scholarly journals Population Stratification in the Gut Microbiota of Bali is Associated with Transitional Lifestyle

2020 ◽  
Author(s):  
Clarissa Asha Febinia ◽  
Safarina G. Malik ◽  
Ratna Djuwita ◽  
I Wayan Weta ◽  
Desak Made Wihandani ◽  
...  

Abstract Background: Human living conditions, such as food availability and the built environment, contribute to environmental forces that influence gut microbiota composition. Understanding the impact of the environment on microbiota assembly and its association with human health has multiple potential applications. Indonesia is a densely populated country that has been undergoing a dramatic societal change for the past two decades. It is distinctive in that it occupies an archipelago that imposes diverse geographic and cultural boundaries. The relationship between diet, microbiota, and health is poorly known in Indonesians and represents a natural study for the interaction between ethnogeographic factors and nutrition in microbiota assembly. Results: Here we show the first comprehensive report of the gut microbiota in adults from Bali, Indonesia (n=41). Their microbiotas clustered into two distinct community types: a Prevotella-rich (Type-P) and a Bacteroides-rich (Type-B) community. The Type-P individuals had lower alpha diversity (p <0.001, Shannon) and more incidence of obesity. The two community types are significantly different in their inter-genus co-abundance pattern (p <0.001, ANOSIM, Wilcoxon test). Further analyses with diet and obesity data showed that the presence of two distinct community types in Bali is a significant confounder for identifying health markers. In a multi-country dataset (n=257), the Bali microbiota indicates a transitional state from a subsistent (Prevotella-dominant) to industrial (Bacteroides-dominant) society. The two largest axes in a Principal Coordinate Analysis of weighted UniFrac distance explained the majority of variance between samples across countries (49.1%). Microbial dissimilarity across populations is significantly associated with Prevotella and Bacteriodes abundance (p <0.001, Generalized Additive Model). Conclusion: Our data showed that lifestyle transitions have a strong influence on the frequency of microbiota community types in a population. The Bali microbiota is undergoing a shift towards a Bacteroides-dominant community which reflects the ongoing transition of nutrition, socio-economy, and lifestyle the society. Although enterotypes obscured the detection of health markers, our findings collectively suggest that enterotypes may be useful in future studies for informing population-level stratification in large heterogenetic datasets.

2021 ◽  
Vol 9 (5) ◽  
pp. 1037
Author(s):  
Craig Resch ◽  
Mihir Parikh ◽  
J. Alejandro Austria ◽  
Spencer D. Proctor ◽  
Thomas Netticadan ◽  
...  

There is an increased interest in the gut microbiota as it relates to health and obesity. The impact of diet and sex on the gut microbiota in conjunction with obesity also demands extensive systemic investigation. Thus, the influence of sex, diet, and flaxseed supplementation on the gut microbiota was examined in the JCR:LA-cp rat model of genetic obesity. Male and female obese rats were randomized into four groups (n = 8) to receive, for 12 weeks, either (a) control diet (Con), (b) control diet supplemented with 10% ground flaxseed (CFlax), (c) a high-fat, high sucrose (HFHS) diet, or (d) HFHS supplemented with 10% ground flaxseed (HFlax). Male and female JCR:LA-cp lean rats served as genetic controls and received similar dietary interventions. Illumine MiSeq sequencing revealed a richer microbiota in rats fed control diets rather than HFHS diets. Obese female rats had lower alpha-diversity than lean female; however, both sexes of obese and lean JCR rats differed significantly in β-diversity, as their gut microbiota was composed of different abundances of bacterial types. The feeding of an HFHS diet affected the diversity by increasing the phylum Bacteroidetes and reducing bacterial species from phylum Firmicutes. Fecal short-chain fatty acids such as acetate, propionate, and butyrate-producing bacterial species were correspondingly impacted by the HFHS diet. Flax supplementation improved the gut microbiota by decreasing the abundance of Blautia and Eubacterium dolichum. Collectively, our data show that an HFHS diet results in gut microbiota dysbiosis in a sex-dependent manner. Flaxseed supplementation to the diet had a significant impact on gut microbiota diversity under both flax control and HFHS dietary conditions.


