scholarly journals Genome Sequence of Segmented Filamentous Bacteria Present in the Human Intestine

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.

scholarly journals Genome sequence of segmented filamentous bacteria present in the human intestine

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Hans Jonsson ◽  
Luisa W. Hugerth ◽  
John Sundh ◽  
Eva Lundin ◽  
Anders F. Andersson
Keyword(s):  
Amino Acid Identity ◽  
Phylogenomic Analysis ◽  
Host Immune System ◽  
Filamentous Bacteria ◽  
Segmented Filamentous Bacteria ◽  
Average Amino Acid Identity ◽  
Specific Manner ◽  
Iga Production ◽  
T Cell Maturation ◽  
Human Specific

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.

scholarly journals 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.

2020 ◽  
Vol 70 (4) ◽  
pp. 2873-2878 ◽  
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.

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

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.

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

1999 ◽  
Vol 67 (4) ◽  
pp. 1992-2000 ◽  
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.

Interactions between gut-associated lymphoid tissue and colonization levels of indigenous, segmented, filamentous bacteria in the small intestine of mice

1998 ◽  
Vol 44 (12) ◽  
pp. 1177-1182 ◽  
Author(s):  
J Snel ◽  
C C Hermsen ◽  
H J Smits ◽  
N A Bos ◽  
WMC Eling ◽  
...  
Keyword(s):  
Small Intestine ◽  
Immune System ◽  
Lymphoid Tissue ◽  
Immune Reaction ◽  
Mucosal Immune System ◽  
Filamentous Bacteria ◽  
Segmented Filamentous Bacteria ◽  
Swiss Mice ◽  
Age Dependent ◽  
Old Mice

Unlike most other indigenous bacteria, segmented filamentous bacteria (SFB) are potent activators of the mucosal immune system. SFB are strongly anchored to the epithelial cells of the small intestine where they have a preference for mucosal lymphoid epithelium. Since SFB are only present in high numbers shortly after weaning, it was investigated whether an SFB-induced immune reaction results in the removal of these bacteria from the small intestine. A correlation was found between age and colonization levels in the small intestines of SFB monoassociated Swiss mice. Five-week-old athymic BALB/c (nu/nu) mice showed lower colonization levels than their heterozygous littermates, but the opposite was found at the age of 12 weeks. However, SFB inoculation of germfree Swiss mice resulted in higher colonization levels in 5-week-old mice when compared with 4-month-old mice. We conclude that SFB colonization levels in the small intestine are likely influenced by the activity of the mucosal immune system. However, an additional age-dependent factor that modulates SFB colonization levels cannot be excluded.Key words: segmented filamentous bacteria, small intestine, gut-associated lymphoid tissue.

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

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)

Influence of Diets Containing Native or BoiledPhaseolus vulgarison Segmented Filamentous Bacteria in the Small Intestine of Mice

1991 ◽  
Vol 4 (3) ◽  
Author(s):  
H. L. B. M. Klaasen ◽  
J. P. Koopman ◽  
M. E. Van Den Brink ◽  
P. M. Scholten ◽  
M. H. Bakker ◽  
...  
Keyword(s):  
Small Intestine ◽  
Filamentous Bacteria ◽  
Segmented Filamentous Bacteria

Influence of Macronutrients on Segmented Filamentous Bacteria in the Small Intestine of Mice

1991 ◽  
Vol 4 (1) ◽  
pp. 47-51 ◽  
Author(s):  
H. L. B. M. Klaasen ◽  
J. P. Koopman ◽  
M. E. Van Den Brink ◽  
P. M. Scholten ◽  
A. C. Beynen
Keyword(s):  
Small Intestine ◽  
Filamentous Bacteria ◽  
Segmented Filamentous Bacteria

scholarly journals Differential Roles of Segmented Filamentous Bacteria and Clostridia in Development of the Intestinal Immune System

1999 ◽  
Vol 67 (7) ◽  
pp. 3504-3511 ◽  
Author(s):  
Yoshinori Umesaki ◽  
Hiromi Setoyama ◽  
Satoshi Matsumoto ◽  
Akemi Imaoka ◽  
Kikuji Itoh
Keyword(s):  
Small Intestine ◽  
Immune System ◽  
Large Intestine ◽  
Immunoglobulin A ◽  
Cell Receptor ◽  
Intraepithelial Lymphocytes ◽  
Filamentous Bacteria ◽  
Segmented Filamentous Bacteria ◽  
Intestinal Immune System ◽  
Gnotobiotic Mice

ABSTRACT The presence of microflora in the digestive tract promotes the development of the intestinal immune system. In this study, to evaluate the roles of two types of indigenous microbe, segmented filamentous bacteria (SFB) and clostridia, whose habitats are the small and large intestines, respectively, in this immunological development, we analyzed three kinds of gnotobiotic mice contaminated with SFB, clostridia, and both SFB and clostridia, respectively, in comparison with germfree (GF) or conventionalized (Cvd) mice associated with specific-pathogen-free flora. In the small intestine, the number of αβ T-cell receptor-bearing intraepithelial lymphocytes (αβIEL) increased in SFB-associated mice (SFB-mice) but not in clostridium-associated mice (Clost-mice). There was no great difference in Vβ usage among GF mice, Cvd mice, and these gnotobiotic mice, although the association with SFB decreased the proportion of Vβ6+ cells in CD8β− subsets to some extent, compared to that in GF mice. The expression of major histocompatibility complex class II molecules on the epithelial cells was observed in SFB-mice but not in Clost-mice. On the other hand, in the large intestine, the ratio of the number of CD4−CD8+ cells to that of CD4+ CD8−cells in αβIEL increased in Clost-mice but not in SFB-mice. On association with both SFB and clostridia, the numbers and phenotypes of IEL in the small and large intestines changed to become similar to those in Cvd mice. In particular, the ratio of the number of CD8αβ+ cells to that of CD8αα+ cells in αβIEL, unusually elevated in the small intestines of SFB-mice, decreased to the level in Cvd mice on contamination with both SFB and clostridia. The number of immunoglobulin A (IgA)-producing cells in the lamina propria was more elevated in SFB-mice than in Clost-mice, not only in the ileum but also in the colon. The number of IgA-producing cells in the colons of Clost-mice was a little increased compared to that in GF mice. Taken together, SFB and clostridia promoted the development of both IEL and IgA-producing cells in the small intestine and that of only IEL in the large intestine, respectively, suggesting the occurrence of compartmentalization of the immunological responses to the indigenous bacteria between the small and large intestines.

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