scholarly journals Impact of demographics on human gut microbial diversity in a US Midwest population

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1514 ◽  
Author(s):  
Jun Chen ◽  
Euijung Ryu ◽  
Matthew Hathcock ◽  
Karla Ballman ◽  
Nicholas Chia ◽  
...  
Keyword(s):  
Alcohol Use ◽  
Gut Microbiota ◽  
Effect Sizes ◽  
Human Gut ◽  
Related Factors ◽  
Β Diversity ◽  
Α Diversity ◽  
Unweighted Unifrac ◽  
Us Midwest ◽  
Comparative Results

The clinical utility of microbiome biomarkers depends on the reliable and reproducible nature of comparative results. Underappreciation of the variation associated with common demographic, health, and behavioral factors may confound associations of interest and generate false positives. Here, we present the Midwestern Reference Panel (MWRP), a resource for comparative gut microbiome studies conducted in the Midwestern United States. We analyzed the relationships between demographic and health behavior-related factors and the microbiota in this cohort, and estimated their effect sizes. Most variables investigated were associated with the gut microbiota. Specifically, body mass index (BMI), race, sex, and alcohol use were significantly associated with microbial β-diversity (P < 0.05, unweighted UniFrac). BMI, race and alcohol use were also significantly associated with microbial α-diversity (P < 0.05, species richness). Tobacco use showed a trend toward association with the microbiota (P < 0.1, unweighted UniFrac). The effect sizes of the associations, as quantified by adjusted R2values based on unweighted UniFrac distances, were small (< 1% for all variables), indicating that these factors explain only a small percentage of overall microbiota variability. Nevertheless, the significant associations between these variables and the gut microbiota suggest that they could still be potential confounders in comparative studies and that controlling for these variables in study design, which is the main objective of the MWRP, is important for increasing reproducibility in comparative microbiome studies.

scholarly journals Impact of demographics on human gut microbial diversity in a US Midwest population

2015 ◽  
Author(s):  
Jun Chen ◽  
Euijung Ryu ◽  
Matthew Hathcock ◽  
Karla Ballman ◽  
Nicholas Chia ◽  
...  
Keyword(s):  
Alcohol Use ◽  
Gut Microbiota ◽  
Effect Sizes ◽  
Human Gut ◽  
Related Factors ◽  
Β Diversity ◽  
Α Diversity ◽  
Unweighted Unifrac ◽  
Us Midwest ◽  
Comparative Results

The clinical utility of microbiome biomarkers depends on the reliable and reproducible nature of comparative results. Underappreciation of the variation associated with common demographic, health, and behavioral factors may confound associations of interest and generate false positives. Here, we present the Midwestern Reference Panel (MWRP), a resource for comparative gut microbiome studies conducted in the Midwestern United States. We analyzed the relationships between demographic and health behavior–related factors and the microbiota in this cohort, and estimated their effect sizes. Most variables investigated were associated with the gut microbiota. Specifically, body mass index (BMI), race, sex, and alcohol use were significantly associated with microbial β-diversity (P < 0.05, unweighted UniFrac). BMI, race and alcohol use were also significantly associated with microbial α-diversity (P < 0.05, species richness). Tobacco use showed a trend toward association with the microbiota (P < 0.1, unweighted UniFrac). The effect sizes of the associations, as quantified by adjusted R2 values based on unweighted UniFrac distances, were small (< 1% for all variables), indicating that these factors explain only a small percentage of overall microbiota variability. Nevertheless, the significant associations between these variables and the gut microbiota suggest that they could still be potential confounders in comparative studies and that controlling for these variables in study design, which is the main objective of the MWRP, is important for increasing reproducibility in comparative microbiome studies.

scholarly journals Impact of demographics on human gut microbial diversity in a US Midwest population

2015 ◽  
Author(s):  
Jun Chen ◽  
Euijung Ryu ◽  
Matthew Hathcock ◽  
Karla Ballman ◽  
Nicholas Chia ◽  
...  
Keyword(s):  
Alcohol Use ◽  
Gut Microbiota ◽  
Effect Sizes ◽  
Human Gut ◽  
Related Factors ◽  
Β Diversity ◽  
Α Diversity ◽  
Unweighted Unifrac ◽  
Us Midwest ◽  
Comparative Results

