The Composition and Diversity of the Gut Microbiota in Children Is Modifiable by the Household Dogs: Impact of a Canine-Specific Probiotic

Metagenomic insights into the resistome, mobilome, and virulome of dogs with diverse lifestyles

BACKGROUND

Dogs-whether pets, rural, or stray-exhibit distinct living styles that influence their fecal microbiota and resistomes, yet these dynamics remain underexplored. This study aimed to analyze and compare the fecal microbiota and resistomes of three groups of dogs (37 pets, 20 rural, and 25 stray dogs) in Shanghai, China.

RESULTS

Metagenomic analysis revealed substantial differences in fecal microbial composition and metabolic activities among the dog groups. Pet dogs displayed the lowest microbial diversity. Using Shapley Additive Explanations (SHAP), an interpretable machine learning approach, Ligilactobacillus emerged as the most diverse genus, with significantly higher SHAP values in stray dogs, suggesting enhanced adaptability to more variable and less controlled environments. Across all samples, 587 antibiotic resistance genes (ARGs) were identified, conferring resistance to 14 antibiotic classes. A striking observation was the detection of mcr-1 in one pet dog, indicating a potential public health risk. The floR gene was identified as a key differentiator in resistance profiles, particularly in pet and rural dogs, likely due to antibiotic exposure in their environments.

CONCLUSION

This study provides the first comprehensive assessment of fecal microbiota and resistome variations among dogs with different lifestyles, revealing a less resilient microbiome and heightened antimicrobial resistance in pet dogs, which could have public health implications.

A 15-day pilot biodiversity intervention with horses in a farm system leads to gut microbiome rewilding in 10 urban Italian children

To provide some glimpses on the possibility of shaping the human gut microbiome (GM) through probiotic exchange with natural ecosystems, here we explored the impact of 15 days of daily interaction with horses on the GM of 10 urban-living Italian children. Specifically, the children were in close contact with the horses in an "educational farm", where they spent almost 10 h/day interacting with the animals. The children's GM was assessed before and after the horse interaction using metabarcoding sequencing and shotgun metagenomics, along with the horses' skin, oral and fecal microbiomes. Targeted metabolomic analysis for GM-produced beneficial metabolites (i.e., short-chain fatty acids) in the children's feces was also performed. Interaction with horses facilitated the acquisition of health-related traits in the children's GM, such as increased diversity, enhanced butyrate production and an increase in several health-promoting species considered to be next-generation probiotics. Among these, the butyrate producers Facecalibacterium prausnitzii and F. duncaniae and a species belonging to the order Christensenellales. Interaction with horses was also associated with increased proportions of Eggerthella lenta, Gordonibacter pamelae and G. urolithinfaciens, GM components known to play a role in the bioconversion of dietary plant polyphenols into beneficial metabolites. Notably, no increase in potentially harmful traits, including toxin genes, was observed. Overall, our pilot study provides some insights on the existence of possible health-promoting exchanges between children and horses microbiomes. It lays the groundwork for an implemented and more systematic enrollment effort to explore the full complexity of human GM rewilding through exchange with natural ecosystems, aligning with the One Health approach.

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.

Fecal microbiota profiles of growing pigs and their relation to growth performance

The early gut microbiota composition is fundamentally important for piglet health, affecting long-term microbiome development and immunity. In this study, the gut microbiota of postparturient dams was compared with that of their offspring in three Finnish pig farms at three growth phases. The differences in fecal microbiota of three study development groups (Good, Poorly, and PrematureDeath) were analyzed at birth (initial exposure phase), weaning (transitional phase), and before slaughter (stable phase). Dam Lactobacillaceae abundance was lower than in piglets at birth. Limosilactobacillus reuteri and Lactobacillus amylovorus were dominantly expressed in dams and their offspring. Altogether 17 piglets (68%) were identified with Lactobacillaceae at the initial exposure phase, divided unevenly among the development groups: 85% of Good, 37.5% of Poorly, and 75% of PrematureDeath pigs. The development group Good was identified with the highest microbial diversity, whereas the development group PrematureDeath had the lowest diversity. After weaning, the abundance and versatility of Lactobacillaceae in piglets diminished, shifting towards the microbiome of the dam. In conclusion, the fecal microbiota of pigs tends to develop towards a similar alpha and beta diversity despite development group and rearing environment.

