scholarly journals Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota

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.

Author(s):  
Ralf Jäger ◽  
Alex E. Mohr ◽  
Katie C. Carpenter ◽  
Chad M. Kerksick ◽  
Martin Purpura ◽  
...  

AbstractPosition statement: The International Society of Sports Nutrition (ISSN) provides an objective and critical review of the mechanisms and use of probiotic supplementation to optimize the health, performance, and recovery of athletes. Based on the current available literature, the conclusions of the ISSN are as follows: Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host (FAO/WHO).Probiotic administration has been linked to a multitude of health benefits, with gut and immune health being the most researched applications.Despite the existence of shared, core mechanisms for probiotic function, health benefits of probiotics are strain- and dose-dependent.Athletes have varying gut microbiota compositions that appear to reflect the activity level of the host in comparison to sedentary people, with the differences linked primarily to the volume of exercise and amount of protein consumption. Whether differences in gut microbiota composition affect probiotic efficacy is unknown.The main function of the gut is to digest food and absorb nutrients. In athletic populations, certain probiotics strains can increase absorption of key nutrients such as amino acids from protein, and affect the pharmacology and physiological properties of multiple food components.Immune depression in athletes worsens with excessive training load, psychological stress, disturbed sleep, and environmental extremes, all of which can contribute to an increased risk of respiratory tract infections. In certain situations, including exposure to crowds, foreign travel and poor hygiene at home, and training or competition venues, athletes’ exposure to pathogens may be elevated leading to increased rates of infections. Approximately 70% of the immune system is located in the gut and probiotic supplementation has been shown to promote a healthy immune response. In an athletic population, specific probiotic strains can reduce the number of episodes, severity and duration of upper respiratory tract infections.Intense, prolonged exercise, especially in the heat, has been shown to increase gut permeability which potentially can result in systemic toxemia. Specific probiotic strains can improve the integrity of the gut-barrier function in athletes.Administration of selected anti-inflammatory probiotic strains have been linked to improved recovery from muscle-damaging exercise.The minimal effective dose and method of administration (potency per serving, single vs. split dose, delivery form) of a specific probiotic strain depends on validation studies for this particular strain. Products that contain probiotics must include the genus, species, and strain of each live microorganism on its label as well as the total estimated quantity of each probiotic strain at the end of the product’s shelf life, as measured by colony forming units (CFU) or live cells.Preclinical and early human research has shown potential probiotic benefits relevant to an athletic population that include improved body composition and lean body mass, normalizing age-related declines in testosterone levels, reductions in cortisol levels indicating improved responses to a physical or mental stressor, reduction of exercise-induced lactate, and increased neurotransmitter synthesis, cognition and mood. However, these potential benefits require validation in more rigorous human studies and in an athletic population.


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 ◽  
...  

Gut Microbes ◽  
2017 ◽  
Vol 8 (5) ◽  
pp. 493-503 ◽  
Author(s):  
Ilias Lagkouvardos ◽  
Jörg Overmann ◽  
Thomas Clavel

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

2013 ◽  
Vol 111 (3) ◽  
pp. 387-402 ◽  
Author(s):  
Susan E. Power ◽  
Paul W. O'Toole ◽  
Catherine Stanton ◽  
R. Paul Ross ◽  
Gerald F. Fitzgerald

The human intestine is colonised by 1013to 1014micro-organisms, the vast majority of which belong to the phyla Firmicutes and Bacteroidetes. Although highly stable over time, the composition and activities of the microbiota may be influenced by a number of factors including age, diet and antibiotic treatment. Although perturbations in the composition or functions of the microbiota are linked to inflammatory and metabolic disorders (e.g. inflammatory bowel diseases, irritable bowel syndrome and obesity), it is unclear at this point whether these changes are a symptom of the disease or a contributing factor. A better knowledge of the mechanisms through which changes in microbiota composition (dysbiosis) promote disease states is needed to improve our understanding of the causal relationship between the gut microbiota and disease. While evidence of the preventive and therapeutic effects of probiotic strains on diarrhoeal illness and other intestinal conditions is promising, the exact mechanisms of the beneficial effects are not fully understood. Recent studies have raised the question of whether non-viable probiotic strains can confer health benefits on the host by influencing the immune system. As the potential health effect of these non-viable bacteria depends on whether the mechanism of this effect is dependent on viability, future research needs to consider each probiotic strain on a case-by-case basis. The present review provides a comprehensive, updated overview of the human gut microbiota, the factors influencing its composition and the role of probiotics as a therapeutic modality in the treatment and prevention of diseases and/or restoration of human health.


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.


2020 ◽  
Author(s):  
Alfonso Benítez-Páez ◽  
Annick V. Hartstra ◽  
Max Nieuwdorp ◽  
Yolanda Sanz

AbstractBackgroundEffective methodologies to accurately identify members of the gut microbiota at the species and strain levels are necessary to unveiling more specific and detailed host-microbe interactions and associations with health and disease.MethodsMinION™ MkIb nanopore-based device and the R9.5 flowcell chemistry were used to sequence and assemble dozens of rrn regions (16S-ITS-23S) derived from the most prevalent bacterial species in the human gut microbiota. As a method proof-of-concept to disclose further strain-level variation, we performed a complementary analysis in a subset of samples derived from an faecal microbiota transplantation (FMT) trial aiming amelioration of glucose and lipid metabolism in overweight subjects with metabolic syndrome.ResultsThe resulting updated rrn database, the data processing pipeline, and the precise control of covariates (sequencing run, sex, age, BMI, donor) were pivotal to accurately estimate the changes in gut microbial species abundance in the recipients after FMT. Furthermore, the rrn methodology described here demonstrated the ability to detect strain-level variation, critical to evaluate the transference of bacteria from donors to recipients as a consequence of the FMT. At this regard, we showed that our FMT trial successfully induced donors’ strain engraftment of e.g. Parabacteroides merdae species in recipients by mapping and assessing their associated single nucleotide variants (SNV).ConclusionsWe developed a methodology that enables the identification of microbiota at species- and strain-level in a cost-effective manner. Despite its error-prone nature and its modest per-base accuracy, the nanopore data showed to have enough quality to estimate single-nucleotide variation. This methodology and data analysis represents a cost-effective manner to trace genetic variability needed for better understanding the health effects of the human microbiome.Trial registrationThe study was prospectively registered at the Dutch Trial registry - NTR4488 (https://www.trialregister.nl/trial/4488).


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