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

2020 ◽  
Author(s):  
Mubanga Hellen Kabwe ◽  
Surendra Vikram ◽  
Khodani Mulaudzi ◽  
Janet K. Jansson ◽  
Thulani P. Makhalanyane
Keyword(s):  
Gut Microbiota ◽  
Smoking Status ◽  
Geographic Location ◽  
Lifestyle Factors ◽  
Size Analysis ◽  
Human Gut ◽  
Related Factors ◽  
Linear Discriminant ◽  
Rural And Urban ◽  
Species Specific

AbstractUnderstanding 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. 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. 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.ImportanceThe past decade has revealed substantial insights regarding the ecological patterns of gut microbiomes. These studies have shown clear differences between the microbiomes of individuals living in urban and rural locations. Yet, in contrast to bacteria we know substantially less regarding the fungal gut microbiota (mycobiome). Here we provide the first insights regarding the mycobiome of individuals from urban and rural locations. We show that these communities are geographically structured. Further we show that lifestyle factors, such as diet and smoking, are strong drivers explaining community variability.

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

2020 ◽  
Author(s):  
Mubanga Kabwe ◽  
Surendra Vikram ◽  
Khodani Mulaudzi ◽  
Janet Jansson ◽  
Thulani Makhalyane
Keyword(s):  
Gut Microbiota ◽  
South African ◽  
Geographic Location ◽  
Size Analysis ◽  
Human Gut ◽  
Linear Discriminant ◽  
Knowledge Deficit ◽  
Rural And Urban ◽  
Its Gene ◽  
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 geographic location was a major driver of gut mycobiota. Other factors such as smoking where also determined gut mycobiota albeit to a lower extent, as explained by the small proportion of total variation. 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 was shown to be a key driver of rural and urban gut mycobiota.

scholarly journals Predictable and host-species specific humanization of the gut microbiota in captive primates

2021 ◽  
Author(s):  
Jennifer Houtz ◽  
Jon Sanders ◽  
Anthony Denice ◽  
Andrew Moeller
Keyword(s):  
Gut Microbiota ◽  
Host Species ◽  
Rrna Gene ◽  
Gene Variants ◽  
Gastrointestinal Dysfunction ◽  
Human Gut ◽  
Captive Populations ◽  
In Captivity ◽  
Species Specific ◽  
Bacterial 16S Rrna Gene

Humans and non-human primates (NHPs) harbor complex gut microbial communities that affect phenotypes and fitness. The gut microbiotas of wild NHPs reflect their hosts’ phylogenetic histories and are compositionally distinct from those of humans, but in captivity the endogenous gut microbial lineages of NHPs can be lost or replaced by lineages found in humans. Despite its potential contributions to gastrointestinal dysfunction, this humanization of the gut microbiota has not been investigated systematically across captive NHP species. Here we show through comparisons of well-sampled wild and captive populations of apes and monkeys that the fraction of the gut microbiota humanized by captivity varies significantly between NHP species but is remarkably reproducible between captive populations of the same NHP species. Conspecific captive populations displayed significantly greater than expected overlap in the sets of bacterial 16S rRNA gene variants that were differentially abundant between captivity and the wild. This overlap was evident even between captive populations residing on different continents but was never observed between heterospecific captive populations. In addition, we developed an approach incorporating human gut microbiota data to rank NHPs’ gut microbial clades based on the propensity of their lineages to be lost or replaced by lineages found in humans in captivity. Relatively few microbial genera displayed reproducible degrees of humanization in different captive host species, but most microbial genera were reproducibly humanized or retained from the wild in conspecific pairs of captive populations. These results demonstrate that the gut microbiotas of captive NHPs display predictable, host-species specific responses to captivity.

scholarly journals Dissecting the collateral damage of antibiotics on gut microbes

2020 ◽  
Author(s):  
Lisa Maier ◽  
Camille V. Goemans ◽  
Mihaela Pruteanu ◽  
Jakob Wirbel ◽  
Michael Kuhn ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Bacteria ◽  
Commensal Bacteria ◽  
Strong Impact ◽  
Collateral Damage ◽  
Microbiota Composition ◽  
Human Gut ◽  
Gut Microbes ◽  
Species Specific ◽  
Gut Microbiota Composition

