Fecal microbiota transplantation as a tool to treat and reduce susceptibility to disease in animals

Phylosymbiosis and Elevated Cancer Risk in Genetically Depauperate Channel Island Foxes

Examination of the host-associated microbiome in wildlife can provide critical insights into the eco-evolutionary factors driving species diversification and response to disease. This is particularly relevant for isolated populations lacking genomic variation, a phenomenon that is increasingly common as human activities create habitat 'islands' for wildlife. Here, we characterised the gut and otic microbial communities of one such species: Channel Island foxes (Urocyon littoralis). The gut microbiome provided evidence of phylosymbiosis by reflecting the host phylogeny, geographic proximity, history of island colonisation and contemporary ecological differences, whereas the otic microbiome primarily reflected geography and disease. Santa Catalina Island foxes are uniquely predisposed to ceruminous gland tumours following infection with Otodectes cynotis ear mites, while San Clemente and San Nicolas Island foxes exhibit ear mite infections without evidence of tumours. Comparative analyses of otic microbiomes revealed that mite-infected Santa Catalina and San Clemente Island foxes exhibited reduced bacterial diversity, skewed abundance towards the opportunistic pathogen Staphylococcus pseudintermedius and disrupted microbial community networks. However, Santa Catalina Island foxes uniquely harboured Fusobacterium and Prevotella bacteria as potential keystone taxa. These bacteria have previously been associated with colorectal cancer and may predispose Santa Catalina Island foxes to an elevated cancer risk. In contrast, mite-infected San Nicolas Island foxes maintained high bacterial diversity and robust microbial community networks, suggesting that they harbour more resilient microbiomes. Considered together, our results highlight the diverse eco-evolutionary factors influencing commensal microbial communities and their hosts and underscore how the microbiome can contribute to disease outcomes.

Fecal microbiota transplants facilitate post-antibiotic recovery of gut microbiota in cheetahs (Acinonyx jubatus)

Burgeoning study of host-associated microbiomes has accelerated the development of microbial therapies, including fecal microbiota transplants (FMTs). FMTs provide host-specific microbial supplementation, with applicability across host species. Studying FMTs can simultaneously provide comparative frameworks for understanding microbial therapies in diverse microbial systems and improve the health of managed wildlife. Ex-situ carnivores, including cheetahs (Acinonyx jubatus), often suffer from intractable gut infections similar to those treated with antibiotics and FMTs in humans, providing a valuable system for testing FMT efficacy. Using an experimental approach in 21 cheetahs, we tested whether autologous FMTs facilitated post-antibiotic recovery of gut microbiota. We used 16S rRNA sequencing and microbial source tracking to characterize antibiotic-induced microbial extirpations and signatures of FMT engraftment for single versus multiple FMTs. We found that antibiotics extirpated abundant bacteria and FMTs quickened post-antibiotic recovery via engraftment of bacteria that may facilitate protein digestion and butyrate production (Fusobacterium). Although multiple FMTs better sustained microbial recovery compared to a single FMT, one FMT improved recovery compared to antibiotics alone. This study elucidated the dynamics of microbiome modulation in a non-model system and improves foundations for reproducible, low-cost, low-dose, and minimally invasive FMT protocols, emphasizing the scientific and applied value of FMTs across species.

Microbiome-based therapies for Parkinson's disease

The human gut microbiome dysbiosis plays an important role in the pathogenesis of Parkinson's disease (PD). The bidirectional relationship between the enteric nervous system (ENS) and central nervous system (CNS) under the mediation of the gut-brain axis control the gastrointestinal functioning. This review article discusses key mechanisms by which modifications in the composition and function of the gut microbiota (GM) influence PD progression and motor control loss. Increased intestinal permeability, chronic inflammation, oxidative stress, α-synuclein aggregation, and neurotransmitter imbalances are some key factors that govern gastrointestinal pathology and PD progression. The bacterial taxa of the gut associated with PD development are discussed with emphasis on the enteric nervous system (ENS), as well as the impact of gut bacteria on dopamine production and levodopa metabolism. The pathophysiology and course of the disease are associated with several inflammatory markers, including TNF-α, IL-1β, and IL-6. Emerging therapeutic strategies targeting the gut microbiome include probiotics, prebiotics, synbiotics, postbiotics, and fecal microbiota transplantation (FMT). The article explored how dietary changes may affect the gut microbiota (GM) and the ways that can affect Parkinson's disease (PD), with a focus on nutrition-based, Mediterranean, and ketogenic diets. This comprehensive review synthesizes current evidence on the role of the gut microbiome in PD pathogenesis and explores its potential as a therapeutic target. Understanding these complex interactions may assist in the development of novel diagnostic tools and treatment options for this neurodegenerative disorder.

The microbiota: a key regulator of health, productivity, and reproductive success in mammals

The microbiota, intensely intertwined with mammalian physiology, significantly impacts health, productivity, and reproductive functions. The normal microbiota interacts with the host through the following key mechanisms: acting as a protective barrier against pathogens, maintain mucosal barrier integrity, assisting in nutrient metabolism, and modulating of the immune response. Therefore, supporting growth and development of host, and providing protection against pathogens and toxic substances. The microbiota significantly influences brain development and behavior, as demonstrated by comprehensive findings from controlled laboratory experiments and human clinical studies. The prospects suggested that gut microbiome influence neurodevelopmental processes, modulate stress responses, and affect cognitive function through the gut-brain axis. Microbiota in the gastrointestinal tract of farm animals break down and ferment the ingested feed into nutrients, utilize to produce meat and milk. Among the beneficial by-products of gut microbiota, short-chain fatty acids (SCFAs) are particularly noteworthy for their substantial role in disease prevention and the promotion of various productive aspects in mammals. The microbiota plays a pivotal role in the reproductive hormonal systems of mammals, boosting reproductive performance in both sexes and fostering the maternal-infant connection, thereby becoming a crucial factor in sustaining mammalian existence. The microbiota is a critical factor influencing reproductive success and production traits in mammals. A well-balanced microbiome improves nutrient absorption and metabolic efficiency, leading to better growth rates, increased milk production, and enhanced overall health. Additionally, it regulates key reproductive hormones like estrogen and progesterone, which are essential for successful conception and pregnancy. Understanding the role of gut microbiota offers valuable insights for optimizing breeding and improving production outcomes, contributing to advancements in agriculture and veterinary medicine. This study emphasizes the critical ecological roles of mammalian microbiota, highlighting their essential contributions to health, productivity, and reproductive success. By integrating human and veterinary perspectives, it demonstrates how microbial communities enhance immune function, metabolic processes, and hormonal regulation across species, offering insights that benefit both clinical and agricultural advancements.

