scholarly journals A genetically adaptable strategy for ribose scavenging in a human gut symbiont plays a diet-dependent role in colon colonization

2019 ◽  
Author(s):  
Robert W. P. Glowacki ◽  
Nicholas A. Pudlo ◽  
Yunus Tuncil ◽  
Ana S. Luis ◽  
Anton I. Terekhov ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Molecular Genetics ◽  
Gut Microbiome ◽  
Phosphate Metabolism ◽  
Human Gut ◽  
Gut Colonization ◽  
Ribose Phosphate ◽  
Gut Symbionts ◽  
The Impact

SummaryEfficient nutrient acquisition in the competitive human gut is essential for microbial persistence. While polysaccharides have been well-studied nutrients for the gut microbiome, other resources such as co-factors and nucleic acids have been less examined. We describe a series of ribose utilization systems (RUSs) that are broadly represented in Bacteroidetes and appear to have diversified to allow access to ribose from a variety of substrates. OneBacteroides thetaiotaomicronRUS variant is critical for competitive gut colonization in a diet-specific fashion. Using molecular genetics, we probed the nature of the ribose source underlying this diet-specific phenotype, revealing that hydrolytic functions in RUS (e.g., to cleave ribonucleosides) are present but dispensable. Instead, ribokinases that are activatedin vivoand participate in cellular ribose-phosphate metabolism are essential. Our results underscore the extensive mechanisms that gut symbionts have evolved to access nutrients and how metabolic context determines the impact of these functionsin vivo.

scholarly journals Low-Molecular-Weight Seaweed-Derived Polysaccharides Lead to Increased Faecal Bulk but Do Not Alter Human Gut Health Markers

Foods ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2988
Author(s):  
Ciara D. Bannon ◽  
Julia Eckenberger ◽  
William John Snelling ◽  
Chloe Elizabeth Huseyin ◽  
Philip Allsopp ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Gut Microbiome ◽  
Controlled Trial ◽  
Bioactive Compound ◽  
Low Molecular Weight ◽  
Fish Analysis ◽  
Gut Health ◽  
Human Gut ◽  
The Impact

Seaweeds are potentially sustainable crops and are receiving significant interest because of their rich bioactive compound content; including fatty acids, polyphenols, carotenoids, and complex polysaccharides. However, there is little information on the in vivo effects on gut health of the polysaccharides and their low-molecular-weight derivatives. Herein, we describe the first investigation into the prebiotic potential of low-molecular-weight polysaccharides (LMWPs) derived from alginate and agar in order to validate their in vivo efficacy. We conducted a randomized; placebo-controlled trial testing the impact of alginate and agar LWMPs on faecal weight and other markers of gut health and on composition of gut microbiota. We show that these LMWPs led to significantly increased faecal bulk (20–30%). Analysis of gut microbiome composition by sequencing indicated no significant changes attributable to treatment at the phylum and family level, although FISH analysis showed an increase in Faecalibacterium prausnitzii in subjects consuming agar LMWP. Sequence analysis of gut bacteria corroborated with the FISH data, indicating that alginate and agar LWMPs do not alter human gut microbiome health markers. Crucially, our findings suggest an urgent need for robust and rigorous human in vivo testing—in particular, using refined seaweed extracts.

scholarly journals 11β-hydroxysteroid dehydrogenase-1 deficiency alters the gut microbiome response to Western diet

2017 ◽  
Vol 232 (2) ◽  
pp. 273-283 ◽  
Author(s):  
Jethro S Johnson ◽  
Monica N Opiyo ◽  
Marian Thomson ◽  
Karim Gharbi ◽  
Jonathan R Seckl ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Gut Microbiome ◽  
Inflammatory Responses ◽  
Hydroxysteroid Dehydrogenase ◽  
Western Diet ◽  
Metabolic Effects ◽  
Chow Diet ◽  
The Family ◽  
The Impact

The enzyme 11β-hydroxysteroid dehydrogenase (11β-HSD) interconverts active glucocorticoids and their intrinsically inert 11-keto forms. The type 1 isozyme, 11β-HSD1, predominantly reactivates glucocorticoids in vivo and can also metabolise bile acids. 11β-HSD1-deficient mice show altered inflammatory responses and are protected against the adverse metabolic effects of a high-fat diet. However, the impact of 11β-HSD1 on the composition of the gut microbiome has not previously been investigated. We used high-throughput 16S rDNA amplicon sequencing to characterise the gut microbiome of 11β-HSD1-deficient and C57Bl/6 control mice, fed either a standard chow diet or a cholesterol- and fat-enriched ‘Western’ diet. 11β-HSD1 deficiency significantly altered the composition of the gut microbiome, and did so in a diet-specific manner. On a Western diet, 11β-HSD1 deficiency increased the relative abundance of the family Bacteroidaceae, and on a chow diet, it altered relative abundance of the family Prevotellaceae. Our results demonstrate that (i) genetic effects on host–microbiome interactions can depend upon diet and (ii) that alterations in the composition of the gut microbiome may contribute to the aspects of the metabolic and/or inflammatory phenotype observed with 11β-HSD1 deficiency.