Author(s):  
Yoshihiro Tomizawa ◽  
Shunya Kurokawa ◽  
Daiki Ishii ◽  
Katsuma Miyaho ◽  
Chiharu Ishii ◽  
...  

Abstract Background The antibacterial effects of psychotropics may be part of their pharmacological effects when treating depression. However, limited studies have focused on gut microbiota in relation to prescribed medication. Method We longitudinally investigated the relationship between patients’ prescribed medications and intestinal bacterial diversity in a naturalistic treatment course for patients with major depressive disorders and anxiety disorders. Patients were recruited and their stool was collected at 3 time points during their usual psychiatric treatments. Gut microbiota were analyzed using 16S rRNA gene sequencing. We examined the impact of psychotropics (i.e., antidepressants, anxiolytics, antipsychotics) on their gut microbial diversity and functions. Results We collected 246 stool samples from 40 patients. Despite no differences in microbial diversity between medication groups at the baseline, over the course of treatment, phylogenic diversity whole-tree diversity decreased in patients on antipsychotics compared with patients without (P = .027), and beta diversity followed this trend. Based on a fixed-effect model, antipsychotics predicted microbial diversity; the higher doses correlated with less diversity based on the Shannon index and phylogenic diversity whole tree (estimate = −0.00254, SE = 0.000595, P &lt; .0001; estimate = −0.02644, SE = 0.00833, P = .002, respectively). Conclusion Antipsychotics may play a role in decreasing the alpha diversity of the gut microbiome among patients with depression and anxiety, and our results indicate a relationship with medication dosage. Future studies are warranted and should consider patients’ types and doses of antipsychotics in order to further elucidate the mechanisms of gut-brain interactions in psychiatric disorders.


Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 180
Author(s):  
Negash Kabtimer Bereded ◽  
Getachew Beneberu Abebe ◽  
Solomon Workneh Fanta ◽  
Manuel Curto ◽  
Herwig Waidbacher ◽  
...  

The gut microbiota of fishes is known to play an essential role in diverse aspects of host biology. The gut microbiota of fish is affected by various environmental parameters, including temperature changes, salinity and diet. Studies of effect of environment on gut microbiota enables to have a further understanding of what comprises a healthy microbiota under different environmental conditions. However, there is insufficient understanding regarding the effects of sampling season and catching site (wild and aquaculture) on the gut microbiota of Nile tilapia. This study characterised gut microbial composition and diversity from samples collected from Lake Tana and the Bahir Dar aquaculture facility centre using 16S rDNA Illumina MiSeq platform sequencing. Firmicutes and Fusobacteria were the most dominant phyla in the Lake Tana samples, while Proteobacteria was the most dominant in the aquaculture samples. The results of differential abundance testing clearly indicated significant differences for Firmicutes, Fusobacteria, Bacteroidetes and Cyanobacteria across sampling months. However, Proteobacteria, Chloroflexi, Fusobacteria and Cyanobacteria were significantly enriched in the comparison of samples from the Lake Tana and aquaculture centre. Significant differences were observed in microbial diversity across sampling months and between wild and captive Nile tilapia. The alpha diversity clearly showed that samples from the aquaculture centre (captive) had a higher diversity than the wild Nile tilapia samples from Lake Tana. The core gut microbiota of all samples of Nile tilapia used in our study comprised Firmicutes, Proteobacteria and Fusobacteria. This study clearly showed the impact of sampling season and catching site (wild and aquaculture) on the diversity and composition of bacterial communities associated with the gut of Nile tilapia. Overall, this is the first study on the effects of sampling season and catching site on the gut microbiota of Nile tilapia in Ethiopia. Future work is recommended to precisely explain the causes of these changes using large representative samples of Nile tilapia from different lakes and aquaculture farms.