Microbiota insights into pet ownership and human health

The relationship between pet and owner has already been studied in several studies. Reviewing and summarizing studies on human and pet microbiota and their effects due to keeping pets is the purpose of the current study. Microbiota of the gut, oral cavity, and skin are unique to each individual, and this is also true of their pets (cats and dogs). Microbiota homeostasis is essential for the health of pets and their owners. Dysbiosis or imbalances in the microbiota can increase the risk of disorder progressions such as IBD or Clostridium difficile infections, among others. The microbial communities of humans change as a result of various factors, such as keeping pets. Pet owners frequently contact domestic dogs and cats, which affects their microbiota. As a result of keeping pets, the microbiota of different areas of the human body has changed, which has been associated with a decrease in pathogenic bacteria and an increase in beneficial bacteria.

The case for microbial intervention at weaning

Weaning, the transition from a milk-based diet to solid food, coincides with the most significant shift in gut microbiome composition in the lifetime of most mammals. Notably, this period also marks a "window of opportunity" where key components of the immune system develop, and host-microbe interactions shape long-term immune homeostasis thereby influencing the risk of autoimmune and inflammatory diseases. This review provides a comprehensive analysis of the changes in nutrition, microbiota, and host physiology that occur during weaning. We explore how these weaning-associated processes differ across species, lifestyles, and regions of the intestine. Using prinicples of microbial ecology, we propose that the weaning transition is an optimal period for microbiome-targeted therapeutic interventions. Additionally, we suggest that replicating features of the weaning microbiome in adults could promote the successful engraftment of probiotics. Finally, we highlight key research areas that could deepen our understanding of the complex relationships between diet, commensal microbes, and the host, informing the development of more effective microbial therapies.

Prevalence of Pentatrichomonas hominis in foxes and raccoon dogs and changes in the gut microbiota of infected female foxes in the Hebei and Henan Provinces in China

Pentatrichomonas hominis (P. hominis) is a zoonotic parasite that affects a wide range of hosts, causing gastrointestinal diseases. The present study aimed to evaluate the prevalence of P. hominis among caged foxes and raccoon dogs and the effect of P. hominis on the gut microbiota in female foxes. A total of 893 fresh fecal samples were collected from the Hebei and Henan Provinces in China. P. hominis was screened based on 18S rRNA gene expression via nested PCR. The difference in the gut microbiota between nine P. hominis-positive and nine P. hominis-negative samples was investigated by 16S rRNA gene sequencing. The total prevalence of P. hominis infection in foxes and raccoon dogs was 31.7% (283/893). The prevalence rates of P. hominis infection were 28.2% (88/312) and 33.6% (195/581) in foxes and raccoon dogs, respectively. Phylogenetic analysis revealed that all P. hominis strains detected in foxes and raccoon dogs in the present study were the zoonotic genotype CC1. Moreover, compared with those in the P. hominis-negative group, the diversity of the gut microbiota in the P. hominis-positive group was lower, and the abundance of Firmicutes and the ratio of Firmicutes/Bacteroidetes (F/B) in the P. hominis-positive group were lower than those in the P. hominis-negative group. We speculate that these differences may be due to indigestion and diarrhea in infected female foxes. Overall, the present study evaluated the prevalence of P. hominis in foxes and raccoon dogs in the Henan and Hebei Provinces and revealed that P. hominis infection interrupted the diversity of the gut microbiota in female foxes.

Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua

BACKGROUND

Early life plays a vital role in the development of the gut microbiome and subsequent health. While many factors that shape the gut microbiome have been described, including delivery mode, breastfeeding, and antibiotic use, the role of household environments is still unclear. Furthermore, the development of the gut antimicrobial resistome and its role in health and disease is not well characterized, particularly in settings with water insecurity and less sanitation infrastructure.

RESULTS

This study investigated the gut microbiome and resistome of infants and young children (ages 4 days-6 years) in rural Nicaragua using Oxford Nanopore Technology's MinION long-read sequencing. Differences in gut microbiome diversity and antibiotic resistance gene (ARG) abundance were examined for associations with host factors (age, sex, height for age z-score, weight for height z-score, delivery mode, breastfeeding habits) and household environmental factors (animals inside the home, coliforms in drinking water, enteric pathogens in household floors, fecal microbial source tracking markers in household floors). We identified anticipated associations of higher gut microbiome diversity with participant age and vaginal delivery. However, novel to this study were the significant, positive associations between ruminant and dog fecal contamination of household floors and gut microbiome diversity. We also identified greater abundance of potential pathogens in the gut microbiomes of participants with higher fecal contamination on their household floors. Path analysis revealed that water quality and household floor contamination independently and significantly influenced gut microbiome diversity when controlling for age. These gut microbiome contained diverse resistome, dominated by multidrug, tetracycline, macrolide/lincosamide/streptogramin, and beta-lactam resistance. We found that the abundance of ARGs in the gut decreased with age. The bacterial hosts of ARGs were mainly from the family Enterobacteriaceae, particularly Escherichia coli.