scholarly journals A Tree of Human Gut Bacterial Species and its Applications to Metagenomics and Metaproteomics Data Analysis

2020 ◽  
Author(s):  
Moses Stamboulian ◽  
Thomas G. Doak ◽  
Yuzhen Ye
Keyword(s):  
Gut Microbiome ◽  
Phylogenetic Trees ◽  
Bacterial Species ◽  
Taxonomic Composition ◽  
Marker Genes ◽  
Missing Information ◽  
Human Gut ◽  
Taxonomic Profiling ◽  
Tree Building ◽  
The Impact

Abstract1BackgroundRecent advances in genome and metagenome sequencing have dramatically enriched the collection of genomes of bacterial species related to human health and diseases. In metagenomic studies phylogenetic trees are commonly used to depict, describe, and compare the bacterial members of the community under study. The most accurate tree-building algorithms now use large sets of marker genes taken from across genomes. However, many of the current bacterial genomes were assembled from metagenomic datasets (i.e., metagenome assembled genomes, MAGs), and often contain missing information. It is therefore important to study how well the phylogeny approach performs on such genomes. Further, phylogeny methods are not perfect and it is important to know how reliable an inferred tree is.ResultsHere we examined the impact of incompleteness of the genomes on the tree reconstruction, and we showed that phylogeny approaches including RAxML (which handles missing data explicitly) and FastTree generally performed well on simulated collection of 400 genomes with missing information. As RAxML is computationally prohibitive for the much larger collections of gut genomes, we chose FastTree to build a unified tree of human-gut associated bacterial species (referred to as gut tree), including more than 3000 genomes, most of which are incomplete. We developed two downstream applications of the gut tree: peptide-centric analysis of metaproteomics datasets; and taxonomic characterization of metagenomic sequences. In both applications, the gut tree provided the basis for quantification of species composition at various taxonomic resolutions.ConclusionsThe gut tree presented in this study provides a useful framework for taxonomic profiling of human gut microbiome. Including MAGs in the tree provides more comprehensive representation of microbial species diversity associated with human gut, important for studying the taxonomic composition of gut microbiome.Availability and ImplementationThe tree construction pipeline and downstream applications of the gut tree are freely available at https://github.com/mgtools/guttree.

scholarly journals Lacticaseibacillus rhamnosus GG and Saccharomyces cerevisiae boulardii supplementation exert protective effects on human gut microbiome following antibiotic administration in vitro

2021 ◽  
pp. 1-16
Author(s):  
C. Duysburgh ◽  
P. Van den Abbeele ◽  
M. Morera ◽  
M. Marzorati
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Gut Microbiome ◽  
Gastrointestinal Symptoms ◽  
Lactobacillus Rhamnosus ◽  
Antibiotic Administration ◽  
Protective Effects ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
The Impact

Antibiotic-induced dysbiosis of the microbial community has been associated with several gastrointestinal symptoms. The impact of repeated administration of Lacticaseibacillus rhamnosus GG (CNCM-I-4798) (formerly known as Lactobacillus rhamnosus GG), Saccharomyces cerevisiae boulardii (CNCM-I-1079) and their combination (associated in Smebiocta/Smectaflora Protect®) in supporting recovery of gut microbiota functionality and composition during and following amoxicillin:clavulanic acid administration was evaluated in vitro. Antibiotic dosage negatively affected SCFA production, coinciding with detrimental effects on Bacteroidetes, Firmicutes and Bifidobacterium spp. in the simulated proximal colon, while Akkermansia muciniphila was significantly reduced in the distal colon. L. rhamnosus GG and S. boulardii were able to thrive in both colon regions upon dosing, with S. boulardii even showing protective effects on the survival of L. rhamnosus GG during antibiotic administration. The impact of the probiotic strains on microbiome recovery revealed that supplementation with L. rhamnosus GG and/or S. boulardii resulted in a stimulating effect on the most abundant bacterial groups within the bacterial community of each donor. For one of the donors tested, co-dosing of L. rhamnosus GG and S. boulardii resulted in superior short-chain fatty acid recovery accompanied by a stronger increase in abundance of Bifidobacteriaceae. Overall, the current study provides first evidence that combined supplementation of L. rhamnosus GG and S. boulardii might be an interesting candidate in limiting detrimental effects of amoxicillin:clavulanic acid on the human gut microbiome, though further studies are warranted to confirm these findings.