Gut bacterial composition shows sex-specific shifts during breeding season in ex situ managed black-footed ferrets

The gut microbiome of mammals engages in a dynamic relationship with the body and contributes to numerous physiological processes integral to overall health. Understanding the factors shaping animal-associated bacterial communities is therefore paramount to the maintenance and management in ex situ wildlife populations. Here, we characterized the gut microbiome of 48 endangered black-footed ferrets (Mustela nigripes) housed at Smithsonian's National Zoo and Conservation Biology Institute (Front Royal, Virginia, USA). We collected longitudinal fecal samples from males and females across two distinct reproductive seasons to consider the role of host sex and reproductive physiology in shaping bacterial communities, as measured using 16S rRNA amplicon sequencing. Within each sex, gut microbial composition differed between breeding and non-breeding seasons, with five bacterial taxa emerging as differentially abundant. Between sexes, female and male microbiomes were similar during non-breeding season but significantly different during breeding season, which may result from sex-specific physiological changes associated with breeding. Finally, we found low overall diversity consistent with other mammalian carnivores alongside high relative abundances of potentially pathogenic microbes such as Clostridium, Escherichia, Paeniclostridium, and (to a lesser degree) Enterococcus-all of which have been associated with gastrointestinal or reproductive distress in mammalian hosts, including black-footed ferrets. We recommend further study of these microbes and possible therapeutic interventions to promote more balanced microbial communities. These results have important implications for ex situ management practices that can improve the gut microbial health and long-term viability of black-footed ferrets.

Interpretation of the effects of rumen acidosis on the gut microbiota and serum metabolites in calves based on 16S rDNA sequencing and non-target metabolomics

Introduction

Rumen acidosis is one of the most common diseases in beef cattle. It severely affects the normal development of calves and poses a significant threat to the farming industry. However, the influence of rumen acidosis on the gut microbiota and serum metabolites of calves is currently unclear.

Objective

The aim of this study is to investigate the changes in the gut microbiota and serum metabolites in calves after rumen acidosis and analyse the correlation.

Methods

Eight calves were selected as the rumen acidosis group, and eight health calves were selected as the healthy group. The faecal gut microbiota and serum metabolites of calves were detected respectively using 16S rDNA high-throughput sequencing and non-target metabolomics. The correlation between gut microbiota and serum metabolites was analyzed by Spearman correlation analysis.

Results

Differential analysis of the diversity and composition of gut microbiota between eight male healthy (Health) and eight male rumen acidosis (Disease) calves revealed that rumen acidosis increased the abundance of the gut microbiota in calves. At the phylum level, compared to the Healthy group, the relative abundance of Proteobacteria in the Disease group significantly decreased (P<0.05), while the relative abundance of Desulfobacterota significantly increased in the Disease group (P<0.05). At the genus level, compared to the Disease group, the relative abundance of Alloprevotella, Muribaculaceae, Succinivibrio, Prevotella, Agathobacter and Parabacteroides significantly increased in the Healthy group (P<0.05), while the relative abundance of Christensenellaceae_R-7 and Monoglobus significantly decreased in the Healthy group (P<0.05). Differential analysis results showed the Healthy group had 23 genera with higher abundance, while the Disease group had 47 genera with higher abundance. Serum metabolomics results revealed the differential metabolites associated with rumen acidosis, including nicotinamide, niacin, L-glutamic acid and carnosine, were mainly enriched in the nicotinate and nicotinamide pathway and the histidine pathway.

Conclusion

The occurrence of rumen acidosis can induce changes in the gut microbiota of calves, with a significant increase of the Christensenellaceae_R-7 genus and a significant decrease of Prevotella and Succinivibrio genera. In addition, the occurrence of rumen acidosis can also induce changes in serum metabolites including niacin, niacinamide, L-glutamine, and carnosine, which may serve as the diagnostic biomarkers of rumen acidosis of calves.

Fecal Microbiota Transplantation in a Domestic Ferret Suffering from Chronic Diarrhea and Maldigestion-Fecal Microbiota and Clinical Outcome: A Case Report

This case report describes the effects of fecal microbiota transplantation (FMT) administered via enema in a 4-year-old spayed, champagne Domestic Ferret (Mustela putorius furo) with chronic diarrhea, maldigestion and weight loss. We aimed to establish a protocol for FMT as a novel therapeutic treatment for chronic diarrhea in domestic ferrets. We mapped the fecal microbiome by 16S rRNA gene amplicon sequencing to track the patient's fecal microbiota throughout the treatment and observation period. Initial oral FMTs were associated with temporary weight improvement but subsequent treatments, via enema and oral delivery, showed varied outcomes. Molecular analysis highlighted distinct gut microbiota composition profiles between the healthy donor and the diseased ferret. The diseased ferret initially exhibited high abundance of Enterobacteriaceae, Escherichia, and Enterobacter, which ultimately normalized to level like those found in the donor ferret. Overall, the gut microbiota of the recipient became more similar to the donor microbiota using a Yue-Clayton theta coefficients analysis. After a restoration of the gut microbiota and clinical improvement, the recipient's symptoms returned indicating that repeated FMTs might be required for long-term resolution of symptoms and complete restructuring of the gut microbiota. Future studies are warranted to map the microbiome of a larger population of domestic ferrets to investigate a potential correlation between fecal microbiota profiles and chronic/acute gastrointestinal disorders.

Integrating microbiome science and evolutionary medicine into animal health and conservation

Microbiome science has provided groundbreaking insights into human and animal health. Similarly, evolutionary medicine - the incorporation of eco-evolutionary concepts into primarily human medical theory and practice - is increasingly recognised for its novel perspectives on modern diseases. Studies of host-microbe relationships have been expanded beyond humans to include a wide range of animal taxa, adding new facets to our understanding of animal ecology, evolution, behaviour, and health. In this review, we propose that a broader application of evolutionary medicine, combined with microbiome science, can provide valuable and innovative perspectives on animal care and conservation. First, we draw on classic ecological principles, such as alternative stable states, to propose an eco-evolutionary framework for understanding variation in animal microbiomes and their role in animal health and wellbeing. With a focus on mammalian gut microbiomes, we apply this framework to populations of animals under human care, with particular relevance to the many animal species that suffer diseases linked to gut microbial dysfunction (e.g. gut distress and infection, autoimmune disorders, obesity). We discuss diet and microbial landscapes (i.e. the microbes in the animal's external environment), as two factors that are (i) proposed to represent evolutionary mismatches for captive animals, (ii) linked to gut microbiome structure and function, and (iii) potentially best understood from an evolutionary medicine perspective. Keeping within our evolutionary framework, we highlight the potential benefits - and pitfalls - of modern microbial therapies, such as pre- and probiotics, faecal microbiota transplants, and microbial rewilding. We discuss the limited, yet growing, empirical evidence for the use of microbial therapies to modulate animal gut microbiomes beneficially. Interspersed throughout, we propose 12 actionable steps, grounded in evolutionary medicine, that can be applied to practical animal care and management. We encourage that these actionable steps be paired with integration of eco-evolutionary perspectives into our definitions of appropriate animal care standards. The evolutionary perspectives proposed herein may be best appreciated when applied to the broad diversity of species under human care, rather than when solely focused on humans. We urge animal care professionals, veterinarians, nutritionists, scientists, and others to collaborate on these efforts, allowing for simultaneous care of animal patients and the generation of valuable empirical data.

