scholarly journals Gut Microbiome Functional and Taxonomic Diversity within an Amazonian semi-nomadic hunter-gatherer group

2019 ◽  
Author(s):  
LC Conteville ◽  
J Oliveira-Ferreira ◽  
AC Vicente
Keyword(s):  
Human Health ◽  
Gut Microbiome ◽  
Human Microbiome ◽  
Gene Families ◽  
Taxonomic Diversity ◽  
South American ◽  
Traditional Group ◽  
Hunter Gatherers ◽  
Functional Features ◽  
Number Of Individuals

AbstractBackgroundHuman gut microbiome profiles have been associated with human health and disease. These profiles have been defined based on microbes’ taxonomy and more recently, on their functionality. Human groups that still maintain traditional modes of subsistence (hunter-gatherers and rural agriculturalists) represent the groups non-impacted by urban-industrialized lifestyles, and therefore study them provide the basis for understanding the human microbiome evolution. The Yanomami is the largest semi-nomadic hunter-gatherer group of the Americas, exploring different niches of the Amazon rainforest in Brazil and Venezuela. In order to extend the analysis of this unique and diverse group, we focused on the gut microbiome of the Yanomami from Brazil and compared with those from Venezuela, and also with other traditional groups from the Amazon, considering taxonomic and functional profiles.ResultsA diversity of taxonomic biomarkers were identified to each South American traditional group studied, including the two Yanomami groups, despite their overall similarity in the taxonomic gut microbiome profiles. Broader levels of functional categories poorly discriminated traditional and urban-industrialized groups. Interestingly, a diversity was observed with the stratification of these categories, clearly segregating those groups. The Yanomami/Brazil gut microbiome presented unique functional features, such as a higher abundance of gene families involved in regulation/cell signaling, motility/chemotaxis, and virulence, contrasting with the microbiomes from the Yanomami/Venezuela and other groups.ConclusionsOur study revealed biomarkers, taxonomic and functional differences between the gut microbiome of Yanomami/Brazil and Yanomami/Venezuela individuals. This intra-Yanomami group diversity was accessed due to the increase number of individuals and group studied. These differences may reflect their semi-nomadic behavior, as well as, the local and seasonal diversity of the vast rainforest niche they explore, despite their shared cultural and genetic background. Overall, their microbiome profiles are shared with South American and African traditional groups, probably due to their lifestyle. The unique features identified within the Yanomami highlight the bias imposed by underrepresented sampling, and factors such as variations over space and time (seasonality) that impact, mainly, the hunter-gatherers. Therefore, to reach knowledge about human microbiome variations and their implications in human health, it is essential to enlarge data concerning the number of individuals, as well as the groups representing different lifestyles.

scholarly journals Biomimetic Gut Model Systems for Development of Targeted Microbial Solutions for Enhancing Warfighter Health and Performance

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Lauren M. Brinkac ◽  
Nandita Rahman ◽  
Loun-Loun Chua ◽  
Sterling Thomas
Keyword(s):  
Human Health ◽  
Gut Microbiome ◽  
Human Microbiome ◽  
Research Priorities ◽  
Performance Outcomes ◽  
Vital Role ◽  
Model Systems ◽  
Experimental Model Systems ◽  
And Performance

ABSTRACT The human gut microbiome plays a vital role in both health and disease states and as a mediator of cognitive and physical performance. Despite major advances in our understanding of the role of gut microbes in host physiology, mechanisms underlying human-microbiome dynamics have yet to be fully elucidated. This knowledge gap represents a major hurdle to the development of targeted gut microbiome solutions influencing human health and performance outcomes. The microbiome as it relates to warfighter health and performance is of interest to the Department of Defense (DoD) with the development of interventions impacting gut microbiome resiliency among its top research priorities. While technological advancements are enabling the development of experimental model systems that facilitate mechanistic insights underpinning human health, disease, and performance, translatability to human outcomes is still questionable. This review discusses some of the drivers influencing the DoD’s interest in the warfighter gut microbiome and describes current in vitro gut model systems supporting direct microbial-host interactions.

scholarly journals Animal welfare risks of global aquaculture

2021 ◽  
Vol 7 (14) ◽  
pp. eabg0677
Author(s):  
Becca Franks ◽  
Christopher Ewell ◽  
Jennifer Jacquet
Keyword(s):  
Animal Welfare ◽  
Taxonomic Diversity ◽  
Aquatic Animal ◽  
Multiple Sources ◽  
Aquatic Animals ◽  
Extreme Risk ◽  
Unknown Species ◽  
High Production ◽  
Species Specific ◽  
Number Of Individuals