scholarly journals Stable Engraftment of a Human Gut Bacterial Microbiome in Double Humanized BLT-mice

2019 ◽  
Author(s):  
Lance Daharsh ◽  
Amanda E. Ramer-Tait ◽  
Qingsheng Li
Keyword(s):  
Immune System ◽  
Gut Microbiome ◽  
Human Disease ◽  
Humanized Mice ◽  
Rrna Gene ◽  
Human Immune System ◽  
Human Gut ◽  
Healthy Human ◽  
Human Immune

AbstractBackgroundHumanized mice featuring a functional human immune system are an important pre-clinical model for examining immune responses to human-specific pathogens. This model has been widely utilized to study human diseases that are otherwise impossible or difficult to investigate in humans or with other animal models. However, one limitation of using humanized mice is their native murine gut microbiome, which significantly differs from the one found in humans. These differences may be even greater for mice housed and bred in specific pathogen free conditions. Given the importance of the gut microbiome to human health and disease, these differences may profoundly impact the ability to translate the results from humanized mice studies to human disease. Further, there is a critical need for improved pre-clinical models to study the complex in vivo relationships of the gut microbiome, immune system, and human disease. We therefore created double humanized mice with both a functional human immune system and stable human-like gut microbiome.ResultsSurgery was performed on NOD.Cg-PrkdcscidII2rgtm1Wjl/SzJ (NSG) mice to create bone-marrow, liver, thymus (BLT) humanized mice. After immune reconstitution, mice were treated with broad spectrum antibiotics to deplete murine gut bacteria and then transplanted with fecal material from healthy human donors. Characterization of 173 fecal samples obtained from 45 humanized mice revealed that double humanized mice had unique 16S rRNA gene profiles consistent with those of the individual human donor samples. Importantly, transplanted human-like gut microbiomes were stable in mice for the duration of the study, up to 14.5 weeks post-transplant. Microbiomes of double humanized mice also harbored predicted functional capacities that more closely resembled those of the human donors compared to humanized mice.ConclusionsHere, we describe successful engraftment of a stable human microbiome in BLT humanized mice to further improve this preclinical humanized mouse model. These double humanized mice represent a unique and tractable new model to study the complex relationships between the human gut microbiome, human immune system, and human disease in vivo.

scholarly journals Vertical Transmission of Gut Microbiome and Antimicrobial Resistance Genes in Infants Exposed to Antibiotics at Birth

2020 ◽  
Author(s):  
Weizhong Li ◽  
Terhi Tapiainen ◽  
Lauren Brinkac ◽  
Hernan A Lorenzi ◽  
Kelvin Moncera ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Vertical Transmission ◽  
Gut Microbiome ◽  
Treated Group ◽  
Control Group ◽  
Gut Colonization ◽  
Antimicrobial Resistance Genes ◽  
Major Route ◽  
Group 10 ◽  
The Impact

Abstract Vertical transmission of maternal microbes is a major route for establishing the gut microbiome in newborns. The impact of perinatal antibiotics on vertical transmission of microbes and antimicrobial resistance is not well understood. Using a metagenomic approach, we analyzed the fecal samples from mothers and vaginally delivered infants from a control group (10 pairs) and a treatment group (10 pairs) receiving perinatal antibiotics. Antibiotic-usage had a significant impact on the main source of inoculum in the gut microbiome of newborns. The control group had significantly more species transmitted from mothers to infants (P = .03) than the antibiotic-treated group. Approximately 72% of the gut microbial population of infants at 3–7 days after birth in the control group was transmitted from their mothers, versus only 25% in the antibiotic-treated group. In conclusion, perinatal antibiotics markedly disturbed vertical transmission and changed the source of gut colonization towards horizontal transfer from the environment to the infants.

scholarly journals Novel approaches for analysing gut microbes and dietary polyphenols: challenges and opportunities

Microbiology ◽  
2010 ◽  
Vol 156 (11) ◽  
pp. 3224-3231 ◽  
Author(s):  
R. A. Kemperman ◽  
S. Bolca ◽  
L. C. Roger ◽  
E. E. Vaughan
Keyword(s):  
Gut Microbiota ◽  
Health Effects ◽  
Fruit And Vegetables ◽  
Human Gut ◽  
Microbial Composition ◽  
Dietary Polyphenols ◽  
Host Health ◽  
The Impact

