Public human microbiome data are dominated by highly developed countries

PLoS Biology, Год журнала: 2022, Номер 20(2), С. e3001536 - e3001536

Опубликована: Фев. 15, 2022

The importance of sampling from globally representative populations has been well established in human genomics. In microbiome research, however, we lack a full understanding the global distribution research studies. This information is crucial to better understand patterns microbiome-associated diseases and extend health benefits this all populations. Here, analyze country origin 444,829 samples that are available world's 3 largest genomic data repositories, including Sequence Read Archive (SRA). 2,592 studies 19 body sites, 220,017 gut microbiome. We show more than 71% with known come Europe, United States, Canada, 46.8% US alone, despite representing only 4.3% population. also find central southern Asia most underrepresented region: Countries such as India, Pakistan, Bangladesh account for quarter world population but make up 1.8% samples. These results demonstrate critical need ensure representation participants

Язык: Английский

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Human microbiome variation associated with race and ethnicity emerges as early as 3 months of age

PLoS Biology, Год журнала: 2023, Номер 21(8), С. e3002230 - e3002230

Опубликована: Авг. 17, 2023

Human microbiome variation is linked to the incidence, prevalence, and mortality of many diseases associates with race ethnicity in United States. However, age at which variability emerges between these groups remains a central gap knowledge. Here, we identify that gut associated arises after 3 months persists through childhood. One-third bacterial taxa vary across caregiver-identified racial categories children are reported also adults. Machine learning modeling childhood microbiomes from 8 cohort studies (2,756 samples 729 children) distinguishes ethnic 87% accuracy. Importantly, predictive genera among top 30 most important when used predict adult self-identified ethnicity. Our results highlight critical developmental window or shortly social environmental factors drive ethnicity-associated may contribute health disparities.

Язык: Английский

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Vaginal microbiomes show ethnic evolutionary dynamics and positive selection of Lactobacillus adhesins driven by a long-term niche-specific process

Cell Reports, Год журнала: 2024, Номер 43(4), С. 114078 - 114078

Опубликована: Апрель 1, 2024

The vaginal microbiome's composition varies among ethnicities. However, the evolutionary landscape of microbiome in multi-ethnic context remains understudied. We perform a systematic analysis 351 samples from 35 pregnant women, addition to two validation cohorts, totaling 462 90 women. Microbiome alpha diversity and community state dynamics show strong ethnic signatures. Lactobacillaceae have higher ratio non-synonymous synonymous polymorphism lower nucleotide than non-Lactobacillaceae all ethnicities, with large repertoire positively selected genes, including mucin-binding cell wall anchor genes. These are driven by long-term process unique human niche. Finally, we propose an model reflecting environmental niches microbes. Our study reveals extensive signatures microbial ecology evolution, highlighting importance studying host-microbiome ecosystem perspective.

Язык: Английский

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Expanding the human gut microbiome atlas of Africa

Nature, Год журнала: 2025, Номер unknown

Опубликована: Янв. 29, 2025

Population studies provide insights into the interplay between gut microbiome and geographical, lifestyle, genetic environmental factors. However, low- middle-income countries, in which approximately 84% of world's population lives1, are not equitably represented large-scale research2-4. Here we present AWI-Gen 2 Microbiome Project, a cross-sectional study sampling 1,801 women from Burkina Faso, Ghana, Kenya South Africa. By engaging with communities that range rural horticultural to post-industrial urban informal settlements, capture far greater breadth diversity. Using shotgun metagenomic sequencing, identify taxa geographic lifestyle associations, including Treponema Cryptobacteroides species loss Bifidobacterium gain populations. We uncover 1,005 bacterial metagenome-assembled genomes, antibiotic susceptibility as factor might drive succinifaciens absence Finally, find an HIV infection signature defined by several previously associated HIV, Dysosmobacter welbionis Enterocloster sp. This represents largest population-representative survey metagenomes African individuals so far, paired extensive clinical biomarkers demographic data, provides opportunity for microbiome-related discovery.

