Genome sequence of segmented filamentous bacteria present in the human intestine

AbstractSegmented filamentous bacteria (SFB) are unique immune modulatory bacteria colonizing the small intestine of a variety of animals in a host-specific manner. SFB exhibit filamentous growth and attach to the host’s intestinal epithelium, offering a physical route of interaction. SFB affect functions of the host immune system, among them IgA production and T-cell maturation. Until now, no human-specific SFB genome has been reported. Here, we report the metagenomic reconstruction of an SFB genome from a human ileostomy sample. Phylogenomic analysis clusters the genome with SFB genomes from mouse, rat and turkey, but the genome is genetically distinct, displaying 65–71% average amino acid identity to the others. By screening human faecal metagenomic datasets, we identified individuals carrying sequences identical to the new SFB genome. We thus conclude that a unique SFB variant exists in humans and foresee a renewed interest in the elucidation of SFB functionality in this environment.

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Genome Sequence of Segmented Filamentous Bacteria Present in the Human Intestine

10.1101/813196 ◽

2019 ◽

Author(s):

Hans Jonsson ◽

Luisa W. Hugerth ◽

John Sundh ◽

Anders F. Andersson

Keyword(s):

Small Intestine ◽

Amino Acid Identity ◽

Phylogenomic Analysis ◽

Filamentous Bacteria ◽

Segmented Filamentous Bacteria ◽

Average Amino Acid Identity ◽

Specific Manner ◽

Iga Production ◽

T Cell Maturation ◽

Human Specific

SummarySegmented filamentous bacteria (SFB) colonize the small intestine of a variety of animals in a host-specific manner. SFB are physically attached to the host’s intestinal epithelium and affect several functions related to the immune system, among them IgA production and T-cell maturation. Until now, no human-specific SFB genome had been described. Here, we report the metagenomic reconstruction of an SFB genome from a human ileostomy sample. Phylogenomic analysis clusters the genome with the SFB genomes from mouse, rat and turkey, but the genome is genetically distinct, displaying 65-71% average amino acid identity to the other genomes, and is tentatively unique for the human small intestine. By screening human faecal metagenomic datasets, we identified individuals carrying sequences identical to the new SFB-genome. We thus conclude that a unique SFB variant exists in humans and we foresee a renewed interest in the elucidation of SFB functionality in this environment.

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Spiribacter aquaticus Leon et al. 2017 is a later heterotypic synonym of Spiribacter roseus Leon et al. 2016. Reclassification of Halopeptonella vilamensis Menes et al. 2016 as Spiribacter vilamensis comb. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004113 ◽

2020 ◽

Vol 70 (4) ◽

pp. 2873-2878 ◽

Cited By ~ 9

Author(s):

María José León ◽

Cristina Galisteo ◽

Antonio Ventosa ◽

Cristina Sánchez-Porro

Keyword(s):

Type Species ◽

Single Species ◽

Amino Acid Identity ◽

The Other ◽

Phylogenomic Analysis ◽

Content Type ◽

Link Type ◽

Average Amino Acid Identity ◽

Single Genus ◽

Type Strains

A comparative taxonomic study of Spiribacter and Halopeptonella species was carried out using a phylogenomic approach based on comparison of the core genome, orthologous average nucleotide identity (OrthoANIu), Genome-to-Genome Distance Calculator (GGDC) and average amino acid identity (AAI). Phylogenomic analysis based on 976 core translated gene sequences obtained from their genomes showed that Spiribacter aquaticus SP30T, S. curvatus UAH-SP71T, S. roseus SSL50T, S. salinus M19-40T and Halopeptonella vilamensis DSM 21056T formed a robust cluster, clearly separated from the remaining species of closely related taxa. AAI between H. vilamensis DSM 21056T and the species of the genus Spiribacter was ≥73.1 %, confirming that all these species belong to the same single genus. On the other hand, S. roseus SSL50T and S. aquaticus SP30T showed percentages of OrthoANIu and digital DNA–DNA hybridization of 98.4 % and 85.3 %, respectively, while these values among those strains and the type strains of the other species of Spiribacter and H. vilamensis DSM 21056T were ≤80.8 and 67.8 %, respectively. Overall, these data show that S. roseus SSL50T and S. aquaticus SP30T constitute a single species and thus that S. aquaticus SP30T should be considered as a later, heterotypic synonym of S. roseus SSL50T based on the rules for priority of names. We propose an emended description of S. roseus , including the features of S. aquaticus . We also propose the reclassification of H. vilamensis as Spiribacter vilamensis comb. nov.

