Biology subjects

Weyrich, L. S.

Publications and source records attributed to Weyrich, L. S..

6 recordsLinked to original sources

bioRxiv2026

Evolutionary Histories and Environments Shape Ugandan and Global Oral Microbiomes

Industrialization has been identified as the single biggest factor driving global microbiome diversity. While many studies examining gut microbiomes attribute these shifts to dietary increases in fat and reductions in protein, oral microbiome responses to industrialization remains debated. The oral microbiome is more resilient due to long-standing coevolution with host tissues and biofilm stability. However, limited geographic and historical representation has constrained our understanding of how these transitions unfolded globally in the oral microbiomes. Here, we investigate oral microbiome variation in Batwa rainforest hunter-gatherers and neighboring Bakiga subsistence farmers from southwestern Uganda, comparing them with publicly available data from Tanzanian, Venezuelan, and industrialized populations from North America, Europe, and Australia. Using 16S rRNA gene sequencing, we characterized salivary microbiota and evaluated differences in local and global diversity, composition, and differential abundance. Ugandan populations contained significant compositional differences but similar levels of diversity, suggesting that shared environments and dietary overlap may shape microbial assemblages despite distinct cultural histories. Globally, strong continental and industrialization effects were observed in the oral microbiome, with all industrial populations clustering separately from people living in other locations. African populations also clustered separately from non-African groups. Oral microbiome diversity was highest in Ugandan individuals and lowest in industrialized populations, mirroring patterns previously observed in the gut microbiome. Together, these findings demonstrate that both geography and subsistence strategy structure global oral microbiome variation. They also clarify the position that oral microbial communities record biocultural transitions and highlight the need to better understand the industrial mechanisms that shape microbial diversity in the oral cavity.

evolutionary biology↗

bioRxiv2025

The sociobiome-oral microbiome pathway in dental caries among Indigenous Australians

Indigenous Australians experience disproportionately high rates of dental caries, yet the biological pathways linking socioeconomic disadvantage to oral health remain unclear. This study examined how individual- and neighbourhood-level socioeconomic status (SES) shape the oral microbiome and mediate dental caries risk in Indigenous adults. A cross-sectional study of 100 Indigenous Australians ([≥]18 years) collected demographic, SES, and oral health behaviour data, followed by dental examinations for dental caries assessment, followed by collection of saliva and plaque samples. The microbiome was profiled using 16S rRNA sequencing, with analyses of microbial diversity, composition, differential abundance, and mediation of SES-caries associations. Saliva exhibited greater observed and Shannon diversity than plaque (both p < 0.01), with significant compositional differences (adonis p < 0.001). In saliva, alpha diversity was reduced with age, secondary education, low income, ownership of a healthcare card, and caries presence (all p < 0.05). SES explained greater variation in saliva than plaque composition, with associations for income (R{superscript 2}=3.8%, p<0.01), education (R{superscript 2}=2.0%, p<0.01), and caries (R{superscript 2}=2.2%, p<0.01). Differentially abundant taxa in low-income and caries groups included Rikenellaceae RC9 gut group, F0058, Filifactor, and Treponema. Mediation analyses showed 75.6% of the income effect on caries was mediated by microbiome shifts (ME=0.28, SE=0.32), compared with 21% for education (ME=0.03, SE=0.02). Socioeconomic disadvantage has a significant impact on the oral microbiome, influencing caries risk through income-related microbial dysbiosis. Saliva emerges as a sensitive biomarker of SES gradients. Addressing oral health inequities requires both structural policies targeting income inequality and microbiome-informed interventions. IMPORTANCEThis research provides novel biological insights into how socioeconomic disadvantage contributes to the higher burden of dental caries among Indigenous Australians. Although social determinants of health are well recognised, the pathways connecting these determinants to oral disease remain unclear. By demonstrating that low income and education affect oral microbiome diversity and composition, and that a significant part of income-related caries risk is mediated through microbiome changes, this study highlights an important mechanism behind oral health inequalities. Identifying saliva as particularly responsive to socioeconomic differences makes it a useful, non-invasive biomarker for tracking risk in vulnerable populations. These findings emphasise the need for two approaches: structural interventions to reduce social and income gaps, and microbiome-based strategies to address microbial imbalance and disease risk. Together, they strengthen the evidence for more effective, culturally sensitive efforts to promote oral health equity.