The clinical utility of microbiome biomarkers depends on the reliable and reproducible nature of comparative results. Underappreciation of the variation associated with common demographic, health, and behavioral factors may confound associations of interest and generate false positives. Here, we present the Midwestern Reference Panel (MWRP), a resource for comparative gut microbiome studies conducted in the Midwestern United States. We analyzed the relationships between demographic and health behavior–related factors and the microbiota in this cohort, and estimated their effect sizes. Most variables investigated were associated with the gut microbiota. Specifically, body mass index (BMI), race, sex, and alcohol use were significantly associated with microbial β-diversity (P < 0.05, unweighted UniFrac). BMI, race and alcohol use were also significantly associated with microbial α-diversity (P < 0.05, species richness). Tobacco use showed a trend toward association with the microbiota (P < 0.1, unweighted UniFrac). The effect sizes of the associations, as quantified by adjusted R2 values based on unweighted UniFrac distances, were small (< 1% for all variables), indicating that these factors explain only a small percentage of overall microbiota variability. Nevertheless, the significant associations between these variables and the gut microbiota suggest that they could still be potential confounders in comparative studies and that controlling for these variables in study design, which is the main objective of the MWRP, is important for increasing reproducibility in comparative microbiome studies.

Association of subjective global assessment of nutritional status with gut microbiota in hemodialysis patients: a case–control study

2020 ◽  
Author(s):  
Ting-Yun Lin ◽  
Szu-Chun Hung
Keyword(s):  
Nutritional Status ◽  
Gut Microbiota ◽  
Global Assessment ◽  
Hemodialysis Patients ◽  
Adverse Outcomes ◽  
Subjective Global Assessment ◽  
Protein Energy Wasting ◽  
Β Diversity ◽  
Protein Energy ◽  
Α Diversity

Abstract Background Protein-energy wasting (PEW) is prevalent and associated with adverse outcomes in patients with chronic kidney disease (CKD). However, the pathogenesis of PEW in CKD patients has not been fully identified. The gut microbiota has been implicated in the regulation of host metabolism and energy balance. Therefore, we aimed to explore the association between nutritional status and the composition of the gut microbiota in hemodialysis patients. Methods Gut microbial diversity and taxonomy were examined in 88 hemodialysis patients with PEW (n = 22) and normal nutritional status (n = 66) who were matched 1:3 for age and sex. Nutritional status was assessed by using the 7-point subjective global assessment (SGA) score (1–3 = severe PEW; 4–5 = moderate PEW and 6–7 = normal nutrition). The gut microbiota was assessed by 16S ribosomal RNA gene sequencing. Results Patients with normal nutritional status had a significantly higher body mass index and physical activity and serum albumin levels, but significantly lower levels of inflammatory cytokines than patients with PEW. The most striking finding was that the α-diversity of the gut microbiota was significantly lower in patients with PEW. In a multivariate analysis, the SGA score was independently and positively associated with α-diversity (P = 0.049). Patients with or without PEW were different with respect to the principal coordinate analysis of β-diversity. Notably, the relative abundance of Faecalibacterium prausnitzii, a butyrate-producing bacteria, was markedly reduced in patients with PEW. Conclusion In hemodialysis patients, PEW assessed with the SGA was associated with gut dysbiosis.

Ongoing Supplementation of Probiotics to Cesarean-Born Neonates during the First Month of Life may Impact the Gut Microbial

2020 ◽  
Author(s):  
Wenqing Yang ◽  
Liang Tian ◽  
Jiao Luo ◽  
Jialin Yu
Keyword(s):  
Gut Microbiota ◽  
Intestinal Microbiota ◽  
Influencing Factor ◽  
Delivery Mode ◽  
Next Generation Sequencing Technology ◽  
Operational Taxonomic Units ◽  
Β Diversity ◽  
Α Diversity ◽  
Clusters Of Orthologous Groups ◽  
And Function

