scholarly journals Recipe for a Healthy Gut: Intake of Unpasteurised Milk Is Associated with Increased Lactobacillus Abundance in the Human Gut Microbiome

Nutrients ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 1468
Author(s):  
Mary I. Butler ◽  
Thomaz F. S. Bastiaanssen ◽  
Caitriona Long-Smith ◽  
Kirsten Berding ◽  
Sabrina Morkl ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Dairy Products ◽  
Human Gut ◽  
Microbiome Composition ◽  
Organic Farm ◽  
Functional Richness ◽  
Genus Lactobacillus ◽  
The Impact ◽  
Milk And Dairy Products

Introduction: The gut microbiota plays a role in gut–brain communication and can influence psychological functioning. Diet is one of the major determinants of gut microbiota composition. The impact of unpasteurised dairy products on the microbiota is unknown. In this observational study, we investigated the effect of a dietary change involving intake of unpasteurised dairy on gut microbiome composition and psychological status in participants undertaking a residential 12-week cookery course on an organic farm. Methods: Twenty-four participants completed the study. The majority of food consumed during their stay originated from the organic farm itself and included unpasteurised milk and dairy products. At the beginning and end of the course, participants provided faecal samples and completed self-report questionnaires on a variety of parameters including mood, anxiety and sleep. Nutrient intake was monitored with a food frequency questionnaire. Gut microbiota analysis was performed with 16S rRNA gene sequencing. Additionally, faecal short chain fatty acids (SCFAs) were measured. Results: Relative abundance of the genus Lactobacillus increased significantly between pre- and post-course time points. This increase was associated with participants intake of unpasteurised milk and dairy products. An increase in the faecal SCFA, valerate, was observed along with an increase in the functional richness of the microbiome profile, as determined by measuring the predictive neuroactive potential using a gut–brain module approach. Conclusions: While concerns in relation to safety need to be considered, intake of unpasteurised milk and dairy products appear to be associated with the growth of the probiotic bacterial genus, Lactobacillus, in the human gut. More research is needed on the effect of dietary changes on gut microbiome composition, in particular in relation to the promotion of bacterial genera, such as Lactobacillus, which are recognised as being beneficial for a range of physical and mental health outcomes.

scholarly journals Alterations in human gut microbiome composition and metabolism after exposure to glyphosate and Roundup and/or a spore-based formulation using the SHIME® technology

2021 ◽  
Author(s):  
Robin Mesnage ◽  
Marta Calatayud ◽  
Cindy Duysburgh ◽  
Massimo Marzorati ◽  
Michael Antoniou
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Large Scale ◽  
Epidemiological Studies ◽  
Human Gut ◽  
Microbiome Composition ◽  
Human Gut Microbiome ◽  
Ammonium Production ◽  
Profiling Techniques ◽  
Microbial Environment

Despite extensive research into the toxicology of the herbicide glyphosate, there are still major unknowns regarding its effects on the human gut microbiome. As a step in addressing this knowledge gap, we describe for the first time the effects of glyphosate and a Roundup glyphosate-based herbicide on infant gut microbiota using SHIME technology, which mimics the entire gastrointestinal tract. SHIME microbiota culture was undertaken in the presence of a concentration of 100 mg/L (corresponding to a dose of 1.6 mg/kg/day) glyphosate and the same glyphosate equivalent concentration of Roundup, which is in the range of the US chronic reference dose, and subjected to molecular profiling techniques to assess outcomes. Roundup and to a lesser extent glyphosate caused an increase in fermentation activity, resulting in acidification of the microbial environment. This was also reflected by an increase in lactate and acetate production concomitant to a decrease in the levels of propionate, valerate, caproate and butyrate. Ammonium production reflecting proteolytic activities was increased by Roundup exposure. Global metabolomics revealed large scale disturbances in metabolite profiles, including an increased abundance of long chain polyunsaturated fatty acids (n3 and n6). Although changes in bacterial composition measured by qPCR and 16S rRNA sequencing were less clear, our results suggested that lactobacilli had their growth stimulated as a result of microenvironment acidification. Co-treatment with the spore-based probiotic formulation MegaSporeBiotic reverted some of the changes in short-chain fatty acid levels. Altogether, our results suggest that glyphosate can exert effects on human gut microbiota at permitted regulatory levels of exposure, highlighting the need for epidemiological studies aimed at evaluating the effects of glyphosate herbicides on human gut microbiome function.