microbiology↗

bioRxiv2022

Neanderthals did not likely consume Physcomitrium patens - a model moss species

This manuscript is discussing the method of Weyrich et al., 2017, "Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus". When studying the dietary profile of a Neanderthal specimen from El Sidron cave (Spain) by sequencing ancient DNA present in calcified dental plaque (calculus) the authors identified a wide-range of potential food sources, including woolly rhinoceros, mushrooms, pine nuts, and moss - namely the less-than-abundant model species Physcomitrium patens. We doubted that Neanderthals were actually eating P. patens. By analyzing the ancient DNA reads using different mapping methods, we show likely a misinterpretation based on the previously used methods. The probability of Neanderthals eating P. patens is the same as eating rice or tomato. However, neither crop was grown in Europe at the time Neanderthals thrived.

evolutionary biology↗

bioRxiv2021

School yard biodiversity determines short-term recovery of disturbed skin microbiota in children

The planting and conservation of biodiverse habitat in urban contexts has been proposed as a public health intervention aimed at reducing the prevalence of non-communicable diseases via microbiome rewilding (Mills et al. 2017; Mills et al. 2019). However, our understanding of the effect of urban biodiversity interventions on the human microbiota remains limited, especially on the skin (Hui et al. 2019; Roslund et al. 2020) and in the context of permanent green spaces (Lehtimaki et al. 2018; Selway et al. 2020). Here, we test the short-term response of experimentally disturbed bacterial communities on the skin of healthy children exposed to different school environments - either a classroom, a sports field, or a biodiverse forest - to understand how exposures to different types of biodiversity may influence skin microbiota. Children exposed to the forest had significantly increased skin microbiota diversity when compared to pre-exposure, an effect that increased over three days suggesting long-term effects. The microbiota on children exposed to the forest had the largest structural and compositional community change compared to children exposed to sports fields, which in turn was larger than those who remained in classrooms. Children exposed to sports fields and forests also acquired new core bacteria after exposure to green spaces, potentially buffering against disturbances to the skin microbiotas diversity, while individuals who remained in the classroom lost microbes throughout the experiment. Overall, we conclude that urban green spaces can have an enriching influence on the diversity of skin microbiota, including core members shared between all children. These findings have important implications for the design and construction of new school yards and public spaces with respect to biodiversity, health, and human microbiota.

ecology↗

bioRxiv2021

Rare genera differentiate urban green space soil bacterial communities in three cities across the world

Vegetation complexity is potentially important for urban green space designs aimed at fostering microbial biodiversity to benefit human health. Exposure to urban microbial biodiversity may influence human health outcomes via immune training and regulation. In this context, improving human exposure to microbiota via biodiversity-centric urban green space designs is an underused opportunity. There is currently little knowledge on the association between vegetation complexity (i.e., diversity and structure) and soil microbiota of urban green spaces. Here, we investigated the association between vegetation complexity and soil bacteria in urban green spaces in Bournemouth, UK; Haikou, China; and the City of Playford, Australia by sequencing the 16S rRNA V4 gene region of soil samples and assessing bacterial diversity. We characterized these green spaces as having low or high vegetation complexity and explored whether these two broad categories contained similar bacterial community compositions and diversity around the world. Within cities, we observed significantly different alpha and beta diversities between vegetation complexities; however, these results varied between cities. Rare genera (< 1 % relative abundance individually, on average 35 % relative abundance when pooled) were most likely to be significantly different in sequence abundance between vegetation complexities and therefore explained much of the differences in microbial communities observed. Overall, general associations exist between soil bacterial communities and vegetation complexity, although these are not consistent between cities. Therefore, more in-depth work is required to be done locally to derive practical actions to assist the conservation and restoration of microbial communities in urban areas.

ecology↗

bioRxiv2018

Biological and cultural drivers of oral microbiota in Medieval and Post-Medieval London, UK

The trillions of microorganisms that live in association with the human body (microbiota) are critical for human health and disease, but there is a limited understanding of how cultural and environmental factors shaped our microbiota diversity through time. However, biomolecular remnants of the human oral microbiota - recovered from the calcified dental plaque (calculus) of our long-dead ancestors - are providing a new means of exploring this key relationship of our evolutionary history. Here, we correlate extensive experimental, archaeological, and biological metadata with 128 ancient dental calculus specimens from Medieval and Post-Medieval London, UK (1066 - 1853 CE). We identify a significant association between microbiota and oral geography (i.e. tooth type and tooth surface), which has confounded ancient microbiota studies to date. By controlling for oral geography, however, we identify the first associations between ancient microbiota and cultural and environmental signatures. We find significant links between ancient British microbiota structure and health, including skeletal markers of stress that may reflect low socioeconomic status. Furthermore, this study provides baseline data to explore factors that drive microbiota differentiation within and between ancient populations and highlights the potential of ancient microbiota to infer detailed health and sociocultural information about the past.

microbiology↗