The unprecedented growth of aquaculture involves well-documented environmental and public-health costs, but less is understood about global animal welfare risks. Integrating data from multiple sources, we estimated the taxonomic diversity of farmed aquatic animals, the number of individuals killed annually, and the species-specific welfare knowledge (absence of which indicates extreme risk). In 2018, FAO reported 82.12 million metric tons of farmed aquatic animals from six phyla and at least 408 species—20 times the number of species of farmed terrestrial animals. The farmed aquatic animal tonnage represents 250 to 408 billion individuals, of which 59 to 129 billion are vertebrates (e.g., carps, salmonids). Specialized welfare information was available for 84 species, only 30% of individuals; the remaining 70% either had no welfare publications or were of an unknown species. With aquaculture growth outpacing welfare knowledge, immediate efforts are needed to safeguard the welfare of high-production, understudied species and to create policies that minimize welfare risks.

scholarly journals Long-term Diet Quality and Gut Microbiome Functionality: A Prospective, Shotgun Metagenomic Study among Urban Chinese Adults

2021 ◽  
Vol 5 (4) ◽  
Author(s):  
Danxia Yu ◽  
Yaohua Yang ◽  
Jirong Long ◽  
Wanghong Xu ◽  
Qiuyin Cai ◽  
...  
Keyword(s):  
Diet Quality ◽  
Gut Microbiome ◽  
Metabolic Pathways ◽  
Gene Families ◽  
Diet Group ◽  
Healthy Diet ◽  
Chinese Adults ◽  
Α Diversity ◽  
Unhealthy Diet

ABSTRACT Background Diet is known to affect human gut microbiome composition; yet, how diet affects gut microbiome functionality remains unclear. Objective We compared the diversity and abundance/presence of fecal microbiome metabolic pathways among individuals according to their long-term diet quality. Methods In 2 longitudinal cohorts, we assessed participants’ usual diets via repeated surveys during 1996–2011 and collected a stool sample in 2015–2018. Participants who maintained a healthy or unhealthy diet (i.e., stayed in the highest or lowest quintile of a healthy diet score throughout follow-up) were selected. Participants were excluded if they reported a history of cancer, cardiovascular disease, diabetes, or hypertension; had diarrhea or constipation in the last 7 d; or used antibiotics in the last 6 mo before stool collection. Functional profiling of shotgun metagenomics was performed using HUMAnN2. Associations of dietary variables and 420 microbial metabolic pathways were evaluated via multivariable-adjusted linear or logistic regression models. Results We included 144 adults (mean age = 64 y; 55% female); 66 had an unhealthy diet and 78 maintained a healthy diet. The healthy diet group had higher Shannon α-diversity indexes of microbial gene families and metabolic pathways (both P < 0.02), whereas β-diversity, as evaluated by Bray-Curtis distance, did not differ between groups (both P > 0.50). At P < 0.01 [false discovery rate (FDR) <0.15], the healthy diet group showed enriched pathways for vitamin and carrier biosynthesis (e.g., tetrahydrofolate, acetyl-CoA, and l-methionine) and tricarboxylic acid (TCA) cycle, and increased degradation (or reduced biosynthesis) of certain sugars [e.g., cytidine monophosphate (CMP)-legionaminate, deoxythymidine diphosphate (dTDP)-l-rhamnose, and sucrose], nucleotides, 4-aminobutanoate, methylglyoxal, sulfate, and aromatic compounds (e.g., catechol and toluene). Meanwhile, several food groups were associated with the CMP-legionaminate biosynthesis pathway at FDR <0.05. Conclusions In a small longitudinal study of generally healthy, older Chinese adults, we found long-term healthy eating was associated with increased α-diversity of microbial gene families and metabolic pathways and altered symbiotic functions relevant to human nutrition and health.

scholarly journals Carbohydrates great and small, from dietary fiber to sialic acids: How glycans influence the gut microbiome and affect human health

Gut Microbes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 1-18
Author(s):  
Joanna K Coker ◽  
Oriane Moyne ◽  
Dmitry A. Rodionov ◽  
Karsten Zengler
Keyword(s):  
Human Health ◽  
Dietary Fiber ◽  
Gut Microbiome ◽  
Sialic Acids

scholarly journals The structure of Brazilian Amazonian gut microbiomes in the process of urbanisation

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Ana Paula Schaan ◽  
Dionison Sarquis ◽  
Giovanna C. Cavalcante ◽  
Leandro Magalhães ◽  
Eliene R. P. Sacuena ◽  
...  
Keyword(s):  
Native American ◽  
Ribosomal Rna ◽  
Gut Microbiome ◽  
Brazilian Amazon ◽  
American People ◽  
South American ◽  
Subsistence Strategy ◽  
Urban Populations ◽  
Gradual Loss ◽  
Agricultural Societies