scholarly journals Examining the Effects of an Anti-Salmonella Bacteriophage Preparation, BAFASAL®, on Ex-Vivo Human Gut Microbiome Composition and Function Using a Multi-Omics Approach

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1734
Author(s):  
Janice Mayne ◽  
Xu Zhang ◽  
James Butcher ◽  
Krystal Walker ◽  
Zhibin Ning ◽  
...  
Keyword(s):  
Food Chain ◽  
Gut Microbiome ◽  
Food Industry ◽  
Ex Vivo ◽  
Human Gut ◽  
Microbiome Composition ◽  
Human Gut Microbiome ◽  
And Function ◽  
The Impact

Salmonella infections (salmonellosis) pose serious health risks to humans, usually via food-chain contamination. This foodborne pathogen causes major food losses and human illnesses, with significant economic impacts. Overuse of antibiotics in the food industry has led to multidrug-resistant strains of bacteria, and governments are now restricting their use, leading the food industry to search for alternatives to secure food chains. Bacteriophages, viruses that infect and kill bacteria, are currently being investigated and used as replacement treatments and prophylactics due to their specificity and efficacy. They are generally regarded as safe alternatives to antibiotics, as they are natural components of the ecosystem. However, when specifically used in the industry, they can also make their way into humans through our food chain or exposure, as is the case for antibiotics. In particular, agricultural workers could be repeatedly exposed to bacteriophages supplemented to animal feeds. To our knowledge, no studies have investigated the effects of such exposure to bacteriophages on the human gut microbiome. In this study, we used a novel in-vitro assay called RapidAIM to investigate the effect of a bacteriophage mixture, BAFASAL®, used in poultry farming on five individual human gut microbiomes. Multi-omics analyses, including 16S rRNA gene sequencing and metaproteomic, revealed that ex-vivo human gut microbiota composition and function were unaffected by BAFASAL® treatment, providing an additional measure for its safety. Due to the critical role of the gut microbiome in human health and the known role of bacteriophages in regulation of microbiome composition and function, we suggest assaying the impact of bacteriophage-cocktails on the human gut microbiome as a part of their safety assessment.

scholarly journals Rice Bran and Quercetin Produce a Positive Synergistic Effect on Human Gut Microbiota, Elevate the Level of Propionate, and Reduce the Population of Enterobacteriaceae family when Determined using a Bioreactor Model

2020 ◽  
Author(s):  
Sudeep Ghimire ◽  
Supapit Wongkuna ◽  
Ranjini Sankaranarayanan ◽  
Elizabeth P. Ryan ◽  
G. Jayarama Bhat ◽  
...  
Keyword(s):  
Synergistic Effect ◽  
Gut Microbiota ◽  
Rice Bran ◽  
Gut Microbiome ◽  
Bacterial Species ◽  
Human Gut ◽  
Food Ingredients ◽  
Microbiome Composition ◽  
Human Gut Microbiota ◽  
Host Health

AbstractDiet is one of the prominent determinants of gut microbiota composition significantly impacting human health. Recent studies with dietary supplements such as rice bran and quercetin have been shown to provide a beneficial impact on the host by positively influencing the gut microbiota. However, the specific bacterial species impacted when rice bran or quercetin is present in the diet is not well understood. Therefore, in this study, we used a minibioreactor array system as a model to determine the effect of quercetin and rice bran individually, as well as in combination, on gut microbiota without the confounding host factors. We found that rice bran exerts higher shift in gut microbiome composition when compared to quercetin. At the species level, Acidaminococcus intestini was the only significantly enriched taxa when quercetin was supplemented, while 15 species were enriched in rice bran supplementation and 13 were enriched when quercetin and rice bran were supplemented in combination. When comparing the short chain fatty acid production, quercetin supplementation significantly enriched isobutyrate production while propionate dominated the quercetin and rice bran combined group. Higher levels of propionate were highly correlated to the lower abundance of the potentially pathogenic Enterobacteriaceae family. These findings suggest that the combination of rice bran and quercetin serve to enrich beneficial bacteria and reduce potential opportunistic pathogens. However, further in vivo studies are necessary to determine the synergistic effect of rice bran and quercetin on host health and immunity.ImportanceRice bran and quercetin are dietary components that shape host health by interacting with the gut microbiome. Both these substrates have been reported to provide nutritional and immunological benefits individually. However, considering the complexity of the human diet, it is useful to determine how the combination of food ingredients such as rice bran and quercetin influences the human gut microbiota. Our study provides insights into how these ingredients influence microbiome composition alone and in combination in vitro. This will allow us to identify which species in the gut microbiome are responsible for biotransformation of these dietary ingredients.. Such information is helpful for the development of synbiotics to improve gut health and immunity.

