Biology subjects

Jha, A. R.

Publications and source records attributed to Jha, A. R..

6 recordsLinked to original sources

bioRxiv2024

Ecological factors that drive microbial communities in culturally diverse fermented foods

Fermented foods are increasingly recognized for their health benefits. Historically, cultures worldwide have relied on fermentation to preserve foods and enhance their digestibility, flavor, aromas, and taste. Despite the abundance of global diversity of fermented foods, the microbial communities in traditionally fermented non-European foods remain largely understudied. Here, we characterized the bacterial and fungal communities in 90 plant and animal based fermented foods from Nepal, South Korea, Ethiopia, and Kazakhstan, all traditionally prepared for household consumption. Our results reveal that these foods host diverse and intricately interconnected ecosystems of bacteria and fungi. Beyond the well-known fermenters such as lactic acid bacteria (LABs), Bacillales, and yeasts (Saccharomycetales), these foods contain additional microbes whose roles in fermentation are not well understood. While the microbial compositions of fermented foods vary by geography and preparation methods, the type of food substrate has the most significant effect on differentiating bacterial communities. Vegetable-based ferments harbor bacterial communities consisting primarily of LABs and potential pathways associated with carbohydrates degradation. Contrastingly, legumes and animal-based fermented foods are enriched with Bacillales and protein and lipid degradation pathways. Moreover, the microbial interactions, characterized via bacteria- bacteria and bacteria-fungi co-occurrence networks, differ significantly across traditionally fermented plants, legumes, and dairy products, indicating that microbial ecosystems vary between traditional fermented foods derived from different substrates. Our findings highlight the underexplored diversity of microbial communities in traditional fermented foods and underscore the need to understand the entire microbial communities present in these foods and their functions when evaluating their effect on nutrition and health.

microbiology↗

bioRxiv2024

Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized

BackgroundLifestyle plays an important role in shaping the gut microbiome. However, its contributions to the oral microbiome remains less clear, due to the confounding effects of geography and methodology in investigations of populations studied to date. Furthermore, while the oral microbiome seems to differ between foraging and industrialized populations, we lack insight into whether transitions to and away from agrarian lifestyles shape the oral microbiota. Given the growing interest in so-called vanishing microbiomes potentially being a risk factor for increased disease prevalence in industrialized populations, it is important that we distinguish lifestyle from geography in the study of microbiomes across populations. ResultsHere, we investigate salivary microbiomes of 63 Nepali individuals representing a spectrum of lifestyles: foraging, subsistence farming (individuals that transitioned from foraging to farming within the last 50 years), agriculturalists (individuals that have transitioned to farming for at least 300 years), and industrialists (expatriates that immigrated to the United States within the last 20 years). We characterize the role of lifestyle in microbial diversity, identify microbes that differ between lifestyles, and pinpoint specific lifestyle factors that may be contributing to differences in the microbiomes across populations. Contrary to prevailing views, when geography is controlled for, oral microbiome alpha diversity does not differ significantly across lifestyles. Microbiome composition, however, follows the gradient of lifestyles from foraging through agrarianism to industrialism, supporting the notion that lifestyle indeed plays a role in the oral microbiome. Relative abundances of several individual taxa, including Streptobacillus and an unclassified Porphyromonadaceae genus, also mirror lifestyle. Finally, we identify specific lifestyle factors associated with microbiome composition across the gradient of lifestyles, including smoking and grain source. ConclusionOur findings demonstrate that by controlling for geography, we can isolate an important role for lifestyle in determining oral microbiome composition. In doing so, we highlight the potential contributions of several lifestyle factors, underlining the importance of carefully examining the oral microbiome across lifestyles to improve our understanding of global microbiomes.

microbiology↗

bioRxiv2022

Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles

Infant microbiome assembly is intensely studied in infants from industrialized nations, but little is known about this process in populations living non-industrialized lifestyles. In this study we deeply sequenced infant stool samples from the Hadza hunter-gatherers of Tanzania and analyzed them in a global meta-analysis. Infant microbiomes develop along lifestyle-associated trajectories, with over twenty percent of genomes detected in the Hadza infant gut representing phylogenetically diverse novel species. Industrialized infants, even those who are breastfed, have microbiomes characterized by a paucity of Bifidobacterium infantis and gene cassettes involved in human milk utilization. Strains within lifestyle-associated taxonomic groups are shared between mother-infant dyads, consistent with early-life inheritance of lifestyle-shaped microbiomes. The population-specific differences in infant microbiome composition and function underscore the importance of studying microbiomes from people outside of wealthy, industrialized nations. Recognition of work on indigenous communitiesResearch involving indigenous communities is needed for a variety of reasons including to ensure that scientific discoveries and understanding appropriately represent all populations and do not only benefit those living in industrialized nations. Special considerations must be made to ensure that this research is conducted ethically and in a non-exploitative manner. In this study we performed deep metagenomic sequencing on fecal samples that were collected from Hadza hunter-gatherers in 2013/2014 and were analyzed in previous publications using different methods (1, 2). A material transfer agreement with the National Institute for Medical Research in Tanzania ensures that stool samples collected are used solely for academic purposes, permission for the study was obtained from the National Institute of Medical Research (MR/53i 100/83, NIMR/HQ/R.8a/Vol.IX/1542) and the Tanzania Commission for Science and Technology, and verbal consent was obtained from the Hadza after the studys intent and scope was described with the help of a translator. The publications that first described these samples included several scientists and Tanzanian field-guides as co-authors for the critical roles they played in sample collection, but as no new samples were collected in this study, only scientists who contributed to the analyses described here were included as co-authors in this publication. It is currently not possible for us to travel to Tanzania and present our results to the Hadza people, however we intend to do so once the conditions of the COVID-19 pandemic allow it.