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Genome-Based Taxonomic Rearrangement of the Order Geobacterales Including the Description of Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov.

Frontiers in Microbiology ◽

10.3389/fmicb.2021.737531 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zhenxing Xu ◽

Yoko Masuda ◽

Xueding Wang ◽

Natsumi Ushijima ◽

Yutaka Shiratori ◽

...

Keyword(s):

Taxonomic Status ◽

Terrestrial Ecosystems ◽

Single Copy ◽

Amino Acid Identity ◽

Taxonomic Structure ◽

Phylogenomic Analysis ◽

Genome Sequences ◽

Average Amino Acid Identity ◽

The Family ◽

Genomic Similarity

Geobacterales is a recently proposed order comprising members who originally belonged to the well-known family Geobacteraceae, which is a key group in terrestrial ecosystems involved in biogeochemical cycles and has been widely investigated in bioelectrochemistry and bioenergy fields. Previous studies have illustrated the taxonomic structure of most members in this group based on genomic phylogeny; however, several members are still in a pendent or chaotic taxonomic status owing to the lack of genome sequences. To address this issue, we performed this taxonomic reassignment using currently available genome sequences, along with the description of two novel paddy soil-isolated strains, designated Red51T and Red69T, which are phylogenetically located within this order. Phylogenomic analysis based on 120 ubiquitous single-copy proteins robustly separated the species Geobacter luticola from other known genera and placed the genus Oryzomonas (fam. Geobacteraceae) into the family ‘Pseudopelobacteraceae’; thus, a novel genus Geomobilimonas is proposed, and the family ‘Pseudopelobacteraceae’ was emended. Moreover, genomic comparisons with similarity indexes, including average amino acid identity (AAI), percentage of conserved protein (POCP), and average nucleotide identity (ANI), showed proper thresholds as genera boundaries in this order with values of 70%, 65%, and 74% for AAI, POCP, and ANI, respectively. Based on this, the three species Geobacter argillaceus, Geobacter pelophilus, and Geobacter chapellei should be three novel genera, for which the names Geomobilibacter, Geoanaerobacter, and Pelotalea are proposed, respectively. In addition, the two novel isolated strains phylogenetically belonged to the genus Geomonas, family Geobacteraceae, and shared genomic similarity values higher than those of genera boundaries, but lower than those of species boundaries with each other and their neighbors. Taken together with phenotypic and chemotaxonomic characteristics similar to other Geomonas species, these two strains, Red51T and Red69T, represent two novel species in the genus Geomonas, for which the names Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov. are proposed, respectively.

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Segmented Filamentous Bacteria Are Potent Stimuli of a Physiologically Normal State of the Murine Gut Mucosal Immune System

Infection and Immunity ◽

10.1128/iai.67.4.1992-2000.1999 ◽

1999 ◽

Vol 67 (4) ◽

pp. 1992-2000 ◽

Cited By ~ 241

Author(s):

Gwen L. Talham ◽

Han-Qing Jiang ◽

Nicolaas A. Bos ◽

John J. Cebra

Keyword(s):