Objective The delivery mode is considered to be a significant influencing factor in the early gut microbiota composition, which is associated with the long-term health of the host. In this study, we tried to explore the effects of probiotics on the intestinal microbiota of C-section neonates. Study Design Twenty-six Chinese neonates were enrolled in this study. The neonates were divided into four groups: VD (natural delivery neonates, n = 3), CD (cesarean-born neonates, n = 9), CDL (cesarean-born neonates supplemented with probiotic at a lower dosage, n = 7), and CDH (cesarean-born neonates supplemented with probiotic at a higher dosage, n = 7). Fecal samples were collected on the 3rd, 7th, and 28th day since birth. The V3–V4 region of the 16S ribosomal ribonucleic acid gene was sequenced by next-generation sequencing technology. Results The α-diversity of the intestinal microbiota of cesarean delivery neonates was significantly lower than that of the naturally delivered neonates on the 28th day (p = 0.005). After supplementation with probiotics for 28 days, the α-diversity and the β-diversity of the gut flora in the cesarean-born infants (CDL28 and CDH28) was similar to that in the vaginally delivery infants. Meanwhile, the abundances of Lactobacillus and Bifidobacterium were significantly increased since the 3rd day of probiotic supplementation. Besides, the sustained supplementation of probiotics to neonates would help improve the abundance of the operational taxonomic units in several different Clusters of Orthologous Groups of proteins. Conclusion This study showed that probiotics supplementation to cesarean-born neonates since birth might impact the diversity and function of gut microbiota. Key Points

scholarly journals A game theory model for gut bacterial nutrient utilization strategies during human infancy

2020 ◽  
Vol 287 (1931) ◽  
pp. 20200824 ◽  
Author(s):  
Inga Leena Angell ◽  
Knut Rudi
Keyword(s):  
Game Theory ◽  
Gut Microbiota ◽  
Nutrient Utilization ◽  
Theory Model ◽  
Ecological Processes ◽  
Β Diversity ◽  
Gut Colonization ◽  
Α Diversity ◽  
Colonization Patterns ◽  
Expanding Population

Despite the fact that infant gut colonization patterns have been extensively studied, we have limited knowledge about the underlying ecological processes. This particularly relates to the ecological choice of nutrient utilization strategies. The aim of the current study was therefore to compare empirically determined nutrient utilization strategies with that expected from a combinatorial game theory model. Observational analyses for 100 mother–child pairs suggested mother–child transmission of specialists with the potential to use few nutrients. Generalists, on the other hand, with the potential to use many nutrients, peaked at three months of age for the children. The level of generalists was gradually replaced with specialists up to 12 months of age. Game theory simulation revealed a competitive advantage of generalists in an expanding population, while more specialized bacteria were favoured with the maturation of the population. This suggests that the observed increase in generalists in the three-month-old children could be due to an immature, expanding gut microbiota population while the increase of specialists at 12 months could be due to population maturation. The simulated and empirical data also correspond with respect to an increased α diversity and a decreased β diversity with the number of simulations and age, respectively. Taken together, game theory simulation of nutrient utilization strategies can therefore provide novel insight into the maturation of the human gut microbiota during infancy.

scholarly journals The gut microbiota of rural and urban individuals is shaped by geography and lifestyle

2020 ◽  
Author(s):  
Mubanga Kabwe ◽  
Surendra Vikram ◽  
Khodani Mulaudzi ◽  
Janet Jansson ◽  
Thulani Makhalyane
Keyword(s):  
Gut Microbiota ◽  
Smoking Status ◽  
Geographic Location ◽  
Size Analysis ◽  
Human Gut ◽  
Related Factors ◽  
Linear Discriminant ◽  
Knowledge Deficit ◽  
Rural And Urban ◽  
Species Specific

Abstract Background Understanding the structure and drivers of gut microbiota remains a major ecological endeavour. Recent studies have shown that several factors including diet, lifestyle and geography may substantially shape the human gut microbiota. However, most of these studies have focused on the more abundant bacterial component and comparatively less is known regarding fungi in the human gut. This knowledge deficit is especially true for rural and urban African populations. Therefore, we assessed the structure and drivers of rural and urban gut mycobiota. Results Our participants (n=100) were balanced by geography and sex. The mycobiota of these geographically separated cohorts was characterized using amplicon analysis of the Internal Transcribed Spacer (ITS) gene. We further assessed biomarker species specific to rural and urban cohorts. In addition to phyla which have been shown to be ubiquitous constituents of gut microbiota, Pichia were key constituents of the mycobiota. We found that several factors including geographic location and lifestyle factors such as the smoking status were major drivers of gut mycobiota. Linear discriminant and the linear discriminant analysis effect size analysis revealed several distinct urban and rural biomarkers. Conclusions Together, our analysis reveals distinct community structure in urban and rural South African individuals. Geography and lifestyle related factors were shown to be key drivers of rural and urban gut microbiota.