CONCLUSIONS

This study identified the role of household environmental contamination in the developing gut microbiome and resistome of young children and infants with a One Health perspective. We found significant relationships between host age, gut microbiome diversity, and the resistome. Understanding the impact of the household environment on the development of the resistome and microbiome in early life is essential to optimize the relationship between environmental exposure and human health. Video Abstract.

Microfiber-loaded bacterial community in indoor fallout and air-conditioner filter dust

Microfibers (MFs) are widely existed in indoor air; however, characteristic of microbiota on MFs is largely unknown. In this study, air-borne MFs were collected from fallout or air-conditioner (AC) filter dust in three types of indoor space including living room, dormitory and office. Both plastic and natural MFs were identified by Fourier transform infrared spectroscopy. Ultramicroscopic observation showed dense biofilms adhering on surfaces of MFs. Fallout MFs contained more bacteria but fewer fungi than MFs from AC filter dust. MFs-loaded bacteria were of highest abundance in living rooms, following dormitories and offices. Bacterial community and its diversity were further analyzed by 16S rRNA High-throughput sequencing. Up to 4540 of bacterium OTUs were shared in these MFs samples, unique OTUs in fallout and AC filter samples accounting for 26.3 % and 25.7 % of the total. Compared to MFs fallout, AC filter MFs contained more species of pathogenic bacteria, such as Betaproteobacteriales and Ralstonia, with obviously different β-diversity between two groups. Phenotypic analysis showed that fallout and AC filter MFs bacteria presented high index values of film formation, oxidative stress tolerance and potential pathogenicity. Overall, these results suggest that abundant bacteria including pathogen can be loaded on MFs, and would pose health risks through delivery of indoor MFs.

Maternal-infant antibiotic resistance genes transference: what do we know?

Resistance to antibiotics is becoming a worldwide threat as infections caused by multidrug-resistant pathogenic microorganisms can overcome antibiotic treatments and spread quickly in the population. In the context of early life, newborns are at increased risk as their immune system is still under development, so infections and acquisition of resistance during childhood have short- and long-term consequences for the health. The moment of birth is the first exposure of infants to possible antibiotic-resistant microorganisms that may colonize their gut and other body sites. Different factors including mode of delivery, previous antibiotic exposure of the mother, gestational age and consumption of antibiotics in early-life have been described to modulate the neonate's microbiota, and thus, the resistome. Other factors, such as lactation, also impact the establishment and development of gut microbiota, but little is known about the role of breastmilk in transferring Antibiotic Resistant Genes (ARG). A deeper understanding of vertical transmission of antibiotic resistance from mothers to their offspring is necessary to determine the most effective strategies for reducing antibiotic resistance in the early life. In this review, we aim to present the current perspective on antibiotic resistances in mother-infant dyads, as well as a new insight on the study of the human gut and breastmilk resistome, and current strategies to overcome this public health problem, toward highlighting the gaps of knowledge that still need to be closed.

Balancing the Risks and Benefits of Pet Ownership in Pediatric Transplant Recipients

In recent decades, the number of pediatric transplantations and their survival rates have increased. Psychological problems and poorer quality of life are notable among children undergoing transplantation and can have long-lasting consequences and affect immunosuppressive therapy adherence. Pet ownership and animal contact have been associated with physical, mental, and social health benefits. Despite these potential benefits, however, companion animals are known to be a source of infection, which is one of the main concerns for clinicians. Because of immunosuppression, these children are particularly vulnerable to infections. Zoonoses comprise a long list of infectious diseases and represent a major public health problem. Nevertheless, many families and most healthcare providers are unaware of these potential risks, and there is a worrisome lack of recommendations to manage the risk-benefit balance, which could pose a risk for acquiring a zoonosis. Furthermore, no data are available on the number of transplanted patients with pets, and this risk-benefit balance is difficult to adequately evaluate. In this document, we review the currently available evidence regarding the epidemiology of zoonotic infections in patients undergoing transplantation, focusing on pediatric patients from a risk-benefit perspective, to help inform decision-making for clinicians. Families and healthcare professionals should be aware of the risks, and clinicians should actively screen for pets and offer comprehensive information as part of routine clinical practice. A multidisciplinary approach will ensure proper care of patients and pets and will establish preventive measures to ensure patients are safe living with their pets.