T Cells ◽

Immune System ◽

Immunoglobulin A ◽

Mucosal Immune System ◽

Filamentous Bacteria ◽

Mesenteric Lymph Nodes ◽

Segmented Filamentous Bacteria ◽

Iga Antibody ◽

Autochthonous Bacteria ◽

Iga Production

ABSTRACT Segmented filamentous bacteria (SFB) are autochthonous bacteria inhabiting the intestinal tracts of many species, including humans. We studied the effect of SFB on the mucosal immune system by monoassociating formerly germfree C3H/HeN mice with SFB. At various time points during 190 days of colonization, fragment cultures of small intestine and Peyer’s patches (PP) were analyzed for total immunoglobulin A (IgA) and SFB-specific IgA production. Also, phenotypic changes indicating germinal center reactions (GCRs) and the activation of CD4+ T cells in PP were determined by using fluorescence-activated cell sorter analyses. A second group of SFB-monoassociated mice was colonized with a gram-negative commensal,Morganella morganii, to determine if the mucosal immune system was again stimulated and to evaluate the effect of prior colonization with SFB on the ability of M. morganii to translocate to the spleen and mesenteric lymph nodes. We found that SFB stimulated GCRs in PP from day 6 after monoassociation, that GCRs only gradually waned over the entire length of colonization, that natural IgA production was increased to levels 24 to 63% of that of conventionally reared mice, and that SFB-specific IgA was produced but accounted for less than 1.4% of total IgA. Also, the proportion of CD4+, CD45RBlow T cells, indicative of activated cells, gradually increased in the PP to the level found in conventionally reared mice. Secondary colonization with M. morganii was able to stimulate GCRs anew, leading to a specific IgA antibody response. Previous stimulation of mucosal immunity by SFB did not prevent the translocation of M. morganii in the double-colonized mice. Our findings generally indicate that SFB are one of the single most potent microbial stimuli of the gut mucosal immune system.

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Description of Acinetobacter kanungonis sp. nov., based on phylogenomic analysis

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004833 ◽

2021 ◽

Vol 71 (6) ◽

Author(s):

Lipika Das ◽

Sushanta Deb ◽

Subrata K. Das

Keyword(s):

Sequence Similarity ◽

Amino Acid Identity ◽

Phylogenomic Analysis ◽

Rrna Gene ◽

Content Type ◽

Link Type ◽

Average Amino Acid Identity ◽

Cellular Components ◽

Reference Strains ◽

Type Strains

A novel strain of a member of the genus Acinetobacter, strain PS-1T, was isolated from the skin of fresh water pufferfish (Tetraodon cutcutia) collected from Mahanadi River, India. Cells were Gram-stain-negative, aerobic, coccoid and non-motile. The predominant polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE) and phospholipid (PL) and the cell wall sugars were glucose, galactose and ribose. The major cellular fatty acids of PS-1T were C18 : 1ω9c (30.67 %), C16 : 1ω7c (19.54 %), C16 : 0 (15.87 %), C12 : 0 (7.35 %) and C12 : 0 3-OH (6.77 %). The genome size was 3.5 Mbp and the DNA G+C content was 41.97 %. Gene ontology study revealed that the major fraction of genes were associated with biological processes (53.99 %) followed by molecular function (30.42 %) and cellular components (15.58 %). Comparisons of 16S rRNA gene sequences revealed 97.94–97.05 % sequence similarity with the closely related type strains of species of the genus Acinetobacter . The average nucleotide identity (ANI) and average amino acid identity (AAI) of PS-1T with reference strains of species of the genus Acinetobacter with validly published names were bellow 95–96 and the corresponding in-silico DNA–DNA hybridization (DDH) values were below 70 %. A phylogenomic tree based on core genome analysis supported these results. Genotypic and phenotypic characteristics of PS-1T indicate that the strain represents a novel species of the genus Acinetobacter and the name Acinetobacter kanungonis sp. nov. is proposed. The type strain is PS-1T (=JCM 34131T=NCIMB 15260T)