scholarly journals Gut Microbiota Profile in Pediatric Patients With Inflammatory Bowel Disease: A Systematic Review

2021 ◽  
Vol 9 ◽  
Author(s):  
Xiaojun Zhuang ◽  
Caiguang Liu ◽  
Shukai Zhan ◽  
Zhenyi Tian ◽  
Na Li ◽  
...  
Keyword(s):  
Systematic Review ◽  
Inflammatory Bowel Disease ◽  
Gut Microbiota ◽  
Bowel Disease ◽  
Pediatric Patients ◽  
Β Diversity ◽  
Α Diversity ◽  
Treatment Naïve ◽  
Inflammatory Bowel ◽  
Pediatric Ibd

Background and Aim: Accumulating evidence have implicated gut microbiota alterations in pediatric and adult patients with inflammatory bowel disease (IBD); however, the results of different studies are often inconsistent and even contradictory. It is believed that early changes in new-onset and treatment-naïve pediatric patients are more informative. We performed a systematic review to investigate the gut microbiota profiles in pediatric IBD and identify specific microbiota biomarkers associated with this disorder.Methods: Electronic databases were searched from inception to 31 July 2020 for studies that observed gut microbiota alterations in pediatric patients with IBD. Study quality was assessed using the Newcastle–Ottawa scale.Results: A total of 41 original studies investigating gut microbiota profiles in pediatric patients with IBD were included in this review. Several studies have reported a decrease in α-diversity and an overall difference in β-diversity. Although no specific gut microbiota alterations were consistently reported, a gain in Enterococcus and a significant decrease in Anaerostipes, Blautia, Coprococcus, Faecalibacterium, Roseburia, Ruminococcus, and Lachnospira were found in the majority of the included articles. Moreover, there is insufficient data to show specific microbiota bacteria associated with disease activity, location, and behavior in pediatric IBD.Conclusions: This systematic review identified evidence for differences in the abundance of some bacteria in pediatric patients with IBD when compared to patients without IBD; however, no clear overall conclusion could be drawn from the included studies due to inconsistent results and heterogeneous methodologies. Further studies with large samples that follow more rigorous and standardized methodologies are needed.

scholarly journals α- and β-Diversity Patterns of Macrophytes and Freshwater Fishes are Driven by Different Factors and Processes in Lakes of the Unexplored Southern Balkan Biodiversity Hotspot

Water ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 1984
Author(s):  
Anthi Oikonomou ◽  
Konstantinos Stefanidis
Keyword(s):  
Species Richness ◽  
Species Turnover ◽  
Biodiversity Hotspot ◽  
Environmental Drivers ◽  
Conservation Strategies ◽  
Compositional Variation ◽  
Related Factors ◽  
Diversity Patterns ◽  
Β Diversity ◽  
Α Diversity

Disentangling the main drivers of species richness and community composition is a central theme in ecology. Freshwater biodiversity patterns have been poorly explored; yet, it has been shown that different freshwater biota have different, often contrasting responses to environmental gradients. In this study, we investigated the relative contribution of geographical and environmental (habitat-, climate- and water quality-related) factors/gradients in shaping the α- and β-diversity patterns of macrophytes and fish in sixteen natural freshwater lakes of an unexplored Balkan biodiversity hotspot, the Southern Balkan Peninsula. We employed generalized linear modeling to identify drivers of α-diversity, and generalized dissimilarity modeling to explore commonalities and dissimilarities of among-biota β-diversity. Species richness of both biota was significantly associated with lake surface area, whereas macrophytes had an inverse response to altitude, compared to fish. Both species turnover and nestedness significantly contributed to the total β-diversity of macrophytes. In contrast, species turnover was the most significant contributor to the total fish β-diversity. We found that the compositional variation of macrophytes is primarily limited by dispersal and ultimately shaped by environmental drivers, resulting in spatially structured assemblages. Fish communities were primarily shaped by altitude, highlighting the role of species sorting. We conclude that among-biota diversity patterns are shaped by different/contrasting factors, and, thus, effective/sustainable conservation strategies should encompass multiple aquatic biota.