AbstractShifts in subsistence strategy among Native American people of the Amazon may be the cause of typically western diseases previously linked to modifications of gut microbial communities. Here, we used 16S ribosomal RNA sequencing to characterise the gut microbiome of 114 rural individuals, namely Xikrin, Suruí and Tupaiú, and urban individuals from Belém city, in the Brazilian Amazon. Our findings show the degree of potential urbanisation occurring in the gut microbiome of rural Amazonian communities characterised by the gradual loss and substitution of taxa associated with rural lifestyles, such as Treponema. Comparisons to worldwide populations indicated that Native American groups are similar to South American agricultural societies and urban groups are comparable to African urban and semi-urban populations. The transitioning profile observed among traditional populations is concerning in light of increasingly urban lifestyles. Lastly, we propose the term “tropical urban” to classify the microbiome of urban populations living in tropical zones.

scholarly journals Guild-based analysis for understanding gut microbiome in human health and diseases

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Guojun Wu ◽  
Naisi Zhao ◽  
Chenhong Zhang ◽  
Yan Y. Lam ◽  
Liping Zhao
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Gut Microbiome ◽  
Association Studies ◽  
Causative Role ◽  
Disease Phenotypes ◽  
Genetic Complexity ◽  
Causative Agents ◽  
Specific Health

AbstractTo demonstrate the causative role of gut microbiome in human health and diseases, we first need to identify, via next-generation sequencing, potentially important functional members associated with specific health outcomes and disease phenotypes. However, due to the strain-level genetic complexity of the gut microbiota, microbiome datasets are highly dimensional and highly sparse in nature, making it challenging to identify putative causative agents of a particular disease phenotype. Members of an ecosystem seldomly live independently from each other. Instead, they develop local interactions and form inter-member organizations to influence the ecosystem’s higher-level patterns and functions. In the ecological study of macro-organisms, members are defined as belonging to the same “guild” if they exploit the same class of resources in a similar way or work together as a coherent functional group. Translating the concept of “guild” to the study of gut microbiota, we redefine guild as a group of bacteria that show consistent co-abundant behavior and likely to work together to contribute to the same ecological function. In this opinion article, we discuss how to use guilds as the aggregation unit to reduce dimensionality and sparsity in microbiome-wide association studies for identifying candidate gut bacteria that may causatively contribute to human health and diseases.

scholarly journals Synthesis of the pentasaccharide repeating unit from Ruminococcus gnavus and measurement of its inflammatory properties

RSC Advances ◽  
2021 ◽  
Vol 11 (24) ◽  
pp. 14357-14361
Author(s):  
Teron Haynie ◽  
Shawn Gubler ◽  
Christoph Drees ◽  
Tanner Heaton ◽  
Tanner Mitton ◽  
...  
Keyword(s):  
Human Health ◽  
Gut Microbiome

The roles played by the gut microbiome in human health are increasingly recognized, and the prevalence of specific microorganisms has been correlated with different diseases.

scholarly journals Cross-kingdom inhibition of bacterial virulence and communication by probiotic yeast metabolites

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Orit Malka ◽  
Dorin Kalson ◽  
Karin Yaniv ◽  
Reut Shafir ◽  
Manikandan Rajendran ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Gut Microbiome ◽  
Bacterial Infections ◽  
Pathogenic Bacteria ◽  
Molecular Mechanisms ◽  
Human Microbiome ◽  
Cell Communication ◽  
Probiotic Yeast ◽  
Gut Pathogen ◽  
Cell Cell

Abstract Background Probiotic milk-fermented microorganism mixtures (e.g., yogurt, kefir) are perceived as contributing to human health, and possibly capable of protecting against bacterial infections. Co-existence of probiotic microorganisms are likely maintained via complex biomolecular mechanisms, secreted metabolites mediating cell-cell communication, and other yet-unknown biochemical pathways. In particular, deciphering molecular mechanisms by which probiotic microorganisms inhibit proliferation of pathogenic bacteria would be highly important for understanding both the potential benefits of probiotic foods as well as maintenance of healthy gut microbiome. Results The microbiome of a unique milk-fermented microorganism mixture was determined, revealing a predominance of the fungus Kluyveromyces marxianus. We further identified a new fungus-secreted metabolite—tryptophol acetate—which inhibits bacterial communication and virulence. We discovered that tryptophol acetate blocks quorum sensing (QS) of several Gram-negative bacteria, particularly Vibrio cholerae, a prominent gut pathogen. Notably, this is the first report of tryptophol acetate production by a yeast and role of the molecule as a signaling agent. Furthermore, mechanisms underscoring the anti-QS and anti-virulence activities of tryptophol acetate were elucidated, specifically down- or upregulation of distinct genes associated with V. cholerae QS and virulence pathways. Conclusions This study illuminates a yet-unrecognized mechanism for cross-kingdom inhibition of pathogenic bacteria cell-cell communication in a probiotic microorganism mixture. A newly identified fungus-secreted molecule—tryptophol acetate—was shown to disrupt quorum sensing pathways of the human gut pathogen V. cholerae. Cross-kingdom interference in quorum sensing may play important roles in enabling microorganism co-existence in multi-population environments, such as probiotic foods and the gut microbiome. This discovery may account for anti-virulence properties of the human microbiome and could aid elucidating health benefits of probiotic products against bacterially associated diseases.

