scholarly journals Cultured microbes represent a substantial fraction of the human and mouse gut microbiota

Gut Microbes ◽  
2017 ◽  
Vol 8 (5) ◽  
pp. 493-503 ◽  
Author(s):  
Ilias Lagkouvardos ◽  
Jörg Overmann ◽  
Thomas Clavel
2021 ◽  
Author(s):  
Xu-Wen Wang ◽  
Yang-Yu Liu

AbstractMany studies have revealed that both host and environmental factors can impact the gut microbial compositions, implying that the gut microbiota is considerably dynamic1–5. In their Article, Ji et al.6 performed comprehensive analysis of multiple high-resolution time series data of human and mouse gut microbiota. They found that both human and mouse gut microbiota dynamics can be characterized by several robust scaling laws describing short- and long-term changes in gut microbiota abundances, distributions of species residence and return times, and the correlation between the mean and the temporal variance of species abundances. They claimed that those scaling laws characterize both short- and long-term dynamics of gut microbiota. However, we are concerned that their interpretation is quite misleading, because all the scaling laws can be reproduced by the shuffled time series with completely randomized time stamps of the microbiome samples.


Microbiome ◽  
2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Xu Zhang ◽  
Zhibin Ning ◽  
Janice Mayne ◽  
Jasmine I. Moore ◽  
Jennifer Li ◽  
...  

2020 ◽  
Vol 150 ◽  
pp. 991-999 ◽  
Author(s):  
Baiyuan Li ◽  
Huahai Chen ◽  
Linyan Cao ◽  
Yunfei Hu ◽  
Dan Chen ◽  
...  

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Chenchen Ma ◽  
Chengcheng Zhang ◽  
Denghui Chen ◽  
Shuaiming Jiang ◽  
Siyuan Shen ◽  
...  

AbstractThe adaptive evolution in indigenous intestinal microbes derived from probiotics is critical to safety and efficacy evaluation of probiotics, yet it is still largely underexplored. Here, through 11 publicly accessible datasets, we demonstrated that probiotic consumption can lead to widespread single-nucleotide variants (SNVs) in the native microbiota. Interestingly, the same probiotic strains introduced far more SNVs in mouse gut than humans. Furthermore, the pattern of probiotics-induced SNVs was highly probiotic-strain specific, and 17 common SNVs in Faecalibacterium prausnitzii genome were identified cross studies, which might lead to changes in bacterial protein structure. Further, nearly 50% of F. prausnitzii SNVs can be inherited for six months in an independent human cohort, whereas the other half only transiently occurred. Collectively, our study substantially extended our understanding of co-evolution of the probiotics and the indigenous gut microbiota, highlighting the importance of assessment of probiotics efficacy and safety in an integrated manner.


2021 ◽  
Author(s):  
Silas Kieser ◽  
Evgeny M. Zdobnov ◽  
Mirko Trajkovski

AbstractMouse is the most used model for studying the impact of microbiota on its host, but the repertoire of species from the mouse gut microbiome remains largely unknown. Here, we construct a Comprehensive Mouse Gut Metagenome (CMGM) catalog by assembling all currently available mouse gut metagenomes and combining them with published reference and metagenome-assembled genomes. The 50’011 genomes cluster into 1’699 species, of which 78.1% are uncultured, and we discovered 226 new genera, 7 new families, and 1 new order. Rarefaction analysis indicates comprehensive sampling of the species from the mouse gut. CMGM enables an unprecedented coverage of the mouse gut microbiome exceeding 90%. Comparing CMGM to the human gut microbiota shows an overlap 64% at the genus, but only 16% at the species level, demonstrating that human and mouse gut microbiota are largely distinct.


Nature ◽  
2016 ◽  
Vol 536 (7615) ◽  
pp. 238-238 ◽  
Author(s):  
Benoit Chassaing ◽  
Omry Koren ◽  
Julia K. Goodrich ◽  
Angela C. Poole ◽  
Shanthi Srinivasan ◽  
...  

2014 ◽  
Vol 45 (3) ◽  
pp. 195-202 ◽  
Author(s):  
Hai-Ning Yu ◽  
Jing Zhu ◽  
Wen-sheng Pan ◽  
Sheng-Rong Shen ◽  
Wei-Guang Shan ◽  
...  

2019 ◽  
Vol 5 (1) ◽  
Author(s):  
Francesca La Carpia ◽  
Boguslaw S. Wojczyk ◽  
Medini K. Annavajhala ◽  
Abdelhadi Rebbaa ◽  
Rachel Culp-Hill ◽  
...  

Abstract Iron is essential for both microorganisms and their hosts. Although effects of dietary iron on gut microbiota have been described, the effect of systemic iron administration has yet to be explored. Here, we show that dietary iron, intravenous iron administration, and chronic transfusion in mice increase the availability of iron in the gut. These iron interventions have consistent and reproducible effects on the murine gut microbiota; specifically, relative abundance of the Parabacteroides and Lactobacillus genera negatively correlate with increased iron stores, whereas members of the Clostridia class positively correlate with iron stores regardless of the route of iron administration. Iron levels also affected microbial metabolites, in general, and indoles, in particular, circulating in host plasma and in stool pellets. Taken together, these results suggest that by shifting the balance of the microbiota, clinical interventions that affect iron status have the potential to alter biologically relevant microbial metabolites in the host.


2020 ◽  
Vol Volume 13 ◽  
pp. 4547-4558
Author(s):  
Si-Lan Gu ◽  
Yiwen Gong ◽  
Jiaying Zhang ◽  
Yunbo Chen ◽  
Zhengjie Wu ◽  
...  

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