Effect of Housing Condition and Diet on the Gut Microbiota of Weanling Immunocompromised Mice

2021 ◽  
Author(s):  
Colleen E Thurman ◽  
Molly M Klores ◽  
Annie E Wolfe ◽  
William T Poueymirou ◽  
Ellen M Levee ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Standard Diet ◽  
Gastrointestinal Microbiota ◽  
Housing Type ◽  
Gastrointestinal Microbiome ◽  
Intrinsic Factors ◽  
Β Diversity ◽  
Α Diversity ◽  
Immunocompromised Mice ◽  
Extrinsic And Intrinsic Factors

Gastrointestinal microbiota are affected by a wide variety of extrinsic and intrinsic factors. In the husbandry of laboratorymice and design of experiments, controlling these factors where possible provides more reproducible results. However, themicrobiome is dynamic, particularly in the weeks immediately after weaning. In this study, we characterized the baselinegastrointestinal microbiota of immunocompromised mice housed under standard conditions for our facility for 6 weeks afterweaning, with housing either in an isolator or in individually ventilated cages and a common antibiotic diet (trimethoprimsulfamethoxazole). We compared these conditions to a group fed a standard diet and a group that was weaned to a standard diet then switched to antibiotic diet after 2 weeks. We found no clear effect of diet on richness and α diversity of the gastrointestinal microbiota. However, diet did affect which taxa were enriched at the end of the experiment. The change to antibiotic diet during the experiment did not convert the gastrointestinal microbiome to a state similar to mice consistently fed antibiotic diet, which may highlight the importance of the initial post-weaning period in the establishment of the gastrointestinal microbiome. We also observed a strong effect of housing type (isolator compared with individually ventilated cage) on the richness, α diversity, β diversity, and taxa enriched over the course of the experiment. Investigating whether the diet or microbiome affects a certain strain’s phenotype is warranted in some cases. However, our findings do not suggest that maintaining immunocompromised mice on antibiotic feed has a clinical benefit when potential pathogens are operationally excluded, nor does it result in a more consistent or controlled microbiome in the post-weaning period.

scholarly journals Impact of Vitamin D Deficit on the Rat Gut Microbiome

Nutrients ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 2564 ◽  
Author(s):  
Iñaki Robles-Vera ◽  
María Callejo ◽  
Ricardo Ramos ◽  
Juan Duarte ◽  
Francisco Perez-Vizcaino
Keyword(s):  
Vitamin D ◽  
Gut Microbiota ◽  
Vitamin D Deficiency ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
Gut Dysbiosis ◽  
Β Diversity ◽  
Α Diversity ◽  
Rat Gut

Inadequate immunologic, metabolic and cardiovascular homeostasis has been related to either an alteration of the gut microbiota or to vitamin D deficiency. We analyzed whether vitamin D deficiency alters rat gut microbiota. Male Wistar rats were fed a standard or a vitamin D-free diet for seven weeks. The microbiome composition was determined in fecal samples by 16S rRNA gene sequencing. The vitamin D-free diet produced mild changes on α- diversity but no effect on β-diversity in the global microbiome. Markers of gut dysbiosis like Firmicutes-to-Bacteroidetes ratio or the short chain fatty acid producing bacterial genera were not significantly affected by vitamin D deficiency. Notably, there was an increase in the relative abundance of the Enterobacteriaceae, with significant rises in its associated genera Escherichia, Candidatus blochmannia and Enterobacter in vitamin D deficient rats. Prevotella and Actinomyces were also increased and Odoribacteraceae and its genus Butyricimonas were decreased in rats with vitamin D-free diet. In conclusion, vitamin D deficit does not induce gut dysbiosis but produces some specific changes in bacterial taxa, which may play a pathophysiological role in the immunologic dysregulation associated with this hypovitaminosis.

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