridium symbiosum (95.6 %), followed by Enterocloster asparagiformis (94.8 %), Enterocloster clostridioformis (94.8 %) and Enterocloster lavalensis (94.6 %). The evolutionary tree based on 16S rRNA gene sequences demonstrated that strain SNUG30386T had split apart at a unique branch point far from other close relatives. Its DNA G+C content was 48.3 mol% calculated from the whole genome sequence. The major cellular fatty acids were C16 : 0 and C14 : 0. Compared to those of the closely related species, strain SNUG30386T showed distinct biochemical activities such as being unable to utilize most of carbon sources except d-glucose and l-arabinose. As a result, based on its unique phylogenetic clade and taxonomic characteristics, we conclude that strain SNUG30386T represents a novel species within the genus Clostridium , for which the name Clostridium fessum sp. nov. is proposed. The type strain of the novel species is SNUG30386T (=KCTC 15633T= JCM 32258T).

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Reclassification of the Clostridium clostridioforme and Clostridium sphenoides clades as Enterocloster gen. nov. and Lacrimispora gen. nov., including reclassification of 15 taxa

Cited by 142 publications

References 78 publications

The Adult Phenylketonuria (PKU) Gut Microbiome

The Adult Phenylketonuria (PKU) Gut Microbiome

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

Clostridium fessum sp. nov., isolated from human faeces

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