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Phylogenomic analysis of the genus Pseudomonas and reclassification of P. humi, P. zeshuii, P. psychrotolerans, P. nitritireducens, P. pharmacofabricae and P. panacis are later heterotypic synonym of P. citronellolis Lang 2007, P. luteola, P. oryzihabitans, P. nitroreducens Lang 2007, P. fluvialis and P. marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980), respectively

10.1101/2021.05.19.444773 ◽

2021 ◽

Author(s):

Ritu Rani Kujur ◽

Sushanta Deb ◽

Subrata K Das

Keyword(s):

Dna Hybridization ◽

Type Species ◽

Genomic Analysis ◽

Amino Acid Identity ◽

Comparative Genomic ◽

Phylogenomic Analysis ◽

Taxonomic Assignment ◽

Genome Database ◽

Average Amino Acid Identity ◽

Genome Comparisons

The present study described the comparative genomic analysis of the validly named species of the genus Pseudomonas to define the taxonomic assignment. Genomic information for 208 type strains was available in the NCBI genome database at the time of conducting this analysis. The ANI, AAI and in silico DNA DNA hybridization (isDDH) data were higher than the threshold values for the twelve strains with their closely related type species. Whole genome comparisons shared 97 - 99 % average nucleotide identity, 97.85 to 99.19 % average amino acid identity and 72.80 to 90.40 % digital DNA DNA hybridization values. Further, the phylogenomic analysis based on the core genome confirmed that P. humi CCA1 and P. citronellolis LMG 18378, P. zeshuii KACC 15471 and P. luteola NBRC 103146, P. oryzihabitans DSM 6835 and P. psychrotolerans DSM 15758, P. nitroreducens DSM 14399 and P. nitritireducens WZBFD3-5A2, P. fluvialis CCM 8778 and P. pharmacofabricae ZYSR67-Z, P. panacis DSM 18529 and P. marginalis DSM 13124 formed a monophyletic clade. Thus, we proposed six type species viz., P. humi CCA1, P. zeshuii KACC 15471, P. psychrotolerans DSM 15758, P. nitritireducens WZBFD3 5A2, P. pharmacofabricae ZYSR67 Z and P. panacis DSM 18529 are the later heterotypic synonym of P. citronellolis Lang 2007, P. luteola, P. oryzihabitans, P. nitroreducens Lang 2007, P. fluvialis and P. marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980), respectively considering the priority date of publication.

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Genome-based reclassification of Amycolatopsis eurytherma as a later heterotypic synonym of Amycolatopsis thermoflava

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004642 ◽

2021 ◽

Author(s):

Priya Singh ◽

Princy Hira ◽

Charu Dogra Rawat ◽

Rup Lal ◽

Utkarsh Sood

Keyword(s):

Type Species ◽

Sequence Similarity ◽

Bacterial Species ◽

Amino Acid Identity ◽

Phylogenomic Analysis ◽

Rrna Gene ◽

Taxonomic Assignment ◽

Content Type ◽

Link Type ◽

Average Amino Acid Identity

The present study was carried out to clarify the taxonomic assignment of two closely related Amycolatopsis species. Genomic information for 48 type strains was available at the time of conducting this analysis. Our analysis showed that two species, viz. Amycolatopsis eurytherma Kim et al. 2002 and Amycolatopsis thermoflava Chun et al. 1999, are conspecific. The 16S rRNA gene sequences of the two species possess 98.85 % sequence similarity. Further, whole-genome comparisons showed that A. eurytherma DSM 44348T and A. thermoflava N1165T shared 98.75 % average nucleotide identity, 98.63 % average amino acid identity and 87.8 % digital DNA–DNA hybridization values. These values exceed the threshold values for bacterial species delineation, indicating that they belong to the same species. Further, the phylogenomic analysis based on the core genome of the strains under study confirmed that A. eurytherma DSM 44348T and A. thermoflava N1165T formed a monophyletic clade. Based on this evidence we propose the reclassification of Amycolatopsis eurytherma Kim et al. 2002 as a later heterotypic synonym of Amycolatopsis thermoflava Chun et al. 1999.

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