AbstractAntibiotics are used for fighting pathogens, but also target our commensal bacteria as a side effect, disturbing the gut microbiota composition and causing dysbiosis and disease1-3. Despite this well-known collateral damage, the activity spectrum of the different antibiotic classes on gut bacteria remains poorly characterized. Having monitored the activities of >1,000 marketed drugs on 38 representative species of the healthy human gut microbiome4, we here characterize further the 144 antibiotics therein, representing all major classes. We determined >800 Minimal Inhibitory Concentrations (MICs) and extended the antibiotic profiling to 10 additional species to validate these results and link to available data on antibiotic breakpoints for gut microbes. Antibiotic classes exhibited distinct inhibition spectra, including generation-dependent effects by quinolones and phylogeny-independence by β-lactams. Macrolides and tetracyclines, two prototypic classes of bacteriostatic protein synthesis inhibitors, inhibited almost all commensals tested. We established that both kill different subsets of prevalent commensal bacteria, and cause cell lysis in specific cases. This species-specific activity challenges the long-standing divide of antibiotics into bactericidal and bacteriostatic, and provides a possible explanation for the strong impact of macrolides on the gut microbiota composition in animals5-8 and humans9-11. To mitigate the collateral damage of macrolides and tetracyclines on gut commensals, we exploited the fact that drug combinations have species-specific outcomes in bacteria12 and sought marketed drugs, which could antagonize the activity of these antibiotics in abundant gut commensal species. By screening >1,000 drugs, we identified several such antidotes capable of protecting gut species from these antibiotics without compromising their activity against relevant pathogens. Altogether, this study broadens our understanding of antibiotic action on gut commensals, uncovers a previously unappreciated and broad bactericidal effect of prototypical bacteriostatic antibiotics on gut bacteria, and opens avenues for preventing the collateral damage caused by antibiotics on human gut commensals.

scholarly journals Structural Characterization of Peptides From Huangjiu and Their Regulation of Hepatic Steatosis and Gut Microbiota Dysbiosis in Hyperlipidemia Mice

2021 ◽  
Vol 12 ◽  
Author(s):  
Ying Shi ◽  
Ruixue Feng ◽  
Jieqi Mao ◽  
Shuangping Liu ◽  
Zhilei Zhou ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Hepatic Steatosis ◽  
High Fat Diet ◽  
Bioactive Peptides ◽  
Size Analysis ◽  
High Fat ◽  
Linear Discriminant ◽  
Wide Range ◽  
Gut Microbiota Dysbiosis

Hyperlipidemia is a chronic disorder that is difficult to cure and usually treated with long-term lipid-reducing drugs. Recent trends have led to the use of diet therapies or food-derived strategies in the treatment of such long-term diseases. The Chinese rice wine (huangjiu) contains a wide range of bioactive peptides that are produced during the multi-species fermentation process. To clarify the regulation effects of lipid metabolism and gut microbiota by huangjiu bioactive peptides, three huangjiu peptides were isolated, purified and characterized by hyper-filtration, macroporous resin, gel filtration separation and structural identification. Meanwhile, a mouse model of high-fat diet-induced hyperlipidemia was established to study the effects of huangjiu peptides on serum biomarker, hepatic metabolism and gut microbiota dysbiosis. Experimental results showed that huangjiu peptides T1 and T2 (HpT1, HpT2) treatment alleviated the increase in serum total cholesterol, triglyceride, low-density lipoprotein cholesterol levels and aberrant hepatic lipid accumulation in the high-fat diet-induced hyperlipidemia mice. Furthermore, HpT2 and HpT1 restored the α-diversity and structure of gut microbial community after hyperlipidemia-induced microbiota disturbance compared with simvastatin and HpT3. The administration of HpT2 and HpT1 regulated the microbiota-mediated gut ecology through alterations of characteristic taxa including Lactobacillus, Ileibacterium, Faecalibaculum and Alloprevotella by linear discriminant analysis effect size analysis. Collectively, our results offer new insights into the abilities of food-derived peptides on alleviation of high-fat diet-induced hyperlipidemia, hepatic steatosis and gut dysbiosis in mice.