Язык: Английский

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American Disgust: Racism, Microbial Medicine, and the Colony Within

The AAG Review of Books, Год журнала: 2025, Номер unknown, С. 1 - 4

Опубликована: Март 5, 2025

Язык: Английский

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Indigenous Knowledge and the Microbiome—Bridging the Disconnect between Colonized Places, Peoples, and the Unseen Influences That Shape Our Health and Well-Being

mSystems, Год журнала: 2023, Номер 8(1)

Опубликована: Янв. 25, 2023

Indigenous Peoples have a rich and long-standing connection with the environments that they descend from-a has informed deep multifaceted understanding of relationship between human well-being environment. Through cultural narratives practices, much this knowledge endured despite ongoing effects colonization had on many peoples across world. These based observation, experimentation, practical application over generations, potential to make compelling contributions our environmental microbiome its health. Furthermore, inclusion perspectives regarding opens pathways those who rarely engage field learnings. Within scientific community, not always been acknowledged as valid are often seen myth or lacking rigor. Thus, paper aims explore an perspective unseen influence health by framing importance natural environment, leadership, future research directions can contribute domain. Although in article reflects experiences, worldviews, two New Zealand Māori authors, it is hoped concepts discussed relate peoples, non-Indigenous advocates, globally.

Язык: Английский

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The vaginal microbiome: A complex milieu affecting risk of human papillomavirus persistence and cervical cancer

Current Problems in Cancer, Год журнала: 2022, Номер 46(4), С. 100877 - 100877

Опубликована: Июнь 9, 2022

Язык: Английский

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Can societal and ethical implications of precision microbiome engineering be applied to the built environment? A systematic review of the literature

Environment Systems & Decisions, Год журнала: 2024, Номер 44(2), С. 215 - 238

Опубликована: Фев. 24, 2024

Abstract The goal of engineering the microbiome built environment is to create places and spaces that are better for human health. Like other emerging technologies, may bring considerable benefits but there has been a lack exploration on its societal implication how engineer in an ethical way. To date, this topic area also not pulled together into singular study any systematic review or analysis. This fills gap by providing first implications microbiomes application knowledge environment. organize guide our analysis, we invoked four major principles (individual good/non-maleficence, collective good/beneficence, autonomy, justice) as framework characterizing categorizing 15 distinct themes emerged from literature. We argue these different can be used explain predict social if addressed adequately help improve public health field further develops at global scales.

Язык: Английский

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Microbial Kin: Relations of Environment and Time

Medical Anthropology Quarterly, Год журнала: 2021, Номер 35(4), С. 511 - 528

Опубликована: Дек. 1, 2021

Microbiome science considers human beings supraorganisms: single ecological units made up of symbiotic assemblages cells and microorganisms. Microbes co-evolve with humans, microbial populations in bodies are determined by environments/exposures including family, food place, health care, race gender inequities, toxic pollution. Microbiomes transgenerational links, disarrangements between different the outside world. This article asserts that microbes kin-kin making environments, across generations. Post/nonhuman theories have debated agency, sociality, ontologies things like microbes, all while appropriating eliding Indigenous scholarship directly address nonhuman Microbial kin evokes formulations necessitate reciprocal, ethical accountability to more-than-human relations. uses fieldwork a transnational microbiome malnutrition project Bangladesh explore what develops for both biological social sciences if we call human-microbe relations kinships, our kin.

Язык: Английский

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Individuality and ethnicity eclipse a short-term dietary intervention in shaping microbiomes and viromes

PLoS Biology, Год журнала: 2022, Номер 20(8), С. e3001758 - e3001758

Опубликована: Авг. 23, 2022

Many diseases linked with ethnic health disparities associate changes in microbial communities the United States, but causes and persistence of ethnicity-associated microbiome variation are not understood. For instance, studies that strictly control for diet across ethnically diverse populations lacking. Here, we performed multiomic profiling over a 9-day period included 4-day controlled vegetarian intervention defined geographic location 36 healthy Black White females similar age, weight, habitual diets, status. We demonstrate individuality ethnicity account roughly 70% to 88% 2% 10% taxonomic variation, respectively, eclipsing effects short-term shaping gut oral microbiomes viromes. Persistent between ethnicities occurs viral taxa various metagenomic functions, including several KEGG orthologs, carbohydrate active enzyme categories, cluster orthologous groups proteins, antibiotic-resistant gene categories. In contrast data, urine plasma metabolites tend decouple from more strongly diet. These longitudinal, profiles paired dietary illuminate previously unrecognized associations viromic features body sites cohorts within single location, highlighting importance accounting human research, determinants, eventual therapies. Trial Registration: ClinicalTrials.gov Identifier: NCT03314194 .

Язык: Английский

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