2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 293-294
Author(s):  
Camila S Marcolla ◽  
Benjamin Willing

Abstract This study aimed to characterize poultry microbiota composition in commercial farms using 16S rRNA sequencing. Animals raised in sanitized environments have lower survival rates when facing pathogenic challenges compared to animals naturally exposed to commensal organisms. We hypothesized that intensive rearing practices inadvertently impair chicken exposure to microbes and the establishment of a balanced gut microbiota. We compared gut microbiota composition of broilers (n = 78) and layers (n = 20) from different systems, including commercial intensive farms with and without in-feed antibiotics, organic free-range farms, backyard-raised chickens and chickens in an experimental farm. Microbial community composition of conventionally raised broilers was significantly different from antibiotic-free broilers (P = 0.012), from broilers raised outdoors (P = 0.048) and in an experimental farm (P = 0.006) (Fig1). Significant community composition differences were observed between antibiotic-fed and antibiotic-free chickens (Fig2). Antibiotic-free chickens presented higher alpha-diversity, higher relative abundance of Deferribacteres, Fusobacteria, Bacteroidetes and Actinobacteria, and lower relative abundance of Firmicutes, Clostridiales and Enterobacteriales than antibiotic-fed chickens (P &lt; 0.001) (Fig3). Microbial community composition significantly changed as birds aged. In experimental farm, microbial community composition was significant different for 7, 21 and 35 day old broilers (P &lt; 0.001), and alpha diversity increased from 7 to 21d (P &lt; 0.024), but not from 21 to 35d; whereas, in organic systems, increases in alpha-diversity were observed from 7d to 21d, and from 21d to 35d (P &lt; 0.05). Broilers and layers raised together showed no differences in microbiota composition and alpha diversity (P &gt; 0.8). It is concluded that production practices consistently impact microbial composition, and that antibiotics significantly reduces microbial diversity. We are now exploring the impact of differential colonization in a controlled setting, to determine the impact of the microbes associated with extensively raised chickens. This study will support future research and the development of methods to isolate and introduce beneficial microbes to commercial systems.


Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2125
Author(s):  
Limin Wei ◽  
Bo Zeng ◽  
Siyuan Zhang ◽  
Feng Li ◽  
Fanli Kong ◽  
...  

The gut microbiota coevolve with the host and can be stably transmitted to the offspring. Host genetics plays a crucial role in the composition and abundance of gut microbiota. Inbreeding can cause a decrease of the host’s genetic diversity and the heterozygosity. In this study, we used 16S rRNA gene sequencing to compare the differences of gut microbiota between the Diannan small-ear pig and Banna minipig inbred, aiming to understand the impact of inbreeding on the gut microbiota. Three dominant bacteria (Stenotrophlomonas, Streptococcus, and Lactobacillus) were steadily enriched in both the Diannan small-ear pig and Banna minipig inbred. After inbreeding, the gut microbiota alpha diversity and some potential probiotics (Bifidobacterium, Tricibacter, Ruminocaccae, Christensenellaceae, etc.) were significantly decreased, while the pathogenic Klebsiella bacteria was significantly increased. In addition, the predicted metagenomic analysis (PICRUSt2) indicated that several amino acid metabolisms (‘‘Valine, leucine, and isoleucine metabolism’’, ‘‘Phenylalanine, tyrosine, and tryptophan biosynthesis’’, ‘‘Histidine metabolism’’) were also markedly decreased after the inbreeding. Altogether our data reveal that host inbreeding altered the composition and the predicted function of the gut microbiome, which provides some data for the gut microbiota during inbreeding.


2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Oi Yee Yeung ◽  
Yuk Fan Ng ◽  
Jiachi Chiou ◽  
Man-sau Wong

Abstract Objectives Gut microbiome in newborn infants affect their gut health and future development. The major nutrient sources for infants aged 2–4 months are breast-milk or infant formula, hence it is worth investigating whether exclusively breastfed or infant formula-fed does affect the early development of the gut microbiota communities. Metagenomics has been applied to analyse the infant fecal samples in the United State and some European countries, however, similar studies were limited in Asia and especially Hong Kong. Methods Three groups of infants aged 2–4 months which were exclusively breastfed (BF), exclusively infant formula-fed (IF) or mix-fed with breast-milk and infant formula (MF) were recruited. Genomic DNA from the fecal sample and breast-milk was extracted and subjected to 16S rRNA next-generation sequencing to understand the gut microbiota profile, the difference of microbiota diversity and community abundance in these three feeding groups. The sequencing results were processed using pipelines Mothur and Qiime2. Results Overall the breast-milk showed higher alpha-diversity than the fecal samples. The 3 predominant Phyla were Proteobacteria, Firmicutes and Bacteroidetes within the fecal samples from all feeding patterns while the 3 dominant Phyla were Firmicutes, Proteobacteria and Actinobacteria in the breastmilk. Higher abundance of the well-known immune-modulating Genera Bifidobacterium and Lactobacillus were found in the fecal samples of BF and MF groups than the IF group whereas IF group harboured highest abundance of Genus Clostridium among 3 fecal groups. A PCoA based on unweighted UniFrac distance showed that the microbiota from the breastmilk clustered and distinctly separated from those of fecal samples. Moreover, the microbiota of MF subjects were close to BF subjects from the PCoA analysis. Conclusions Our preliminary results suggested that partial feeding with breast-milk could still maintain the major gut community composition as in the BF group. Feeding pattern affect the gut microbiota in Hong Kong infants aged 2–4 month and probiotic genera Bifidobacterium and Lactobacillus were found in the breast-milk, and fecal samples of BF and MF groups. Funding Sources Health and Medical Research Fund, Food and Health Bureau, The Government of the Hong Kong Special Administrative Region.