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 Changes in oral microbiota after the initiation of chemotherapy in patients with hematopoietic tumors

2021 ◽  
Author(s):  
Michi Omori ◽  
Kato-kogoe Nahoko ◽  
Shoichi Sakaguchi ◽  
Eri Komori ◽  
Kazuya Inoue ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Alpha Diversity ◽  
Size Analysis ◽  
Oral Microbiota ◽  
Linear Discriminant ◽  
Chemotherapy Group ◽  
Salivary Microbiota ◽  
Before And After ◽  
Unweighted Unifrac ◽  
Induced Changes

Abstract Background Recently, the gut microbiota has been shown to play an important role in the response and resistance to chemotherapy. Although there is much knowledge about chemotherapy-induced changes in the gut microbiota, chemotherapy-associated changes in the oral microbiota remain unclear. Herein, we aimed to evaluate the changes in oral microbiota associated with the initiation of chemotherapy in patients with malignant hematopoietic tumors. Methods Oral samples were collected before and 8–20 days after the start of chemotherapy from 50 patients with malignant hematopoietic tumors who were starting chemotherapy for the first time. The 16S ribosomal RNA gene sequencing of bacterial DNA extracted from oral samples was performed to compare the oral microbiota before and after the initiation of chemotherapy. Results The richness or evenness of diversity in the ‘after start of chemotherapy’ group decreased significantly, compared with the ‘before start of chemotherapy’ group (alpha-diversity; observed operational taxonomic units (OTUs) index, p < 0.001; and Shannon’s index, p < 0.001). The overall salivary microbiota structure between the pre- and post-chemotherapy groups differed significantly (beta-diversity; unweighted UniFrac distances, p = 0.001; and weighted UniFrac distances, p = 0.003). Linear discriminant analysis effect size analysis demonstrated an increased abundance of species of certain genera, such as Staphylococcus, and decreased abundance of species of some genera, such as Streptococcus and Neisseria, in the ‘after-chemotherapy’ group, compared with those in the ‘before-chemotherapy’ group. The amounts and trends of change in the oral microbiota before and after the start of chemotherapy differed among the subjects. Of the 25 bacterial genera whose prevalence changed significantly before and after the start of chemotherapy, the proportion of oral commensals such as Streptococcus and Neisseria decreased in many subjects. In contrast, Staphylococcus and Pseudomonas were detected only in a few subjects, but their relative abundance increased significantly after the start of chemotherapy. Conclusions The oral microbiota of patients with hematopoietic tumors changed markedly after the initiation of chemotherapy. Our findings are expected to aid the elucidation of the pathogenesis of oral mucositis, which is an adverse event of chemotherapy, and the development of treatment methods for this condition.

scholarly journals Effects of changes on gut microbiota in children with acute Kawasaki disease

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9698
Author(s):  
Jie Shen ◽  
Yinghe Ding ◽  
Zuocheng Yang ◽  
Xueyan Zhang ◽  
Mingyi Zhao
Keyword(s):  
Kawasaki Disease ◽  
Gut Microbiota ◽  
High Throughput Sequencing ◽  
Diversity Index ◽  
Venous Blood ◽  
Size Analysis ◽  
Quantitative Detection ◽  
Control Group ◽  
Healthy Children ◽  
Linear Discriminant