microbiology↗

bioRxiv2022

Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes

The gut microbiome is a key modulator of immune and metabolic health. Human microbiome data is biased towards industrialized populations, providing limited understanding of the distinct and diverse non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing and strain cultivation on 351 fecal samples from the Hadza, hunter-gatherers in Tanzania, and comparative populations in Nepal and California. We recover 94,971 total genomes of bacteria, archaea, bacteriophages, and eukaryotes, 43% of which are absent from existing unified datasets. Analysis of in situ growth rates, genetic pN/pS signatures, high-resolution strain tracking, and 124 gut-resident species vanishing in industrialized populations reveals differentiating dynamics of the Hadza gut microbiome. Industrialized gut microbes are enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource that expands our understanding of microbes capable of colonizing the human gut and clarifies the extensive perturbation brought on by the industrialized lifestyle.

microbiology↗

bioRxiv2020

Risk factors associated with canine overweightness and obesity in an owner-reported survey

BackgroundOverweightness and obesity in dogs are associated with negative health outcomes. A better understanding of risk factors associated with canine weight is fundamental to identifying preventative interventions and treatments. In this cross-sectional study, we used a direct to consumer approach to collect body condition scores (BCS), as well as demographic, diet, and lifestyle data on 4,446 dogs. BCS was assessed by owners using a 9-point system and categorized as ideal (BCS 4-5), overweight (BCS 6), and obese (BCS 7+). Following univariate analyses, a stepwise procedure was used to select variables which were included in multivariate logistic regression models. One model was created to compare ideal to all overweight and obese dogs, and another was created to compare ideal to obese dogs only. We then used Elastic Net selection and XGBoost variable importance measures to validate these results. ResultsOverall, 1,480 (33%) of dogs were reported to be overweight or obese, of which 356 (8% total) of dogs were reported to be obese. Seven factors were significantly associated with both overweightness/obesity and obesity alone in all three analyses (stepwise, Elastic Net, and XGBoost): diet composition, probiotic supplementation, treat quantity, exercise, age, food motivation level, and pet appetite. Neutering was also associated with overweightness/obesity in all analyses. ConclusionsThis study recapitulated established risk factors associated with BCS (age, exercise, neutering). Moreover, we elucidated associations between previously examined risk factors and BCS (diet composition, treat consumption, and temperament) and identified a novel factor (probiotic supplementation). Specifically, relative to dogs on fresh food diets, BCS was higher in dogs eating dry food both alone and in combination with other foods. Furthermore, dogs receiving probiotics, but not other forms of supplementation, were more likely to have an ideal BCS. Future studies should corroborate these findings with experimental manipulations.

bioinformatics↗

bioRxiv2018

Gut microbiome transition across a lifestyle gradient in Himalaya

The composition of the gut microbiome in industrialized populations differs from those living traditional lifestyles. However, it has been difficult to separate the contributions of human genetic and geographic factors from lifestyle/modernization. Here, we characterize the stool bacterial composition of four Himalayan populations to investigate how the gut community changes in response to shifts in human lifestyles. These groups led seminomadic hunting-gathering lifestyles until transitioning to varying dependence upon farming. The Tharu began farming 250-300 years ago, the Raute and Raji transitioned 30-40 years ago, and the Chepang retain many aspects of a foraging lifestyle. We assess the contributions of dietary and environmental factors on their gut microbiota and find that the gut microbiome composition is significantly associated with lifestyle. The Chepang foragers harbor elevated abundance of taxa associated with foragers around the world. Conversely, the gut microbiomes of populations that have transitioned to farming are more similar to those of Americans, with agricultural dependence and several associated lifestyle and environmental factors correlating with the extent of microbiome divergence from the foraging population. For example, our results show that drinking water source and solid cooking fuel are significantly associated with the gut microbiome. Despite the pronounced differences in gut bacterial composition across populations, we found little differences in alpha diversity across populations. These findings in genetically similar populations living in the same geographical region establish the key role of lifestyle in determining human gut microbiome composition and point to the next challenging steps of isolating dietary effects from other factors that change during modernization.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC=\"FIGDIR/small/253450_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (108K):\norg.highwire.dtl.DTLVardef@68f595org.highwire.dtl.DTLVardef@d33792org.highwire.dtl.DTLVardef@e56314org.highwire.dtl.DTLVardef@1cbbba2_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