Evaluation of the safety and efficacy of fecal microbiota transplantations in bottlenose dolphins (Tursiops truncatus) using metagenomic sequencing

AIMS

Gastrointestinal disease is a leading cause of morbidity in bottlenose dolphins (Tursiops truncatus) under managed care. Fecal microbiota transplantation (FMT) holds promise as a therapeutic tool to restore gut microbiota without antibiotic use. This prospective clinical study aimed to develop a screening protocol for FMT donors to ensure safety, determine an effective FMT administration protocol for managed dolphins, and evaluate the efficacy of FMTs in four recipient dolphins.

METHODS AND RESULTS

Comprehensive health monitoring was performed on donor and recipient dolphins. Fecal samples were collected before, during, and after FMT therapy. Screening of donor and recipient fecal samples was accomplished by in-house and reference lab diagnostic tests. Shotgun metagenomics was used for sequencing. Following FMT treatment, all four recipient communities experienced engraftment of novel microbial species from donor communities. Engraftment coincided with resolution of clinical signs and a sustained increase in alpha diversity.

CONCLUSION

The donor screening protocol proved to be safe in this study and no adverse effects were observed in four recipient dolphins. Treatment coincided with improvement in clinical signs.

Microbiome Responses to Fecal Microbiota Transplantation in Cats with Chronic Digestive Issues

There is growing interest in the application of fecal microbiota transplants (FMTs) in small animal medicine, but there are few published studies that have tested their effects in the domestic cat (Felis catus). Here we use 16S rRNA gene sequencing to examine fecal microbiome changes in 46 domestic cats with chronic digestive issues that received FMTs using lyophilized stool that was delivered in oral capsules. Fecal samples were collected from FMT recipients before and two weeks after the end of the full course of 50 capsules, as well as from their stool donors (N = 10), and other healthy cats (N = 113). The fecal microbiomes of FMT recipients varied with host clinical signs and dry kibble consumption, and shifts in the relative abundances of Clostridium, Collinsella, Megamonas, Desulfovibrio and Escherichia were observed after FMT. Overall, donors shared 13% of their bacterial amplicon sequence variants (ASVs) with FMT recipients and the most commonly shared ASVs were classified as Prevotella 9, Peptoclostridium, Bacteroides, and Collinsella. Lastly, the fecal microbiomes of cats with diarrhea became more similar to the microbiomes of age-matched and diet-matched healthy cats compared to cats with constipation. Overall, our results suggest that microbiome responses to FMT may be modulated by the FMT recipient's initial presenting clinical signs, diet, and their donor's microbiome.

Coprophagy rapidly matures juvenile gut microbiota in a precocial bird

Coprophagy is a behavior where animals consume feces, and has been observed across a wide range of species, including birds and mammals. The phenomenon is particularly prevalent in juveniles, but the reasons for this remain unclear. One hypothesis is that coprophagy enables offspring to acquire beneficial gut microbes that aid development. However, despite the potential importance of this behavior, studies investigating the effects in juveniles are rare. Here we experimentally test this idea by examining how ingestion of adult feces by ostrich chicks affects their gut microbiota development, growth, feeding behavior, pathogen abundance, and mortality. We conducted extensive longitudinal experiments for 8 weeks, repeated over 2 years. It involved 240 chicks, of which 128 were provided daily access to fresh fecal material from adults and 112 were simultaneously given a control treatment. Repeated measures, behavioral observations, and DNA metabarcoding of the microbial gut community, both prior to and over the course of the experiment, allowed us to evaluate multiple aspects of the behavior. The results show that coprophagy causes (a) marked shifts to the juvenile gut microbiota, including a major increase in diversity and rapid maturation of the microbial composition, (b) higher growth rates (fecal-supplemented chicks became 9.4% heavier at 8 weeks old), (c) changes to overall feeding behavior but no differences in feed intake, (d) lower abundance of a common gut pathogen (Clostridium colinum), and (e) lower mortality associated with gut disease. Together, our results suggest that the behavior of coprophagy in juveniles is highly beneficial and may have evolved to accelerate the development of gut microbiota.

Pilot evaluation of a single oral fecal microbiota transplantation for canine atopic dermatitis

The gut microbiota has been suggested to be involved in the pathogenesis of canine atopic dermatitis (cAD). However, the gut microbiota has not been well characterized in dogs with atopic dermatitis (AD). In addition, the efficacy of fecal microbiota transplantation (FMT) in dogs with AD remains unclear. This research, therefore, aimed to characterize the gut microbiota of dogs with AD and conduct pilot evaluation of the efficacy of a single oral FMT on clinical signs and the gut microbiota of dogs with AD. For these purposes, we used 12 dogs with AD and 20 healthy dogs. The 16S rRNA analysis of the fecal microbiota revealed significant differences between 12 dogs with AD and 20 healthy dogs. Next, a single oral FMT was performed in 12 dogs with AD as a single-arm, open-label clinical trial for 56 days. A single oral FMT significantly decreased Canine Atopic Dermatitis Extent and Severity Index (CADESI)-04 scores from day 0 (median score, 16.5) to day 56 (8) and Pruritus Visual Analog Scale (PVAS) scores from days 0 (median score, 3) to day 56 (1). Furthermore, a single oral FMT changed the composition of the fecal microbiota of dogs with AD at the phylum and genus levels. The number of common amplicon sequence variants in the fecal microbiota between donor dogs and dogs with AD was positively correlated with CADESI-04 and PVAS reduction ratios 56 days after FMT. Our findings suggest that the gut microbiota plays a pivotal role in the pathogenesis of cAD, and that oral FMT could be a new therapeutic approach targeting the gut microbiota in cAD.

Chicken cecal microbiota reduces abdominal fat deposition by regulating fat metabolism

Cecal microbiota plays an essential role in chicken health. However, its contribution to fat metabolism, particularly in abdominal fat deposition, which is a severe problem in the poultry industry, is still unclear. Here, chickens at 1, 4, and 12 months of age with significantly (p < 0.05) higher and lower abdominal fat deposition were selected to elucidate fat metabolism. A significantly (p < 0.05) higher mRNA expression of fat anabolism genes (ACSL1, FADS1, CYP2C45, ACC, and FAS), a significantly (p < 0.05) lower mRNA expression of fat catabolism genes (CPT-1 and PPARα) and fat transport gene APOAI in liver/abdominal fat of high abdominal fat deposition chickens indicated that an unbalanced fat metabolism leads to excessive abdominal fat deposition. Parabacteroides, Parasutterella, Oscillibacter, and Anaerofustis were found significantly (p < 0.05) higher in high abdominal fat deposition chickens, while Sphaerochaeta was higher in low abdominal fat deposition chickens. Further, Spearman correlation analysis indicated that the relative abundance of cecal Parabacteroides, Parasutterella, Oscillibacter, and Anaerofustis was positively correlated with abdominal fat deposition, yet cecal Sphaerochaeta was negatively correlated with fat deposition. Interestingly, transferring fecal microbiota from adult chickens with low abdominal fat deposition into one-day-old chicks significantly (p < 0.05) decreased Parabacteroides and fat anabolism genes, while markedly increased Sphaerochaeta (p < 0.05) and fat catabolism genes (p < 0.05). Our findings might help to assess the potential mechanism of cecal microbiota regulating fat deposition in chicken production.

