Variation in Microbial Exposure at the Human-Animal Interface and the Implications for Microbiome-Mediated Health Outcome

Associations between fecal contamination of the household environment and enteric pathogen detection in children living in Maputo, Mozambique

Environmental exposure to enteric pathogens is generally assessed using fecal indicators but relationships between markers of fecal contamination and actual exposure to enteric pathogens remain poorly characterized. We investigated whether Escherichia coli and two human fecal markers (HF183 and Mnif) in urban Mozambican household soil and drinking water were associated with detection in child stool of eight bacteria, three viruses, and three protozoa measured by multiplex reverse-transcription PCR and soil transmitted helminths assessed by microscopy. We used mixed-effects logistic regression with marginal standardization to obtain a pooled estimate of the overall indicator-pathogen relationship while simultaneously estimating pathogen-specific associations that accounted for assessing multiple pathogens per sample. At least one pathogen was detected in 88% (169/192) of child stools. Increasing drinking water E. coli gene concentration was associated with higher Ascaris prevalence, while human HF183 in drinking water was weakly associated with lower prevalence of the most common pathogens but was infrequently detected. No fecal marker in soil was clearly associated with any pathogen. We did not find evidence to support human markers as reliable indicators of enteric pathogen carriage in a high-prevalence domestic setting and recommend targeting enteric pathogens directly.

Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans

Dynamic interspecific interactions and environmental factors deeply impact the composition of microbiotic communities in the gut. These factors intertwined with the host's genetic background and social habits cooperate synergistically as a hidden force modulating the host's physiological and health determinants, with certain bacterial species being maintained from generation to generation. Firmicutes, one of the dominant bacterial phyla present across vertebrate classes, exhibits a wide range of functional capabilities and colonization strategies. While ecological scenarios involving microbial specialization and metabolic functions have been hypothesized, the specific mechanisms that sustain the persistence of its microbial taxa in a high diversity of hosts remain elusive. This study fills this gap by investigating the Firmicutes metabolic mechanisms contributing to their prevalence and heritability in the host gut on metagenomes-assembled bacterial genomes collected from 351 vertebrate samples, covering 18 food-producing animals and humans, specific breeds and closely-related species. We observed that taxa belonging to Acetivibrionaceae, Clostridiaceae, Lachnospiraceae, Ruminococcaceae, and the not well understood CAG-74 family were evolutionarily shared across all hosts. These prevalent taxa exhibit metabolic pathways significantly correlated with extra-host survival mechanisms, cell adhesion, colonization and host transmission, highlighted by sporulation, glycan biosynthesis, bile acid metabolism, and short-chain fatty acid encoded genes. Our findings provide a deeper understanding of the ecological foundations governing distinct transmission modes, effective colonization establishment, and maintenance of Firmicutes, offering new perspectives on both well-known and poorly characterized species.

Comparative analysis based on shared amplicon sequence variants reveals that cohabitation influences gut microbiota sharing between humans and dogs

Introduction

The One Health concept is a comprehensive understanding of the interaction between humans, animals, and the environment. The cohabitation of humans and pets positively affects their physical, mental, and social well-being. It is recognized as an essential factor from the One Health perspective. Furthermore, a healthy balance in the gut microbiome is essential for good health, and the changes in the gut microbiome associated with cohabitation between humans and pets could potentially affect various aspects of the health of both hosts. Therefore, elucidating the sharing of gut bacteria between humans and pets associated with cohabitation is important for understanding One Health. However, most studies have examined sharing at the taxonomic level, and it remains unclear whether the same bacteria are transferred between humans and pets, and whether they mutually influence each other.

Methods

Here, microbiome analysis and shared 16S rRNA gene amplicon sequence variant (ASV) analysis were conducted before the start of cohabitation between humans and dogs, as well as at 2 weeks, 1 month, and 3 months after cohabitation.

Results

16S rRNA gene ASVs analysis indicated that gut microbes have been transferred between humans and dogs. The overall structure of the gut microbiota within human-dog pairs remained unchanged after 3 months of adaptation. However, 11ASVs were shared within human-dog pairs. Many shared ASVs were highly abundant within each host, and this high abundance may be considered a factor that influences bacterial transfer between hosts.

Discussion

Our results provide important insights into the potential for the transfer of gut bacteria between humans and dogs. These findings are considered crucial for understanding the impact of human-dog cohabitation on various aspects of health.

Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes

Understanding human, animal, and environmental microbiota is essential for advancing global health and combating antimicrobial resistance (AMR). We investigate the oral and gut microbiota of 48 animal species in captivity, comparing them to those of wildlife animals. Specifically, we characterize the microbiota composition, metabolic pathways, AMR genes, and biosynthetic gene clusters (BGCs) encoding the production of specialized metabolites. Our results reveal a high diversity of microbiota, with 585 novel species-level genome bins (SGBs) and 484 complete BGCs identified. Functional gene analysis of microbiomes shows diet-dependent variations. Furthermore, by comparing our findings to wildlife-derived microbiomes, we observe the impact of captivity on the animal microbiome, including examples of converging microbiome compositions. Importantly, our study identifies AMR genes against commonly used veterinary antibiotics, as well as resistance to vancomycin, a critical antibiotic in human medicine. These findings underscore the importance of the 'One Health' approach and the potential for zoonotic transmission of pathogenic bacteria and AMR. Overall, our study contributes to a better understanding of the complexity of the animal microbiome and highlights its BGC diversity relevant to the discovery of novel antimicrobial compounds.

A taste of wilderness: supplementary feeding of red deer (Cervus elaphus) increases individual bacterial microbiota diversity but lowers abundance of important gut symbionts

The gut microbiome plays a crucial role in the health and well-being of animals. It is especially critical for ruminants that depend on this bacterial community for digesting their food. In this study, we investigated the effects of management conditions and supplemental feeding on the gut bacterial microbiota of red deer (Cervus elaphus) in the Bavarian Forest National Park, Germany. Fecal samples were collected from free-ranging deer, deer within winter enclosures, and deer in permanent enclosures. The samples were analyzed by high-throughput sequencing of the 16 S rRNA gene. The results showed that the gut bacterial microbiota differed in diversity, abundance, and heterogeneity within and between the various management groups. Free-ranging deer exhibited lower alpha diversity compared with deer in enclosures, probably because of the food supplementation available to the animals within the enclosures. Free-living individuals also showed the highest beta diversity, indicating greater variability in foraging grounds and plant species selection. Moreover, free-ranging deer had the lowest abundance of potentially pathogenic bacterial taxa, suggesting a healthier gut microbiome. Winter-gated deer, which spent some time in enclosures, exhibited intermediate characteristics between free-ranging and all-year-gated deer. These findings suggest that the winter enclosure management strategy, including supplementary feeding with processed plants and crops, has a significant impact on the gut microbiome composition of red deer. Overall, this study provides important insights into the effects of management conditions, particularly winter enclosure practices, on the gut microbiome of red deer. Understanding these effects is crucial for assessing the potential health implications of management strategies and highlights the value of microbiota investigations as health marker.

Longitudinal dynamics of farmer and livestock nasal and faecal microbiomes and resistomes

Globally, half a billion people are employed in animal agriculture and are directly exposed to the associated microorganisms. However, the extent to which such exposures affect resident human microbiomes is unclear. Here we conducted a longitudinal profiling of the nasal and faecal microbiomes of 66 dairy farmers and 166 dairy cows over a year-long period. We compare farmer microbiomes to those of 60 age-, sex- and ZIP code-matched people with no occupational exposures to farm animals (non-farmers). We show that farming is associated with microbiomes containing livestock-associated microbes; this is most apparent in the nasal bacterial community, with farmers harbouring a richer and more diverse nasal community than non-farmers. Similarly, in the gut microbial communities, we identify more shared microbial lineages between cows and farmers from the same farms. Additionally, we find that shared microbes are associated with antibiotic resistance genes. Overall, our study demonstrates the interconnectedness of human and animal microbiomes.

Microbiome One Health model for a healthy ecosystem

The attention on microbiome research and its translation to application deployment is escalating along with diffused hype. There is real excitement in this new science, leveraging the growing potential of advances in molecular biology and sequencing techniques. Yet, despite the substantial efforts provided by the scientific communities, the true significance of research achievements requires coordinated and constructive actions across interdisciplinary fields. Individual researchers, universities, small and large companies, venture capitalists, and governments play a fundamental role in fostering collaboration and promoting knowledge that will benefit each other and sustain global prosperity. Making meaningful connections across different fields and getting a new perspective on how technological developments interrelate are the main drivers for creativity and progress. To help the broader innovation community focus on potentially new cross-sectorial developments, the One Health-microbiome-centric approach, defined here as "Microbiome One Health " , is considered as the efficient, holistic approach to product and service exploitations meant to preserve human well-being within a healthy ecosystem. The model opposes the biomedical system and generalizes the "One World-One Health ™" concept. The focus will be given to Nutrition as a driver of health and the food system for its commercial exploitation microbiome-centric, specifically at the interface of human/animal/agricultural. Remarkably, at the interface of humans/animals, the interaction with pets, specifically dogs, has been recognized as a driving force of novel microbiome exploitation.