scholarly journals Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6554 ◽  
Author(s):  
Ksenia M. Klimina ◽  
Artem S. Kasianov ◽  
Elena U. Poluektova ◽  
Kirill V. Emelyanov ◽  
Viktoriya N. Voroshilova ◽  
...  
Keyword(s):  
Disease Prevention ◽  
Gut Microbiota ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Health Assessment ◽  
Probiotic Bacteria ◽  
Microbiota Composition ◽  
Unique Genotype ◽  
Functional Biomarkers

Recent research has indicated that in addition to the unique genotype each individual may also have a unique microbiota composition. Difference in microbiota composition may emerge from both its species and strain constituents. It is important to know the precise composition especially for the gut microbiota (GM), since it can contribute to the health assessment, personalized treatment, and disease prevention for individuals and groups (cohorts). The existing methods for species and strain composition in microbiota are not always precise and usually not so easy to use. Probiotic bacteria of the genus Bifidobacterium and Lactobacillus make an essential component of human GM. Previously we have shown that in certain Bifidobacterium and Lactobacillus species the RelBE and MazEF superfamily of toxin-antitoxin (TA) systems may be used as functional biomarkers to differentiate these groups of bacteria at the species and strain levels. We have composed a database of TA genes of these superfamily specific for all lactobacilli and bifidobacteria species with complete genome sequence and confirmed that in all Lactobacillus and Bifidobacterium species TA gene composition is species and strain specific. To analyze composition of species and strains of two bacteria genera, Bifidobacterium and Lactobacillus, in human GM we developed TAGMA (toxin antitoxin genes for metagenomes analyses) software based on polymorphism in TA genes. TAGMA was tested on gut metagenomic samples. The results of our analysis have shown that TAGMA can be used to characterize species and strains of Lactobacillus and Bifidobacterium in metagenomes.

scholarly journals Complete Genome Sequence of Lactobacillus reuteri Byun-re-01, Isolated from Mouse Small Intestine

2018 ◽  
Vol 7 (17) ◽  
Author(s):  
Dongjun Kim ◽  
Mun-ju Cho ◽  
Seungchan Cho ◽  
Yongjun Lee ◽  
Sung June Byun ◽  
...  
Keyword(s):  
Small Intestine ◽  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Lactobacillus Reuteri ◽  
Probiotic Bacteria ◽  
Content Type ◽  
Mouse Small Intestine

Lactic acid bacteria (LAB) are generally recognized as safe (GRAS) and serve as probiotic bacteria when consumed in adequate amounts. Here, we report the complete genome sequence of Lactobacillus reuteri Byun-re-01, isolated from mouse small intestine.

scholarly journals Complete Genome Sequence of Bifidobacterium longum JDM301

2010 ◽  
Vol 192 (15) ◽  
pp. 4076-4077 ◽  
Author(s):  
Yan-Xia Wei ◽  
Zhuo-Yang Zhang ◽  
Chang Liu ◽  
Yong-Zhang Zhu ◽  
Yong-Qiang Zhu ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Bifidobacterium Longum ◽  
Probiotic Bacteria ◽  
Probiotic Properties ◽  
Human Gastrointestinal Tract ◽  
Gram Positive Bacteria ◽  
Commercial Strain

ABSTRACT Bifidobacteria, known as probiotic bacteria, are high-G+C Gram-positive bacteria which naturally inhabit the human gastrointestinal tract and vagina. Recently, we completely sequenced Bifidobacterium longum JDM301, which is a widely used Chinese commercial strain with several probiotic properties.

scholarly journals Complete Genome Sequence of Alistipes indistinctus Strain 2BBH45, Isolated from the Feces of a Healthy Japanese Male

2021 ◽  
Vol 10 (2) ◽  
Author(s):  
Yusuke Ogata ◽  
Mitsuo Sakamoto ◽  
Moriya Ohkuma ◽  
Masahira Hattori ◽  
Wataru Suda
Keyword(s):  
Gut Microbiota ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Human Gut ◽  
Content Type ◽  
Human Gut Microbiota ◽  
Japanese Male

ABSTRACT The genus Alistipes is one of the members of the human gut microbiota. Here, we report the complete genome sequence of Alistipes indistinctus strain 2BBH45, harboring plasmid p2BBH45.

scholarly journals The complete genome sequence ofExiguobacterium arabatumW-01 reveals potential probiotic functions

2017 ◽  
Vol 6 (5) ◽  
pp. e00496 ◽  
Author(s):  
Meinan Cong ◽  
Qingling Jiang ◽  
Xiaojin Xu ◽  
Lixing Huang ◽  
Yongquan Su ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome

scholarly journals Complete Genome Sequence of a Hepatitis E Virus Genotype 1e Strain from an Outbreak in Nigeria, 2017

2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Olusola Anuoluwapo Akanbi ◽  
Dominik Harms ◽  
Bo Wang ◽  
Oluyinka Oladele Opaleye ◽  
Olufisayo Adesina ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Hepatitis E Virus ◽  
Hepatitis E ◽  
Sub Saharan Africa ◽  
Genotype 1 ◽  
Virus Genotype ◽  
Sub Saharan

Hepatitis E virus genotype 1 (HEV-1) is associated with large epidemics. Notably, HEV subtype 1e (HEV-1e) has caused HEV outbreaks in sub-Saharan Africa.

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