The human and animals' malignant melanoma: comparative tumor models and the role of microbiome in dogs and humans

Currently, the most progressively occurring incident cancer is melanoma. The mouse is the most popular model in human melanoma research given its various benefits as a laboratory animal. Nevertheless, unlike humans, mice do not develop melanoma spontaneously, so they need to be genetically manipulated. In opposition, there are several reports of other animals, ranging from wild to domesticated animals, that spontaneously develop melanoma and that have cancer pathways that are similar to those of humans. The influence of the gut microbiome on health and disease is being the aim of many recent studies. It has been proven that the microbiome is a determinant of the host's immune status and disease prevention. In human medicine, there is increasing evidence that changes in the microbiome influences malignant melanoma progression and response to therapy. There are several similarities between some animals and human melanoma, especially between canine and human oral malignant melanoma as well as between the gut microbiome of both species. However, microbiome studies are scarce in veterinary medicine, especially in the oncology field. Future studies need to address the relevance of gut and tissue microbiome for canine malignant melanoma development, which results will certainly benefit both species in the context of translational medicine.

Comparing invasive and noninvasive faecal sampling in wildlife microbiome studies: A case study on wild common cranes

In ecological and conservation studies, responsible researchers strive to obtain rich data while minimizing disturbance to wildlife and ecosystems. We assessed if samples collected noninvasively can be used for faecal microbiome research, comparing microbiota of noninvasively collected faecal samples to those collected from trapped common cranes at the same sites over the same periods. We found significant differences in faecal microbial composition (alpha and beta diversity), which likely did not result from noninvasive sample exposure to soil contaminants, as assessed by comparing bacterial oxygen use profiles. Differences might result from trapped birds' exposure to sedatives or stress. We conclude that if all samples are collected in the same manner, comparative analyses are valid, and noninvasive sampling may better represent host faecal microbiota because there are no trapping effects. Experiments with fresh and delayed sample collection can elucidate effects of environmental exposures on microbiota. Further, controlled tests of stressing or sedation may unravel how trapping affects wildlife microbiota.

Fecal microbiota transplants modulate the gut microbiome of a two-toed sloth (Choloepus didactylus)

The microbes inhabiting an animal's gastrointestinal tracts, collectively known as the gut microbiome, are vital to animal health and wellbeing. For animals experiencing gut distress or infection, modulation of the gut microbiome, for example, via fecal microbiota transplant (FMT), provides a possible disease prevention and treatment method. The beneficial microbes present in the donor's transplanted feces can help combat pathogens, assist in digestion, and rebalance the recipient's microbiota. Investigating the efficacy of FMTs in animal health is a crucial step toward improving management strategies for species under human care. We present a case study of the use of FMTs in a two-toed sloth experiencing abnormally large, clumped, and frequent stools. We used 16 S rRNA amplicon sequencing of fecal samples to (a) compare the microbiomes of the FMT donor, a healthy, cohoused conspecific, and the FMT recipient and (b) assess the influence of multiple rounds of FMTs on the recipient's microbiome and stool consistency and frequency over time. In response to the FMTs, we found that the recipient's microbiome showed trends toward increased diversity, shifted community composition, and altered membership that more resembled the community of the donor. FMT treatment was also associated with marked, yet temporary, alleviation of the recipient's abnormal bowel movements, suggesting a broader impact on gut health. Our results provide valuable preliminary evidence that FMT treatments can augment the recipient's gut microbiome, with potential implications for animal health and management.

Stability and volatility shape the gut bacteriome and Kazachstania slooffiae dynamics in preweaning, nursery and adult pigs

The gut microbiome plays important roles in the maintenance of health and pathogenesis of diseases in the growing host. In order to fully comprehend the interplay of the gut microbiome and host, a foundational understanding of longitudinal microbiome, including bacteria and fungi, development is necessary. In this study, we evaluated enteric microbiome and host dynamics throughout the lifetime of commercial swine. We collected a total of 234 fecal samples from ten pigs across 31 time points in three developmental stages (5 preweaning, 15 nursery, and 11 growth adult). We then performed 16S rRNA gene amplicon sequencing for bacterial profiles and qPCR for the fungus Kazachstania slooffiae. We identified distinct bacteriome clustering according to the host developmental stage, with the preweaning stage exhibiting low bacterial diversity and high volatility amongst samples. We further identified clusters of bacteria that were considered core, increasing, decreasing or stage-associated throughout the host lifetime. Kazachstania slooffiae was absent in the preweaning stage but peaked during the nursery stage of the host. We determined that all host growth stages contained negative correlations between K. slooffiae and bacterial genera, with only the growth adult stage containing positive correlates. Our stage-associated bacteriome results suggested the neonate contained a volatile gut microbiome. Upon weaning, the microbiome became relatively established with comparatively fewer perturbations in microbiome composition. Differential analysis indicated bacteria might play distinct stage-associated roles in metabolism and pathogenesis. The lack of positive correlates and shared K. slooffiae-bacteria interactions between stages warranted future research into the interactions amongst these kingdoms for host health. This research is foundational for understanding how bacteria and fungi develop singularly, as well as within a complex ecosystem in the host's gut environment.

Microbiota Transplantation in Day-Old Broiler Chickens Ameliorates Necrotic Enteritis via Modulation of the Intestinal Microbiota and Host Immune Responses

A microbiota transplant (MT) originating from mature adult chicken ceca and propagated in bioreactors was administered to day-old broiler chicks to ascertain the degree to which, and how, the MT affects Clostridium perfringens (Cp)-incited necrotic enteritis (NE). Using a stress predisposition model of NE, birds administered the MT and challenged with Cp showed fewer necrotic lesions, and exhibited a substantially higher α- and β-diversity of bacteria in their jejunum and ceca. Birds challenged with Cp and not administered the MT showed decreased Lactobacillus and increased Clostridium sensu strico 1 in the jejunum. In ceca, Megamonas, a genus containing butyrate-producing bacteria, was only present in birds administered the MT, and densities of this genus were increased in birds challenged with Cp. Metabolite profiles in cecal digesta were altered in birds administered the MT and challenged with the pathogen; 59 metabolites were differentially abundant following MT treatment, and the relative levels of short chain fatty acids, butyrate, valerate, and propionate, were decreased in birds with NE. Birds administered the MT and challenged with Cp showed evidence of enhanced restoration of intestinal barrier functions, including elevated mRNA of MUC2B, MUC13, and TJP1. Likewise, birds administered the MT exhibited higher mRNA of IL2, IL17A, and IL22 at 2-days post-inoculation with Cp, indicating that these birds were better immunologically equipped to respond to pathogen challenge. Collectively, study findings demonstrated that administering a MT containing a diverse mixture of microorganisms to day-old birds ameliorated NE in broilers by increasing bacterial diversity and promoting positive immune responses.