Background Kawasaki disease (KD) is an acute febrile illness of early childhood. The exact etiology of the disease remains unknown. At present, research on KD is mostly limited to susceptibility genes, infections, and immunity. However, research on the correlation between gut microbiota and KD is rare. Methods Children with a diagnosis of acute KD and children undergoing physical examination during the same period were included. At the time of admission, the subjects’ peripheral venous blood and feces were collected. Faecal samples were analyzed for bacterial taxonomic content via high-throughput sequencing. The abundance, diversity, composition, and characteristic differences of the gut microbiota in KD and healthy children were compared by alpha diversity, beta diversity, linear discriminant analysis and LDA effect size analysis. Blood samples were used for routine blood examination, biochemical analysis, and immunoglobulin quantitative detection. Results Compared with the control group, the community richness and structure of gut microbiota in the KD group was significantly reduced (Chao1 richness estimator, mean 215.85 in KD vs. mean 725.76 in control, p < 0.01; Shannon diversity index, mean 3.32 in KD vs. mean 5.69 in control, p < 0.05). LEfSe analysis identified two strains of bacteria significantly associated with KD: Bacteroidetes and Dorea. Bacteroidetes were enriched in healthy children (mean 0.16 in KD vs. mean 0.34 in control, p < 0.05). Dorea was also enriched in healthy children but rarely existed in children with KD (mean 0.002 in KD vs. mean 0.016 in control, p < 0.05). Compared with the control, IgA and IgG in the KD group decreased (IgA, median 0.68 g/L in KD vs. median 1.06 g/L in control, p < 0.001; IgG, median 6.67 g/L in KD vs. median 9.71 g/L in control, p < 0.001), and IgE and IgM levels were not significantly changed. Conclusions Dysbiosis of gut microbiota occurs in children with acute KD and may be related to the etiology or pathogenesis of KD. It is worth noting that for the first time, we found that Dorea, a hydrogen-producing bacterium, was significantly reduced in children with acute KD. Overall, our results provide a theoretical basis for the prevention or diagnosis of KD based on intestinal microecology.

scholarly journals Gut Microbiota Influences Plasmodium Falciparum Malaria Susceptibility

2021 ◽  
Author(s):  
Aly Kodio ◽  
Drissa Coulibaly ◽  
Safiatou Doumbo ◽  
Salimata Konaté ◽  
Abdoulaye Kassoum Koné ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Plasmodium Falciparum Malaria ◽  
Gut Bacteria ◽  
Size Analysis ◽  
Healthy Children ◽  
Linear Discriminant ◽  
At Risk Populations ◽  
Lactobacillus Ruminis ◽  
Bacteria And Fungi ◽  
The Impact

The gut microbiota has recently been associated with susceptibility/resistance to malaria in animal models and humans, yet the impact of the gut microbiota on the risk of a malaria attack remains to be assessed. This study aims at assessing the influence of the gut microbiota on malaria attacks and Plasmodium parasit&aelig;mia in children living in a malaria-endemic area in Mali. Three hundred healthy children were included in a 16-months cohort study in Bandiagara. Their gut bacteria and fungi community structures were characterised via 16S and ITS metabarcoding from stool samples collected at inclusion. Clinician team monitored the occurrence of malaria attacks. Asymptomatic carriage of Plasmodium was assessed by qPCR. Over the 16-month period, 107 (36%) children experienced at least one occurrence of malaria attacks, and 82 (27%) at least one asymptomatic Plasmodium parasit&aelig;mia episode. A higher gut bacteria richness was independently associated with susceptibility to asymptomatic parasit&aelig;mia episodes and malaria attacks; while the Shannon H diversity and Chao-1 richness index of gut fungi community structure was relatively homogeneous in children who were and were not infected with P. falciparum. Using a linear discriminant effect size analysis of operational taxonomic units assigned to the species level, 17 bacteria, including Clostridiaceae, Eubacteriaceae, Senegalimassilia sp., Atopobiaceae and Lachnosipraceae, and seven fungi, including Dioszegia fristigensis, Ogataea polymorpha and Cutaneotrichosporon cyanovorans, were associated with susceptibility; whereas eight bacteria, including, Bifidobacterium spp., Weissela confusa and Peptostreptococcacea, and 3 fungi, Malassezia sp., Niesslia exosporoides, and Didymocrea leucaenae, were associated with resistance to malaria. Moreover, 15 bacteria, including Coproccus eutactus, Terrisporobacter petrolearius, Klebsiella pneumoniae and Ruminococcaceae, and 13 fungi, including Wallemia mellicola, were associated with susceptibility, whereas 19 bacteria, including Bifidobacterium spp., Bacteroides fragilis, Peptostreptococcacea, and Lactobacillus ruminis, and three fungi, including Cryptococcus neoformans, were associated with resistance to asymptomatic Plasmodium parasit&aelig;mia episodes. Further studies are needed to confirm these findings that point the way towards strategies aiming to reduce the risk of malaria by modulating gut microbiota components in at-risk populations.

Sign in / Sign up

Export Citation Format

Share Document