Polyphenols, ubiquitously present in the food we consume, may modify the gut microbial composition and/or activity, and moreover, may be converted by the colonic microbiota to bioactive compounds that influence host health. The polyphenol content of fruit and vegetables and derived products is implicated in some of the health benefits bestowed on eating fruit and vegetables. Elucidating the mechanisms behind polyphenol metabolism is an important step in understanding their health effects. Yet, this is no trivial assignment due to the diversity encountered in both polyphenols and the gut microbial composition, which is further confounded by the interactions with the host. Only a limited number of studies have investigated the impact of dietary polyphenols on the complex human gut microbiota and these were mainly focused on single polyphenol molecules and selected bacterial populations. Our knowledge of gut microbial genes and pathways for polyphenol bioconversion and interactions is poor. Application of specific in vitro or in vivo models mimicking the human gut environment is required to analyse these diverse interactions. A particular benefit can now be gained from next-generation analytical tools such as metagenomics and metatranscriptomics allowing a wider, more holistic approach to the analysis of polyphenol metabolism. Understanding the polyphenol–gut microbiota interactions and gut microbial bioconversion capacity will facilitate studies on bioavailability of polyphenols in the host, provide more insight into the health effects of polyphenols and potentially open avenues for modulation of polyphenol bioactivity for host health.

THE IMPACT OF ORALLY ADMINISTERED ANTIBIOTICS ON HUMAN GUT COLONIZATION BY CANDIDA ALBICANS

Mycoses ◽  
2002 ◽  
Vol 45 (S2) ◽  
pp. 37-37
Author(s):  
S. Maraki ◽  
E. Mavromanolakis ◽  
M. Dialynas ◽  
S. Kavvalos ◽  
G. Samonis ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Human Gut ◽  
Gut Colonization ◽  
The Impact

scholarly journals Metagenomics Reveals Impact of Urbanisation in Central India on the Human Gut Microbiome and its Antimicrobial Resistance Profiles

2019 ◽  
Author(s):  
Tanya Monaghan ◽  
Tim J. Sloan ◽  
Stephen R. Stockdale ◽  
Adam M. Blanchard ◽  
Richard D. Emes ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Gut Microbiome ◽  
Human Gut ◽  
Metabolic Potential ◽  
Urban Populations ◽  
Human Gut Microbiome ◽  
Rural And Urban ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
The Impact

Abstract Background The impact of the rapid urbanisation of low- and middle-income countries on the human gut microbiome remains grossly understudied. Whilst the effect of urbanisation on the bacterial populations of the human gut microbiome have been documented, little is known about the influence of diet and antibiotics on the bacteriome, its virome, and antibiotic resistome. Here, we use shotgun metagenomics to comprehensively characterise the bacterial and viral fractions of the human gut microbiome, and their encoded functions, from two divergent Central Indian populations (rural agriculturalists from Melghat and an urban population in Nagpur). Additionally, we investigate cohorts with and without diarrhoea, and the potential burden of Clostridioides difficile, associated with widespread unregulated use of antibiotics in India. Results We observed distinct rural-urban differences in the gut microbiome, including viral diversity and composition, with geography exhibiting a greater influence than diarrhoeal status. Urban microbiomes were enriched in metabolic pathways responsible for degradation of drugs and organic compounds, which were predicted to relate to replacement of rural-enriched Prevotella spp. and fermentative Clostridiales with Enterobacteriaceae and Bacteroides spp. By linking phages present in the microbiome to their bacterial hosts through CRISPR spacers, a shift from Prevotella- and Eubacterium-infecting phages to Bacteroides- and Parabacteroides-infecting phages was observed in rural and urban populations, respectively. Additionally, the auxiliary metabolic potential of rural-associated phage populations was enriched for carbon and amino acid energy harvesting potential, compared to urban-associated phages. A core set of antimicrobial resistance genes was identified in both populations, particularly those conferring resistance to macrolides, tetracyclines and 1stgeneration cephalosporins, with the majority also showing evidence of resistance to fluoroquinolones, aminoglycosides and sulphonamides. In a subgroup of urban subjects with diarrhoea and high antibiotic exposure, most of whom tested positive for C. difficile toxin, evidence of resistance to fosfomycin, glycopeptides, daptomycin, 3rd generation cephalosporins and carbapenems was widespread. Conclusions We report distinct differences in antimicrobial resistance gene profiles as well as a marked variation in the burden of C. difficile disease between rural and urban populations. The key drivers of variation in urban and rural Indian microbiomes are geography, diet, industrial and healthcare exposures.

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.

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