Impacts of Gut Microbiota on the Immune System and Fecal Microbiota Transplantation as a Re-Emerging Therapy for Autoimmune Diseases

The enormous and diverse population of microorganisms residing in the digestive tracts of humans and animals influence the development, regulation, and function of the immune system. Recently, the understanding of the association between autoimmune diseases and gut microbiota has been improved due to the innovation of high-throughput sequencing technologies with high resolutions. Several studies have reported perturbation of gut microbiota as one of the factors playing a role in the pathogenesis of many diseases, such as inflammatory bowel disease, recurrent diarrhea due to Clostridioides difficile infections. Restoration of healthy gut microbiota by transferring fecal material from a healthy donor to a sick recipient, called fecal microbiota transplantation (FMT), has resolved or improved symptoms of autoimmune diseases. This (re)emerging therapy was approved for the treatment of drug-resistant recurrent C. difficile infections in 2013 by the U.S. Food and Drug Administration. Numerous human and animal studies have demonstrated FMT has the potential as the next generation therapy to control autoimmune and other health problems. Alas, this new therapeutic method has limitations, including the risk of transferring antibiotic-resistant pathogens or transmission of genes from donors to recipients and/or exacerbating the conditions in some patients. Therefore, continued research is needed to elucidate the mechanisms by which gut microbiota is involved in the pathogenesis of autoimmune diseases and to improve the efficacy and optimize the preparation of FMT for different disease conditions, and to tailor FMT to meet the needs in both humans and animals. The prospect of FMT therapy includes shifting from the current practice of using the whole fecal materials to the more aesthetic transfer of selective microbial consortia assembled in vitro or using their metabolic products.

Investigation of Host-Microbe-Parasite Interactions in an In Vitro 3D Model of the Vertebrate Gut

In vitro models of the gut-microbiome axis are in high demand. Conventionally, intestinal monolayers grown on Transwell setups are used to test the effects of commensals/pathogens on the barrier integrity, both under homeostatic and pathophysiological conditions. While such models remain valuable for deepening the understanding of host-microbe interactions, often, they lack key biological components that mediate this intricate crosstalk. Here, a 3D in vitro model of the vertebrate intestinal epithelium, interfaced with immune cells surviving in culture for over 3 weeks, is developed and applied to proof-of-concept studies of host-microbe interactions. More specifically, the establishment of stable host-microbe cocultures is described and functional and morphological changes in the intestinal barrier induced by the presence of commensal bacteria are shown. Finally, evidence is provided that the 3D vertebrate gut models can be used as platforms to test host-microbe-parasite interactions. Exposure of gut-immune-bacteria cocultures to helminth "excretory/secretory products" induces in vivo-like up-/down-regulation of certain cytokines. These findings support the robustness of the modular in vitro cell systems for investigating the dynamics of host-microbe crosstalk and pave the way toward new approaches for systems biology studies of pathogens that cannot be maintained in vitro, including parasitic helminths.

Canine Fecal Microbiota Transplantation: Current Application and Possible Mechanisms

Fecal microbiota transplantation (FMT) is an emerging therapeutic option for a variety of diseases, and is characterized as the transfer of fecal microorganisms from a healthy donor into the intestinal tract of a diseased recipient. In human clinics, FMT has been used for treating diseases for decades, with promising results. In recent years, veterinary specialists adapted FMT in canine patients; however, compared to humans, canine FMT is more inclined towards research purposes than practical applications in most cases, due to safety concerns. Therefore, in order to facilitate the application of fecal transplant therapy in dogs, in this paper, we review recent applications of FMT in canine clinical treatments, as well as possible mechanisms that are involved in the process of the therapeutic effect of FMT. More research is needed to explore more effective and safer approaches for conducting FMT in dogs.

Case Report: Oral Fecal Microbiota Transplantation in a Dog Suffering From Relapsing Chronic Diarrhea-Clinical Outcome and Follow-Up

The present case report describes the effects of orally administered fecal microbiota transplantation (FMT) (frozen capsules) in a dog suffering from relapsing chronic diarrhea, needing a continuous low prednisolone dose to maintain the condition under acceptable control. Through FMT, we aimed at evaluating the possibility of improving the clinical score and/or reducing/suspending steroid administration. During a first period of strict monitoring (21 days), the canine inflammatory bowel disease activity index (CIBDAI) score passed from mild to clinically insignificant disease. Furthermore, two additional gastrointestinal signs that had been reported, bloating and episodes of painful defecation, rapidly improved (bloating) or even resolved (painful defecation). The patient was then followed for 18 months (to the authors' knowledge, the longest follow-up time ever reported in a dog), during which no serious relapses occurred and no increase in prednisolone dose was necessary. No adverse clinical effects were ever reported during monitoring. The present description provides a further experience increasing those already present in the veterinary literature, in which an agreement on how to use FMT has not yet been achieved although strongly needed and recommended.

The Age of Next-Generation Therapeutic-Microbe Discovery: Exploiting Microbe-Microbe and Host-Microbe Interactions for Disease Prevention

Humans are considered "superorganisms," harboring a diverse microbial collective that outnumbers human cells 10 to 1. Complex and gravely understudied host- and microbe-microbe interactions-the product of millions of years of host-microbe coevolution-govern the superorganism in almost every aspect of life functions and overall well-being. Abruptly disrupting these interactions via extrinsic factors has undesirable consequences for the host. On the other hand, supplementing commensal or beneficial microbes may mitigate perturbed interactions or enhance the interactive relationships that ultimately benefit all parties. Hence, immense efforts have focused on dissecting the innumerable host- and microbe-microbe relationships to characterize if a "positive" or "negative" interaction is at play and to exploit such behavior for broader implications. For example, microbiome research has worked to identify and isolate naturally antipathogenic microbes that may offer therapeutic potential either in a direct, one-on-one application or by leveraging its unique metabolic properties. However, the discovery and isolation of such desired therapeutic microbes from complex microbiota have proven challenging. Currently, there is no conventional technique to universally and functionally screen for these microbes. With this said, we first describe in this review the historical (probiotics) and current (fecal microbiota or defined consortia) perspectives on therapeutic microbes, present the discoveries of therapeutic microbes through exploiting microbe-microbe and host-microbe interactions, and detail our team's efforts in discovering therapeutic microbes via our novel microbiome screening platform. We conclude this minireview by briefly discussing challenges and possible solutions with therapeutic microbes' applications and paths ahead for discovery.