scholarly journals Unraveling the Gut Microbiome of the Invasive Small Indian Mongoose (Urva auropunctata) in the Caribbean

2021 ◽  
Vol 9 (3) ◽  
pp. 465
Author(s):  
Anne A. M. J. Becker ◽  
KC Hill ◽  
Patrick Butaye
Keyword(s):  
Relative Abundance ◽  
Gut Microbiome ◽  
Taxonomic Diversity ◽  
Caribbean Islands ◽  
Microbial Profile ◽  
Vegetation Zones ◽  
Males And Females ◽  
The Caribbean ◽  
Metabolic Properties ◽  
Small Indian Mongoose

Small Indian mongooses (Urva auropunctata) are among the most pervasive predators to disrupt the native ecology on Caribbean islands and are strongly entrenched in their areas of introduction. Few studies, however, have considered the microbial ecology of such biological invasions. In this study, we investigated the gut microbiota of invasive small Indian mongooses in terms of taxonomic diversity and functional potential. To this end, we collected fecal samples from 60 free-roaming mongooses trapped in different vegetation zones on the island Saint Kitts. The core gut microbiome, assessed by 16S rRNA amplicon gene sequencing on the Ion S5TM XL platform, reflects a carnivore-like signature with a dominant abundance of Firmicutes (54.96%), followed by Proteobacteria (13.98%) and Fusobacteria (12.39%), and a relatively minor contribution of Actinobacteria (10.4%) and Bacteroidetes (6.40%). Mongooses trapped at coastal sites exhibited a higher relative abundance of Fusobacterium spp. whereas those trapped in scrubland areas were enriched in Bacteroidetes, but there was no site-specific difference in predicted metabolic properties. Between males and females, beta-diversity was not significantly different and no sex-specific strategies for energy production were observed. However, the relative abundance of Gammaproteobacteria, and more specifically, Enterobacteriaceae, was significantly higher in males. This first description of the microbial profile of small Indian mongooses provides new insights into their bioecology and can serve as a springboard to further elucidating this invasive predator’s impact throughout the Caribbean.

Gut Feeling

2016 ◽  
Vol 33 (S1) ◽  
pp. S504-S505
Author(s):  
C. Cotta ◽  
G. Jesus ◽  
V. Vila Nova ◽  
C. Moreira
Keyword(s):  
Mental Disorders ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Bacterial Infections ◽  
Human Microbiome ◽  
Dietary Interventions ◽  
Scientific Databases ◽  
Antibiotic Drugs ◽  
Microbiome Research ◽  
Competing Interest

IntroductionThere is growing evidence of the importance of nutrition in mental disorders. Gut microbiota, influenced by environmental factors such as diet and stress, has been proposed as one of the players on a dynamic called gut-brain axis, which is thought to have an influence on behaviour and mental health.Objectives and aimsTo summarize recent evidence on the topic, and its potential role in psychiatric interventions.MethodsThe authors review updated literature collected from online scientific databases.ResultsThe development of the brain itself has been shown to be influenced by the gut microbiome. Research demonstrates that the composition of the microbiota has influence on behaviour through neuroendocrine and other neuroactive messengers production by the bacteria within the gut lumen. Studies in germ-free animals, animals exposed to bacterial infections, probiotic suplements or antibiotic drugs suggest a role for the gut microbiota in the regulation of anxiety, mood, cognition and pain. The gut microbiome has been implicated in brain disorders including anxiety and depression, multiple sclerosis, Alzheimer's disease, Parkinson's disease, and autism.ConclusionsThe treatment of mental disorders is usually based on pharmacological and psychotherapeutic interventions, and little attention is given to dietary interventions. The emerging field of research focused on the human microbiome suggests an important role for the gut microbiota in influencing brain development, behaviour and mood in humans, and points new strategies for developing novel therapeutics for mental disorders.Disclosure of interestThe authors have not supplied their declaration of competing interest.

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