Noncontiguous finished genome sequence and description of Streptococcus timonensis sp. nov. isolated from the human stomach

Ricaboni, Davide; Mailhe, Morgane; Lagier, Jean-Christophe; Michelle, Caroline; Armstrong, Nicholas; Bittar, Fadi; Vitton, Véronique; Benezech, Alban; Raoult, Didier; Million, Matthieu

doi:10.1016/j.nmni.2016.11.013

Cited by 7 publications

(9 citation statements)

References 36 publications

(44 reference statements)

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“…2a ), whereas 23 (6%) species were bacteria already described in human other site but not in the gut and were isolated for the first time in the human gut in this study, 4 (1%) were known species from the environment but were isolated for the first time in humans, and 37 (10%) were new bacterial species isolated for the first time (Additional file 5 : Table S4) of which we identified 17 new genera. All these new prokaryote species have undergone whole genome sequencing and described using the taxonogenomic approach [ 19 – 21 ]. They have been deposited in a strain collection: the Collection de Souches de l’Unité des Rickettsies (CSUR).…”

Section: Resultsmentioning

confidence: 99%

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RETRACTED ARTICLE: Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing

et al. 2018

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BackgroundMost studies on the human microbiota have analyzed stool samples, although a large proportion of the absorption of nutrients takes place in upper gut tract. We collected samples from different locations along the entire gastrointestinal tract from six patients who had simultaneously undergone upper endoscopy and colonoscopy, to perform a comprehensive analysis using culturomics with matrix assisted laser desorption ionisation - time of flight (MALDI-TOF) identification and by metagenomics targeting the 16S ribosomal ribonucleic acid (rRNA) gene.ResultsUsing culturomics, we isolated 368 different bacterial species, including 37 new species. Fewer species were isolated in the upper gut: 110 in the stomach and 106 in the duodenum, while 235 were isolated from the left colon (p < 0.02). We isolated fewer aero-intolerant species in the upper gut: 37 from the stomach and 150 from the left colon (p < 0.004). Using metagenomics, 1,021 species were identified. The upper gut microbiota was revealed to be less rich than the lower gut microbiota, with 37,622 reads from the stomach, 28,390 from the duodenum, and 79,047 from the left colon (p < 0.009). There were fewer reads for aero-intolerant species in the upper gut (8,656 in the stomach, 5,188 in the duodenum and 72,262 in the left colon, p < 0.02).Patients taking proton pump inhibitors (PPI) were then revealed to have a higher stomach pH and a greater diversity of species in the upper digestive tract than patients not receiving treatment (p < 0.001).ConclusionSignificant modifications in bacterial composition and diversity exist throughout the gastrointestinal tract. We suggest that the upper gut may be key to understanding the relationship between the gut microbiota and health.Electronic supplementary materialThe online version of this article (10.1186/s12866-018-1304-7) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

“…Consequently, this work again contributes towards shedding light on part of bacterial dark matter [ 12 , 25 ]. All of them will be comprehensively described using taxonogenomics [ 19 – 21 ].…”

Section: Discussionmentioning

confidence: 99%

RETRACTED ARTICLE: Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing

et al. 2018

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“…These similarities are in line with another newly identified Streptococcus strain exhibiting 98.7 and 92.6% similarities of 16S rRNA and rpoB gene sequences between the Streptococcus timonensis sp. nov. and the Streptococcus infantis strain JCM 10157 T ( Ricaboni et al, 2017 ). There were also essential differences of G + C contents and genome sequence lengths between Streptococcus strain E24 and eight other streptococci, but also within the 8 streptococci species, which has been described also for other Streptococcus strains ( Thompson et al, 2013 ) and attributed to frequent occurrence of horizontal gene transfers ( Bellanger et al, 2009 ; Harvey et al, 2011 ; Zhang et al, 2011 ).…”