Informal nutrition symposium: leveraging the microbiome (and the metabolome) for poultry production

Knowledge of gut microbiology of poultry has advanced from a limited ability to culture relatively few microbial species, to attempting to understand the complex interactions between the bird and its microbiome. The Informal Nutrition Symposium 2021 was intended to help poultry scientists to make sense of the implications of the vast amounts of information being generated by researchers. This paper represents a compilation of the talks given at the symposium by leading international researchers in this field. The symposium began with an overview of the historical developments in the field of intestinal microbiology and microbiome research in poultry. Next, the systemic effects of the microbiome on health in the context of the interplay between the intestinal microbiota and the immune system were presented. Because the microbiome and the host communicate and influence each other, the novel field of kinomics (the study of protein phosphorylation) as used in the study of the poultry microbiome was discussed. Protein phosphorylation is a rapid response to the complex of signals among the microbiome, intestinal lumen metabolites, and the host. Then, a description of why an understanding of the role of microbial endocrinology in poultry production can lead to new understanding of the mechanisms by which the gut microbiota and the host can interact in defined mechanisms that ultimately determine health, pathogenesis of infectious disease, and behavior was given. Finally, a view forward was presented underscoring the importance of understanding mechanisms in microbiomes in other organ systems and other species. Additionally, the importance of the development of new -omics platforms and data management tools to more completely understand host microbiomes was stressed.

Nonpharmacological Treatment Strategies for the Management of Canine Chronic Inflammatory Enteropathy—A Narrative Review

Chronic inflammatory enteropathy (CIE) refers to a heterogeneous group of idiopathic diseases of the dog characterised by persistent gastrointestinal (GI) clinical signs. If conventional dietary treatment alone would be unsuccessful, management of CIE is traditionally attained by the use of pharmaceuticals, such as antibiotics and immunosuppressive drugs. While being rather effective, however, these drugs are endowed with side effects, which may impact negatively on the animal’s quality of life. Therefore, novel, safe and effective therapies for CIE are highly sought after. As gut microbiota imbalances are often associated with GI disorders, a compelling rationale exists for the use of nonpharmacological methods of microbial manipulation in CIE, such as faecal microbiota transplantation and administration of pre-, pro-, syn- and postbiotics. In addition to providing direct health benefits to the host via a gentle modulation of the intestinal microbiota composition and function, these treatments may also possess immunomodulatory and epithelial barrier-enhancing actions. Likewise, intestinal barrier integrity, along with mucosal inflammation, are deemed to be two chief therapeutic targets of mesenchymal stem cells and selected vegetable-derived bioactive compounds. Although pioneering studies have revealed encouraging findings regarding the use of novel treatment agents in CIE, a larger body of research is needed to address fully their mode of action, efficacy and safety.

In-Vitro Characterization of Growth Inhibition against the Gut Pathogen of Potentially Probiotic Lactic Acid Bacteria Strains Isolated from Fermented Products

Lactic acid bacteria (LAB) are probiotic candidates that may restore the balance of microbiota populations in intestinal microbial ecosystems by controlling pathogens and thereby promoting host health. The goal of this study was to isolate potential probiotic LAB strains and characterize their antimicrobial abilities against pathogens in intestinal microbiota. Among 54 LAB strains isolated from fermented products, five LAB strains (NSMJ15, NSMJ16, NSMJ23, NSMJ42, and NFFJ04) were selected as potential probiotic candidates based on in vitro assays of acid and bile salt tolerance, cell surface hydrophobicity, adhesion to the intestinal epithelium, and antagonistic activity. Phylogenetic analysis based on 16S rRNA genes showed that they have high similarities of 99.58-100% to Lacticaseibacillus&nbsp;paracasei strains NSMJ15 and NFFJ04, Lentilactobacillus parabuchneri NSMJ16, Levilactobacillus&nbsp;brevis NSMJ23, and Schleiferilactobacillus harbinensis NSMJ42. To characterize their antimicrobial abilities against pathogens in intestinal microbiota, the impact of cell-free supernatant (CFS) treatment in 10% (v/v) fecal suspensions prepared using pooled cattle feces was investigated using in vitro batch cultures. Bacterial community analysis using rRNA amplicon sequencing for control and CFS-treated fecal samples at 8 and 16 h incubation showed the compositional change after CFS treatment for all five LAB strains. The changed compositions were similar among them, but there were few variable increases or decreases in some bacterial groups. Interestingly, as major genera that could exhibit pathogenicity and antibiotic resistance, the members of Bacillus, Escherichia, Leclercia, Morganella, and Vagococcus were decreased at 16 h in all CFS-treated samples. Species-level classification suggested that the five LAB strains are antagonistic to gut pathogens. This study showed the probiotic potential of the five selected LAB strains; in particular, their antimicrobial properties against pathogens present in the intestinal microbiota. These strains would therefore seem to play an important role in modulating the intestinal microbiome of the host.

Review: Can early-life establishment of the piglet intestinal microbiota influence production outcomes?

The gastrointestinal tract microbiota is involved in the development and function of many body processes. Studies demonstrate that early-life microbial colonisation is the most important time for shaping intestinal and immune development, with perturbations to the microbiota during this time having long-lasting negative implications for the host. Piglets face many early-life events that shape the acquisition and development of their intestinal microbiota. The pork industry has a unique advantage in that the producer has a degree of control over what piglets are exposed to, providing conditions that allow for optimum piglet growth and development. An influx of publications within this area has occurred in recent times and with this, interest surrounding its application in pork production has increased. However, it can be difficult to distinguish which research is of most relevance to industry in terms of delivering repeatable and reliable production outcomes. In this review, we describe the literature surrounding research within pigs, predominantly during the preweaning period that has either provided solutions to industry problems or is generating information targeted at addressing relevant industry issues, with the focus being on studies demonstrating causation where possible. This review will provide a basis for the development of new studies targeted at understanding how to better support initial intestinal microbiota colonisation in order to improve piglet health and survival.

Antibiotics and fecal transfaunation differentially affect microbiota recovery, associations, and antibiotic resistance in lemur guts

BACKGROUND

Antibiotics alter the diversity, structure, and dynamics of host-associated microbial consortia, including via development of antibiotic resistance; however, patterns of recovery from microbial imbalances and methods to mitigate associated negative effects remain poorly understood, particularly outside of human-clinical and model-rodent studies that focus on outcome over process. To improve conceptual understanding of host-microbe symbiosis in more naturalistic contexts, we applied an ecological framework to a non-traditional, strepsirrhine primate model via long-term, multi-faceted study of microbial community structure before, during, and following two experimental manipulations. Specifically, we administered a broad-spectrum antibiotic, either alone or with subsequent fecal transfaunation, to healthy, male ring-tailed lemurs (Lemur catta), then used 16S rRNA and shotgun metagenomic sequencing to longitudinally track the diversity, composition, associations, and resistomes of their gut microbiota both within and across baseline, treatment, and recovery phases.