scholarly journals What Is the Role of Gut Microbiota in Obesity Prevalence? A Few Words about Gut Microbiota and Its Association with Obesity and Related Diseases

2021 ◽  
Vol 10 (1) ◽  
pp. 52
Author(s):  
Julita Tokarek ◽  
Joanna Gadzinowska ◽  
Ewelina Młynarska ◽  
Beata Franczyk ◽  
Jacek Rysz
Keyword(s):  
Gut Microbiota ◽  
Molecular Mechanisms ◽  
Obesity Prevalence ◽  
Microbiome Composition ◽  
Obstructive Sleep ◽  
Genus Lactobacillus ◽  
Prevalence Of Obesity ◽  
Lifestyle Disease ◽  
The Impact

Obesity is becoming the most dangerous lifestyle disease of our time, and its effects are already being observed in both developed and developing countries. The aim of this study was to investigate the impact of gut microbiota on the prevalence of obesity and associated morbidities, taking into consideration underlying molecular mechanisms. In addition to exploring the relationship between obesity and fecal microorganisms with their metabolites, the study also focused on the factors that would be able to stimulate growth and remodeling of microbiota. Assessed articles were carefully classified according to a predetermined criterion and were critically appraised and used as a basis for conclusions. The considered articles and reviews acknowledge that intestinal microbiota forms a multifunctional system that might significantly affect human homeostasis. It has been proved that alterations in the gut microbiota are found in obese and metabolically diseased patients. The imbalance of microbiome composition, such as changes in Bacteroidetes/Firmicutes ratio and presence of different species of genus Lactobacillus, might promote obesity and comorbidities (type 2 diabetes mellitus, hypertension, dyslipidemia, depression, obstructive sleep apnea). However, there are also studies that contradict this theory. Therefore, further well-designed studies are needed to improve the knowledge about the influence of microbiota, its metabolites, and probiotics on obesity.

scholarly journals Comprehensive mouse gut metagenome catalog reveals major difference to the human counterpart

2021 ◽  
Author(s):  
Silas Kieser ◽  
Evgeny M. Zdobnov ◽  
Mirko Trajkovski
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
New Order ◽  
Human Gut ◽  
Rarefaction Analysis ◽  
Human Counterpart ◽  
The Impact ◽  
Human And Mouse ◽  
Gut Metagenome ◽  
Mouse Gut Microbiota

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.

scholarly journals Acquired interbacterial defense systems protect against interspecies antagonism in the human gut microbiome

2018 ◽  
Author(s):  
Benjamin D. Ross ◽  
Adrian J. Verster ◽  
Matthew C. Radey ◽  
Danica T. Schmidtke ◽  
Christopher E. Pope ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Gene Clusters ◽  
Protective Capacity ◽  
Human Gut ◽  
Microbiome Composition ◽  
Toxin Resistance ◽  
Human Gut Microbiome ◽  
Bacterial Antagonism ◽  
The Impact

AbstractThe impact of direct interactions between co-resident microbes on microbiome composition is not well understood. Here we report the occurrence of acquired interbacterial defense (AID) gene clusters in bacterial residents of the human gut microbiome. These clusters encode arrays of immunity genes that protect against type VI secretion toxin-mediated intra- and inter-species bacterial antagonism. Moreover, the clusters reside on mobile elements and we demonstrate that their transfer is sufficient to confer toxin resistance in vitro and in gnotobiotic mice. Finally, we identify and validate the protective capacity of a recombinase-associated AID subtype (rAID-1) present broadly in Bacteroidales genomes. These rAID-1 gene clusters have a structure suggestive of active gene acquisition and include predicted immunity factors of toxins deriving from diverse organisms. Our data suggest that neutralization of contact-dependent interbacterial antagonism via AID systems shapes human gut microbiome ecology.