2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Li Cui ◽  
Tingting Zhao ◽  
Haibing Hu ◽  
Wen Zhang ◽  
Xiuguo Hua

Objectives.We aimed to explore the impact of gut microbiota in coronary heart disease (CHD) patients through high-throughput sequencing.Methods.A total of 29 CHD in-hospital patients and 35 healthy volunteers as controls were included. Nucleic acids were extracted from fecal samples, followed byαdiversity and principal coordinate analysis (PCoA). Based on unweighted UniFrac distance matrices, unweighted-pair group method with arithmetic mean (UPGMA) trees were created.Results.After data optimization, an average of121312±19293reads in CHD patients and234372±108725reads in controls was obtained. Reads corresponding to 38 phyla, 90 classes, and 584 genera were detected in CHD patients, whereas 40 phyla, 99 classes, and 775 genera were detected in controls. The proportion of phylum Bacteroidetes (56.12%) was lower and that of phylum Firmicutes was higher (37.06%) in CHD patients than those in the controls (60.92% and 32.06%,P<0.05). PCoA and UPGMA tree analysis showed that there were significant differences of gut microbial compositions between the two groups.Conclusion.The diversity and compositions of gut flora were different between CHD patients and healthy controls. The incidence of CHD might be associated with the alteration of gut microbiota.


2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 401.2-401
Author(s):  
Y. Braun-Moscovici ◽  
S. Ben Simon ◽  
K. Dolnikov ◽  
S. Giryes ◽  
D. Markovits ◽  
...  

Background:A growing body of evidence suggests that the gut microbiota plays a significant role in the development of autoimmune diseases. Altered microbiota composition was associated with gastrointestinal and extraintestinal features in systemic sclerosis (SSc) patients.Objectives:To look for differences in gut microbiota between SSc patients regarding disease duration, disease subset and occurrence of digital ulcers (DU).Methods:SSc patients seen at our center were recruited in a prospective study. The exclusion criteria included antibiotic or probiotic treatment during the month prior to recruitment, recent hospitalization, BMI>30, diabetes mellitus or concomitant inflammatory bowel disease. Fecal samples were processed and 16S rRNA gene sequences were analyzed using the QIIME2 packageWeighted (quantitative) and unweighted (qualitative) UniFrac distances, alpha diversity for richness and homogeneity, taxa plots for species and phyla and ANCOM analyses were performed.Results:During July 2018-May 2019, 26 SSc patients (mean age [SD] 53[12.7] years) and disease duration 8.8 [7.1] years) fulfilled the criteria and were willing to participate in the study. Thirteen patients had diffuse SSc, 16 patients had active DU, 8 patients had Raynaud’s phenomenon only without DU, 2 patients had past DU. The microbiota was significantly more similar between patients without active DU compared to those with active DU (P=0.024), but species richness did not differ. Patients with SSc duration less than 6 years had significantly different microbiota compared to long-lasting SSc (unweighted PCoA – q=0.031). Significant variations concerning quantitative and qualitative UniFrac distances (q=0.063, q=0.005) and species richness (q=0.009) were found among patients with diffuse compared to limited SSc. Limited SSc was associated with greater species richness. Taxa plot analysis revealed higher relative abundance of Firmicutes in diffuse disease and of Actinobacteria and Bacteroidetes in limited SSc.Conclusion:Disease duration, disease subset and active DU were associated with shifts in the microbiome of SSc patients. The impact of these changes on disease progression needs further elucidation.Figure:Disclosure of Interests:Yolanda Braun-Moscovici: None declared, Shira Ben Simon: None declared, Katya Dolnikov: None declared, Sami Giryes: None declared, Doron Markovits: None declared, Yonit Tavor: None declared, Kohava Toledano: None declared, Alexandra Balbir-Gurman Consultant of: Novartis, Omry Koren: None declared


PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8168
Author(s):  
Diana H. Taft ◽  
Samir Akre ◽  
Nicolas Madrid ◽  
Andre Knoesen ◽  
David A. Mills ◽  
...  

Dedicated lactation rooms are a modern development as mothers return to work while still providing breastmilk to their absent infants. This study describes the built environment microbiome of lactation rooms and daycares, and explores the influence of temperature and humidity on the microbiome of lactation rooms. Sterile swabs were used to collect samples from five different sites in lactation rooms at University of California, Davis and from five different sites in daycares located in Davis, California. DNA from the swabs was extracted and the V4 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Temperature and relative humidity data were collected on a subset of the lactation rooms. Sampled lactation rooms could be either dedicated lactation rooms or could also serve other functions (e.g., combined lactation room and restroom lounge). The majority of sequence reads were identified as belonging to family Moraxellaceae, with 73% of all reads included in analysis identified as an unknown species of Acinetobacter. Alpha diversity was analyzed using the Shannon index, while beta diversity was analyzed using unweighted and weighted UniFrac distance. The Jaccard distance was used to measure amount of change at sampling locations between time points for analysis of the impact of temperature and humidity on the microbiome. There were significant differences in the beta diversity of the microbiome of lactation rooms by room type. There were also significant differences in the beta diversity of the microbiome by sample collection location. There were no significant differences in either alpha or beta diversity associated with room temperature or humidity. Additional studies are needed to understand if the differences in lactation room type may result in differences in the breastmilk microbiome of milk collected in those rooms, and to what extent any such differences may influence the infant microbiome.


2021 ◽  
Author(s):  
Robert E. Shapiro ◽  
Victor J. Gallardo ◽  
Edoardo Caronna ◽  
Patricia Pozo-Rosich

Importance: COVID-19 has not impacted people or countries uniformly. This disparity has prompted investigations to identify clinical and genetic predictors of COVID-19 mortality. Headache, a COVID-19 symptom, has been associated with positive disease prognosis. It is logical to consider whether primary headache disorders, among the most prevalent and disabling diseases globally, may also be associated with reduced viral mortality and thereby may have arisen as adaptive host defences. Objective: To study the relationship between COVID-19 mortality and primary headache disorders. Main outcome measure: Using a generalized additive model regression (GAM), we analysed data across 171 nations to identify variables which impact COVID-19 mortality rates (demographics, national wealth and government effectiveness, pandemic management indexes, latitude of the country's capital, prevalence of headache disorders and other diseases). We performed similar analyses of seasonal influenza mortality. Separately, we meta-analysed studies of COVID-19 inpatient survival reporting headache, using PRISMA guidelines. Results: In the global population-level analysis, we observed that a higher prevalence of headache disorders was associated with a higher COVID-19 mortality rate, and represented the main variable contributing to differences in COVID-19 mortality rates between countries (37.8%; F value=10.68). By contrast, we observed a negative trend between the prevalence of headache disorders and influenza death rates. Controversially, when considering headache as a symptom of COVID-19, in the 48 meta-analysed studies we observed a significantly higher risk ratio of survival (RR:2.178 [1.882-2.520], p<0.0001) among COVID-19 inpatients with headache. Conclusions and Relevance: Headache as a primary disorder is more prevalent in nations with higher COVID-19 mortality, whereas headache as a COVID-19 symptom is associated with enhanced survival. Further studies should clarify whether primary headache disorders represent a risk factor for mortality for COVID-19 or, rather, whether this association reflects evolutionary adaptive processes to enhance survival that, in the case of COVID-19, are insufficiently protective.


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