RESULTS

Antibiotic treatment resulted in a drastic decline in microbial diversity and a dramatic alteration in community composition. Whereas microbial diversity recovered rapidly regardless of experimental group, patterns of microbial community composition reflected long-term instability following treatment with antibiotics alone, a pattern that was attenuated by fecal transfaunation. Covariation analysis revealed that certain taxa dominated bacterial associations, representing potential keystone species in lemur gut microbiota. Antibiotic resistance genes, which were universally present, including in lemurs that had never been administered antibiotics, varied across individuals and treatment groups.

CONCLUSIONS

Long-term, integrated study post antibiotic-induced microbial imbalance revealed differential, metric-dependent evidence of recovery, with beneficial effects of fecal transfaunation on recovering community composition, and potentially negative consequences to lemur resistomes. Beyond providing new perspectives on the dynamics that govern host-associated communities, particularly in the Anthropocene era, our holistic study in an endangered species is a first step in addressing the recent, interdisciplinary calls for greater integration of microbiome science into animal care and conservation.

MAP, Johne's disease and the microbiome; current knowledge and future considerations

Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne's disease in ruminants. As an infectious disease that causes reduced milk yields, effects fertility and, eventually, the loss of the animal, it is a huge financial burden for associated industries. Efforts to control MAP infection and Johne's disease are complicated due to difficulties of diagnosis in the early stages of infection and challenges relating to the specificity and sensitivity of current testing methods. The methods that are available contribute to widely used test and cull strategies, vaccination programmes also in place in some countries. Next generation sequencing technologies have opened up new avenues for the discovery of novel biomarkers for disease prediction within MAP genomes and within ruminant microbiomes. Controlling Johne's disease in herds can lead to improved animal health and welfare, in turn leading to increased productivity. With current climate change bills, such as the European Green Deal, targeting livestock production systems for more sustainable practices, managing animal health is now more important than ever before. This review provides an overview of the current knowledge on genomics and detection of MAP as it pertains to Johne's disease.

[Use of antimicrobials in acute canine diarrhea - overview of potential risks, indications and alternatives]

In Germany, antibiotics are frequently used in dogs with gastrointestinal disorders such as acute diarrhea. In line with global efforts to limit antibiotic use, this literature review aims to provide a guideline for the rational and judicious use of antibiotics in acute canine diarrhea. Antibiotics can lead to gastrointestinal side effects and may exert a negative influence on the intestinal microbiota in addition to increasing the occurrence of resistant bacteria. There is also evidence that chronic immunological diseases may be triggered by the administration of antibiotics. Therefore, these should not be administered in uncomplicated acute diarrhea without signs of sepsis or systemic inflammatory reaction. In addition, enteropathogenic bacteria usually do not play a role in the etiology of acute diarrhea. For select clinical entities such as acute hemorrhagic diarrhea syndrome, antibiotic therapy should only be recommended in cases displaying signs of bacterial translocation with subsequent sepsis. In the case of parvovirosis, on the other hand, the administration of antibiotics is unavoidable due to the immunological incompetence of the dog caused by the accompanying severe neutropenia.

Successful outcome after a single endoscopic fecal microbiota transplantation in a Shiba dog with non-responsive enteropathy during the treatment with chlorambucil

A 7-year 6-month-old, castrated male Shiba dog presented with a 1-month history of lethargy, anorexia, vomiting, and frequent watery diarrhea. Weight loss, hypoalbuminemia, anemia, and leukocytosis were detected at the first visit. The dog was diagnosed with non-responsive enteropathy (NRE) based on clinical and histopathological examinations. Since the dog did not respond to the immunosuppressive drugs, fecal microbiota transplantation (FMT) was performed during the treatment with chlorambucil. A single endoscopic FMT into the cecum and colon drastically recovered clinical signs and clinicopathological abnormalities and corrected dysbiosis in the dog. No recurrence or adverse events were observed. The present case report suggests that FMT, possibly together with chlorambucil, might be a treatment option for NRE in Shiba dogs that have poorer prognosis compared with other dog breeds.

Alternatives to Antibiotics: A Symposium on the Challenges and Solutions for Animal Health and Production

Antibiotics have improved the length and quality of life of people worldwide and have had an immeasurable influence on agricultural animal health and the efficiency of animal production over the last 60 years. The increased affordability of animal protein for a greater proportion of the global population, in which antibiotic use has played a crucial part, has resulted in a substantial improvement in human quality of life. However, these benefits have come with major unintended consequences, including antibiotic resistance. Despite the inherent benefits of restricting antibiotic use in animal production, antibiotics remain essential to ensuring animal health, necessitating the development of novel approaches to replace the prophylactic and growth-promoting benefits of antibiotics. The third International Symposium on “Alternatives to Antibiotics: Challenges and Solutions in Animal Health and Production” in Bangkok, Thailand was organized by the USDA Agricultural Research Service, Faculty of Veterinary Science, Chulalongkorn University and Department of Livestock Development-Thailand Ministry of Agriculture and Cooperative; supported by OIE World Organization for Animal Health; and attended by more than 500 scientists from academia, industry, and government from 32 nations across 6 continents. The focus of the symposium was on ensuring human and animal health, food safety, and improving food animal production efficiency as well as quality. Attendees explored six subject areas in detail through scientific presentations and panel discussions with experts, and the major conclusions were as follows: (1) defining the mechanisms of action of antibiotic alternatives is paramount to enable their effective use, whether they are used for prevention, treatment, or to enhance health and production; (2) there is a need to integrate nutrition, health, and disease research, and host genetics needs to be considered in this regard; (3) a combination of alternatives to antibiotics may need to be considered to achieve optimum health and disease management in different animal production systems; (4) hypothesis-driven field trials with proper controls are needed to validate the safety, efficacy, and return of investment (ROI) of antibiotic alternatives.

Spatial heterogeneity of bacterial colonization across different gut segments following inter-species microbiota transplantation

BACKGROUND

The microbiota presents a compartmentalized distribution across different gut segments. Hence, the exogenous microbiota from a particular gut segment might only invade its homologous gut location during microbiota transplantation. Feces as the excreted residue contain most of the large-intestinal microbes but lack small-intestinal microbes. We speculated that whole-intestinal microbiota transplantation (WIMT), comprising jejunal, ileal, cecal, and colonic microbiota, would be more effective for reshaping the entire intestinal microbiota than conventional fecal microbiota transplantation fecal microbiota transplantation (FMT).