Section: Discussionmentioning

confidence: 99%

“…In recent decades, due to improved phenotypic and molecular identification methods and with the development of the new taxonogenomics concept ( Fournier et al, 2015 ), the genus Streptococcus has been significantly expanded with the addition of many newly discovered species ( Huch et al, 2013 ; Ricaboni et al, 2017 ); more than 110 species are now recognized within the genus Streptococcus 1 . With 16S rRNA gene sequence analyses revealed that Streptococcus species were clustered into six groups comprising S. anginosus , S. mitis , S. mutans , S. bovis , S. pyogenes , and S. salivarius ( Kawamura et al, 1995 ).…”

Section: Introductionmentioning

confidence: 99%

Streptococcus xiaochunlingii sp. nov. E24 Isolated From the Oropharynx of Healthy Chinese Children

Zou

Sun

et al. 2020

Front. Microbiol.

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A Gram-positive, α-hemolytic, catalase-negative, facultative anaerobic and non-motile coccus was isolated form throat swabs taken from the oropharynx of healthy children. The genome was shown to be 1.950,659 bp long and contained 42.03 mol% G + C bases with 1,942 protein-coding and 53 RNA coding genes. The results of 16S rRNA gene sequencing strongly suggested that the strain is a member of the Streptococcus genus, with 98.04, 98.11, and 97.34% similarities to Streptococcus australis ATCC 700641 T , Streptococcus rubneri LMG 27207 T and Streptococcus parasanguinis ATCC 15912 T , respectively. A sodA gene comparison exhibited a sequence identity of 92.6% with the closest strain Streptococcus australis ATCC 700641 T . In silico DNA-DNA hybridization showed a highest DNA similarity value of 52% with Streptococcus australis ATCC 700641 T . Comparing 18 biochemical traits, the similarities of the Streptococcus strain E24 were 72% with Streptococcus rubneri LMG 27207 T , 78% with Streptococcus australis ATCC 700641 T and 44% with Streptococcus parasanguinis ATCC 15912 T . We suggest that based on the genotypic and phenotypic results that the strain E24 is a novel species of the Streptococcus genus and propose the name Streptococcus xiaochunlingii sp. nov. E24.

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“…Recently, a strain of a Gram‐positive, facultative anaerobic and nonmotile coccus isolated from gastric lavage of a patient was sequenced. Based on phenotypic and genomic analysis, the validation of Streptococcus timonensis as a new member of the Streptococcus genus has been proposed . Actual isolation of microbial members of the human gastric microbiota enables in vitro and in vivo studies to be carried out to extend our knowledge of the gastric microbiota.…”

Section: Gastric and Gut Microbiotamentioning

confidence: 99%

Other Helicobacters, gastric and gut microbiota

et al. 2017

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The current article is a review of the most important and relevant literature published in 2016 and early 2017 on non-Helicobacter pylori Helicobacter infections in humans and animals, as well as interactions between H. pylori and the microbiota of the stomach and other organs. Some putative new Helicobacter species were identified in sea otters, wild boars, dogs, and mice. Many cases of Helicobacter fennelliae and Helicobacter cinaedi infection have been reported in humans, mostly in immunocompromised patients. Mouse models have been used frequently as a model to investigate human Helicobacter infection, although some studies have investigated the pathogenesis of Helicobacters in their natural host, as was the case for Helicobacter suis infection in pigs. Our understanding of both the gastric and gut microbiome has made progress and, in addition, interactions between H. pylori and the microbiome were demonstrated to go beyond the stomach. Some new approaches of preventing Helicobacter infection or its related pathologies were investigated and, in this respect, the probiotic properties of Saccharomyces, Lactobacillus and Bifidobacterium spp. were confirmed.

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Noncontiguous finished genome sequence and description of Streptococcus timonensis sp. nov. isolated from the human stomach

Cited by 7 publications

References 36 publications

RETRACTED ARTICLE: Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing

RETRACTED ARTICLE: Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing

Streptococcus xiaochunlingii sp. nov. E24 Isolated From the Oropharynx of Healthy Chinese Children

Other Helicobacters, gastric and gut microbiota

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