Domestic Environment and Gut Microbiota: Lessons from Pet Dogs

Accumulating data show the involvement of intestinal microbiota in the development and maintenance of numerous diseases. Many environmental factors influence the composition and function of the gut microbiota. An animal model subjected to the same environmental constraints that will allow better characterization of the microbiota–host dialogue is awaited. The domestic dog has physiological, dietary and pathological characteristics similar to those of humans and shares the domestic environment and lifestyle of its owner. This review exposes how the domestication of dogs has brought them closer to humans based on their intrinsic and extrinsic similarities which were discerned through examining and comparing the current knowledge and data on the intestinal microbiota of humans and canines in the context of several spontaneous pathologies, including inflammatory bowel disease, obesity and diabetes mellitus.

Associations of early-life pet ownership with asthma and allergic sensitization: a meta-analysis of >77,000 children from the EU Child Cohort Network

BACKGROUND

Studies examining associations of early-life cat and dog ownership with childhood asthma have reported inconsistent results. Several factors could explain these inconsistencies, including type of pet, timing and degree of exposure.

OBJECTIVE

To study associations of early-life cat and dog ownership with school-age asthma, including the role of type (cat versus dog), timing (never, prenatal or early childhood) and degree (number) of ownership, and the role of allergic sensitisation.

METHODS

We used harmonised data from 77,434 mother-child dyads aged 5-11 years from nine birth cohorts in the EU Child Cohort Network. Associations were examined through the DataSHIELD platform using adjusted logistic regression models, fitted separately for each cohort and combined using random-effects meta-analysis.

RESULTS

Early-life cat and dog ownership ranged between 12-45% and 7-47% respectively, and prevalence of asthma between 2-20%. There was no overall association between either cat or dog ownership and asthma (OR: 0.97 (95% CI: 0.87-1.09) and 0.92 (0.85-1.01), respectively). Timing and degree of ownership did not strongly influence associations. Cat and dog ownership were also not associated with cat- and dog-specific allergic sensitisation (OR: 0.92 (0.75-1.13) and 0.93 (0.57-1.54), respectively). However, cat- and dog-specific allergic sensitisation were strongly associated with school-age asthma (OR: 6.69 (4.91-9.10) and 5.98 (3.14-11.36), respectively). There was also some indication of an interaction between ownership and sensitisation, suggesting that ownership may exacerbate the risks associated with pet-specific sensitisation, but offer some protection against asthma in the absence of sensitisation.

CONCLUSION

Our findings do not support early-life cat and dog ownership in themselves increasing the risk of school-age asthma, but suggest that ownership may potentially exacerbate the risks associated with cat- and dog-specific allergic sensitisation.

Dogs' Microbiome From Tip to Toe

Microbiota and microbiome, which refers, respectively, to the microorganisms and conjoint of microorganisms and genes are known to live in symbiosis with hosts, being implicated in health and disease. The advancements and cost reduction associated with high-throughput sequencing techniques have allowed expanding the knowledge of microbial communities in several species, including dogs. Throughout their body, dogs harbor distinct microbial communities according to the location (e.g., skin, ear canal, conjunctiva, respiratory tract, genitourinary tract, gut), which have been a target of study mostly in the last couple of years. Although there might be a core microbiota for different body sites, shared by dogs, it is likely influenced by intrinsic factors such as age, breed, and sex, but also by extrinsic factors such as the environment (e.g., lifestyle, urban vs rural), and diet. It starts to become clear that some medical conditions are mediated by alterations in microbiota namely dysbiosis. Moreover, understanding microbial colonization and function can be used to prevent medical conditions, for instance, modulation of gut microbiota of puppies is more effective to ensure a healthy gut than interventions in adults. This paper gathers current knowledge of dogs' microbial communities, exploring their function, implications in the development of diseases, and potential interactions among communities while providing hints for further research.