scholarly journals The Impact of Anthelmintic Treatment on Human Gut Microbiota Based on Cross-Sectional and Pre- and Postdeworming Comparisons in Western Kenya

mBio ◽  
2019 ◽  
Vol 10 (2) ◽  
Author(s):  
Alice V. Easton ◽  
Mariam Quiñones ◽  
Ivan Vujkovic-Cvijin ◽  
Rita G. Oliveira ◽  
Stella Kepha ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Intestinal Parasites ◽  
Fold Change ◽  
Rrna Gene ◽  
Human Gut ◽  
Microbial Composition ◽  
Content Type ◽  
Average Fold Change ◽  
The Impact

ABSTRACT Murine studies suggest that the presence of some species of intestinal helminths is associated with changes in host microbiota composition and diversity. However, studies in humans have produced varied conclusions, and the impact appears to vary widely depending on the helminth species present. To demonstrate how molecular approaches to the human gut microbiome can provide insights into the complex interplay among disparate organisms, DNA was extracted from cryopreserved stools collected from residents of 5 rural Kenyan villages prior to and 3 weeks and 3 months following albendazole (ALB) therapy. Samples were analyzed by quantitative PCR (qPCR) for the presence of 8 species of intestinal parasites and by MiSeq 16S rRNA gene sequencing. Based on pretreatment results, the presence of neither Ascaris lumbricoides nor Necator americanus infection significantly altered the overall diversity of the microbiota in comparison with age-matched controls. Following ALB therapy and clearance of soil-transmitted helminths (STH), there were significant increases in the proportion of the microbiota made up by Clostridiales (P = 0.0002; average fold change, 0.57) and reductions in the proportion made up by Enterobacteriales (P = 0.0004; average fold change, −0.58). There was a significant posttreatment decrease in Chao1 richness, even among individuals who were uninfected pretreatment, suggesting that antimicrobial effects must be considered in any posttreatment setting. Nevertheless, the helminth-associated changes in Clostridiales and Enterobacteriales suggest that clearance of STH, and of N. americanus in particular, alters the gut microbiota. IMPORTANCE The gut microbiome is an important factor in human health. It is affected by what we eat, what medicines we take, and what infections we acquire. In turn, it affects the way we absorb nutrients and whether we have excessive intestinal inflammation. Intestinal worms may have an important impact on the composition of the gut microbiome. Without a complete understanding of the impact of mass deworming programs on the microbiome, it is impossible to accurately calculate the cost-effectiveness of such public health interventions and to guard against any possible deleterious side effects. Our research examines this question in a “real-world” setting, using a longitudinal cohort, in which individuals with and without worm infections are treated with deworming medication and followed up at both three weeks and three months posttreatment. We quantify the impact of roundworms and hookworms on gut microbial composition, suggesting that the impact is small, but that treatment of hookworm infection results in significant changes. This work points to the need for follow-up studies to further examine the impact of hookworm on the gut microbiota and determine the health consequences of the observed changes.

scholarly journals Effect of fructans, prebiotics and fibres on the human gut microbiome assessed by 16S rRNA-based approaches: a review

2020 ◽  
Vol 11 (2) ◽  
pp. 101-129 ◽  
Author(s):  
K.S. Swanson ◽  
W.M. de Vos ◽  
E.C. Martens ◽  
J.A. Gilbert ◽  
R.S. Menon ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Human Gut ◽  
Beta Glucan ◽  
Dietary Fibres ◽  
Sequencing Studies ◽  
Resistant Starches ◽  
The Impact

The inherent and diverse capacity of dietary fibres, nondigestible oligosaccharides (NDOs) and prebiotics to modify the gut microbiota and markedly influence health status of the host has attracted rising interest. Research and collective initiatives to determine the composition and diversity of the human gut microbiota have increased over the past decade due to great advances in high-throughput technologies, particularly the 16S ribosomal RNA (rRNA) sequencing. Here we reviewed the application of 16S rRNA-based molecular technologies, both community wide (sequencing and phylogenetic microarrays) and targeted methodologies (quantitative PCR, fluorescent in situ hybridisation) to study the effect of chicory inulin-type fructans, NDOs and specific added fibres, such as resistant starches, on the human intestinal microbiota. Overall, such technologies facilitated the monitoring of microbiota shifts due to prebiotic/fibre consumption, though there are limited community-wide sequencing studies so far. Molecular studies confirmed the selective bifidogenic effect of fructans and galactooligosaccharides (GOS) in human intervention studies. Fructans only occasionally decreased relative abundance of Bacteroidetes or stimulated other groups. The sequencing studies for various resistant starches, polydextrose and beta-glucan showed broader effects with more and different types of gut microbial species being enhanced, often including phylotypes of Ruminococcaceae. There was substantial variation in terms of magnitude of response and in individual responses to a specific fibre or NDO which may be due to numerous factors, such as initial presence and relative abundance of a microbial type, diet, genetics of the host, and intervention parameters, such as intervention duration and fibre dose. The field will clearly benefit from a more systematic approach that will support defining the impact of prebiotics and fibres on the gut microbiome, identify biomarkers that link gut microbes to health, and address the personalised response of an individual’s microbiota to prebiotics and dietary fibres.

scholarly journals Examining the effects of an anti-Salmonella bacteriophage preparation, BAFASAL, on ex vivo human gut microbiome composition and function using a multi-omics approach

2021 ◽  
Author(s):  
Janice Mayne ◽  
Xu Zhang ◽  
James Butcher ◽  
Krystal Walker ◽  
Zhibin Ning ◽  
...  
Keyword(s):  
Food Chain ◽  
Gut Microbiome ◽  
Ex Vivo ◽  
Human Gut ◽  
Microbiome Composition ◽  
Human Gut Microbiome ◽  
Salmonella Infections ◽  
And Function ◽  
The Impact

Salmonella infections (salmonellosis) pose serious health risks to humans, usually via contamination in our food chain. This foodborne pathogen causes major food losses and human illnesses that result in significant economic impacts. Pathogens such as Salmonella have traditionally been kept at bay through the use of antibiotics, but antibiotic overuse within the food industry has led to the development of numerous multidrug-resistant bacterial strains. Thus, governments are now restricting antibiotic use, forcing the industry to search for alternatives to secure safe food chains. Bacteriophages, viruses that infect and kill bacteria, are currently being investigated and used as replacement treatments and prophylactics due to their specificity and efficacy. They are generally regarded as safe alternatives to antibiotics as they are natural components of the ecosystem. One example is BAFASEL, a commercial bacteriophage mixture that specifically targets Salmonella and is currently approved for use in poultry farming. However, when specifically used in the industry they can also make their way into humans through our food chain or exposure as is the case for antibiotics. In particular, agricultural workers could be repeatedly exposed to bacteriophages supplemented in animal feeds. To the best of our knowledge, no studies have investigated the effects of such exposure to bacteriophages on the human gut microbiome. In this study, we used a novel in vitro assay called RapidAIM to investigate BAFASAL's potential impact on five individual human gut microbiomes. Multi-omics analyses, including 16S rRNA gene sequencing and metaproteomic, revealed that ex vivo human gut microbiota composition and function were unaffected by BAFASAL treatment providing an additional measure for its safety. Due to the critical role of the gut microbiome in human health and the known role of bacteriophages in regulation of microbiome composition and function, we suggest assaying the impact of bacteriophage-cocktails on the human gut microbiome as a part of their safety assessment.

scholarly journals Taxonomic signatures of cause-specific mortality risk in human gut microbiome

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Aaro Salosensaari ◽  
Ville Laitinen ◽  
Aki S. Havulinna ◽  
Guillaume Meric ◽  
Susan Cheng ◽  
...  
Keyword(s):  
Mortality Risk ◽  
Gut Microbiome ◽  
Human Gut ◽  
Cross Sectional ◽  
Microbiome Composition ◽  
Human Gut Microbiome ◽  
Non Invasive ◽  
Sequencing Technologies

AbstractThe collection of fecal material and developments in sequencing technologies have enabled standardised and non-invasive gut microbiome profiling. Microbiome composition from several large cohorts have been cross-sectionally linked to various lifestyle factors and diseases. In spite of these advances, prospective associations between microbiome composition and health have remained uncharacterised due to the lack of sufficiently large and representative population cohorts with comprehensive follow-up data. Here, we analyse the long-term association between gut microbiome variation and mortality in a well-phenotyped and representative population cohort from Finland (n = 7211). We report robust taxonomic and functional microbiome signatures related to the Enterobacteriaceae family that are associated with mortality risk during a 15-year follow-up. Our results extend previous cross-sectional studies, and help to establish the basis for examining long-term associations between human gut microbiome composition, incident outcomes, and general health status.

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