RESULTS

We modeled the compartmentalized colonization of the gut microbiota via transplanting the microbiota from jejunum, ileum, cecum, and colon, respectively, into the germ-free mice. Transplanting jejunal or ileal microbiota induced more exogenous microbes' colonization in the small intestine (SI) of germ-free mice rather than the large intestine (LI), primarily containing Proteobacteria, Lactobacillaceae, and Cyanobacteria. Conversely, more saccharolytic anaerobes from exogenous cecal or colonic microbiota, such as Bacteroidetes, Prevotellaceae, Lachnospiraceae, and Ruminococcaceae, established in the LI of germ-free mice that received corresponding intestinal segmented microbiota transplantation. Consistent compartmentalized colonization patterns of microbial functions in the intestine of germ-free mice were also observed. Genes related to nucleotide metabolism, genetic information processing, and replication and repair were primarily enriched in small-intestinal communities, whereas genes associated with the metabolism of essential nutrients such as carbohydrates, amino acids, cofactors, and vitamins were mainly enriched in large-intestinal communities of germ-free mice. Subsequently, we compared the difference in reshaping the community structure of germ-free mice between FMT and WIMT. FMT mainly transferred LI-derived microorganisms and gene functions into the recipient intestine with sparse SI-derived microbes successfully transplanted. However, WIMT introduced more SI-derived microbes and associated microbial functions to the recipient intestine than FMT. Besides, WIMT also improved intestinal morphological development as well as reduced systematic inflammation responses of recipients compared with FMT.

CONCLUSIONS

Segmented exogenous microbiota transplantation proved the spatial heterogeneity of bacterial colonization along the gastrointestinal tract, i.e., the microbiota from one specific location selectively colonizes its homologous gut region. Given the lack of exogenous small-intestinal microbes during FMT, WIMT may be a promising alternative for conventional FMT to reconstitute the microbiota across the entire intestinal tract. Video Abstract.

Understanding the effects of dietary components on the gut microbiome and human health

The gut microbiome is the complex microbial ecosystem found in the gastrointestinal tract of humans and animals. It plays a vital role in host development, physiology and metabolism, and has been implicated as a factor in brain function, behavior, mental health, and many disease states. While many factors, including host genetics and environmental factors, contribute to the composition of the gut microbiome, diet plays a large role. Microorganisms differ in their nutrient requirements, and alterations in host dietary composition can have strong impacts on the microbial inhabitants of the gastrointestinal tract. The health implications of these dietary and microbial changes are relevant as various global populations consume diets comprised of different macronutrient ratios, and many diets promote alterations to recommended macronutrient ratios to promote health. This review will outline the ways in which specific macro- and micronutrients impact the gut microbiome and host health.

Comparative analysis of the pulmonary microbiome in healthy and diseased pigs

The lungs possess an effective antimicrobial system and a strong ability to eliminate microorganisms in healthy organisms, and were once considered sterile. With the development of culture-independent sequencing technology, the richness and diversity of porcine lung microbiota have been gaining attention. In order to study the relationship between lung microbiota and porcine respiratory disease complex (PRDC), the lung microbiota in healthy and diseased swine bronchoalveolar lavage fluids were analyzed and compared using the Illumina MiSeq sequencing platform. The predominant microbial communities of healthy and diseased swine were similar at the phylum level, mainly composed of Proteobacteria, Firmicutes, Tenericutes, and Bacteroidetes. However, the bacterial taxonomic communities of healthy and diseased swine differed at the genus level. The higher relative abundances of Lactococcus, Enterococcus, Staphylococcus, and Lactobacillus genera in healthy swine might provide more benefits for lung health, while the enhanced richness of Streptococcus, Haemophilus, Pasteurella, and Bordetella genera in diseased swine might be closely related to pathogen invasion and the occurrence of respiratory disease. In conclusion, the observed differences in the richness and diversity of lung microbiota can provide novel insights into their relationship with PRDC. Analyses of swine lung microbiota communities might produce an effective strategy for the control and prevention of respiratory tract infections.

Repeated Inoculation of Young Calves With Rumen Microbiota Does Not Significantly Modulate the Rumen Prokaryotic Microbiota Consistently but Decreases Diarrhea

The complex rumen microbiota exhibits some degree of host specificity. The undeveloped simple rumen microbiota is hypothetically more amendable. The objective of this study was to investigate if the rumen prokaryotic microbial assemblage of young calves can be reprogrammed by oral inoculation with rumen microbiota of adult cows. Twenty newborn male calves were randomly assigned to four groups (n = 5 per group), with two groups being orally inoculated with rumen microbiota (fresh rumen fluid) collected from two lactating dairy cows, while the other two groups receiving autoclaved rumen fluid collected from another two donor cows. Each calf was orally drenched with 100, 200, 300, 400, and 500 mL of the rumen fluid at d3, d7, d21, d42, and d50, respectively, after birth. The inoculation with rumen microbiota did not affect (P > 0.05) feed intake, average daily gain (ADG), heart girth, or feed conversion ratio but significantly (P < 0.01) lowered instance of diarrhea. At the age of 77 days (27 days post-weaning), all the calves were slaughtered for the sampling of rumen content and determination of empty rumen weight. Rumen fermentation characteristics were not affected (P > 0.05) by the inoculation. Rumen prokaryotic microbiota analysis using metataxonomics (targeting the V4 region of the 16S rRNA genes) showed that the calf rumen prokaryotic microbiota differed from that of the donors. Two Succinivibrionaceae OTUs, two Prevotella OTUs, and one Succiniclasticum OTU were predominant (relative abundance > 2%) in the donors, but only one Succinivibrionaceae OTU was found in the calves. On the other hand, five other Prevotella OTUs were predominant (>3%) in the calves, but none of them was a major OTU in the donors. No correlation was observed in relative abundance of major OTUs or genera between the donor and the calves. Principal coordinates analysis (PCoA) based on weighted UniFrac distance showed no significant (P > 0.05) difference in the overall rumen prokaryotic microbiota profiles among the four calf groups, and principal component analysis (PCA) based on Bray-Curtis dissimilarity showed no significant (P > 0.05) difference in functional features predicted from the detected taxa. Nor the calf rumen microbiota showed any clustering with their donor's. Repeated oral inoculation with rumen microbiota probably has a limited effect on the development of rumen microbiota, and the rumen microbiota seems to develop following a program determined by the host and other factors.

Temporal Dynamics of the Gut Bacteriome and Mycobiome in the Weanling Pig

Weaning is a period of environmental changes and stress that results in significant alterations to the piglet gut microbiome and is associated with a predisposition to disease, making potential interventions of interest to the swine industry. In other animals, interactions between the bacteriome and mycobiome can result in altered nutrient absorption and susceptibility to disease, but these interactions remain poorly understood in pigs. Recently, we assessed the colonization dynamics of fungi and bacteria in the gastrointestinal tract of piglets at a single time point post-weaning (day 35) and inferred interactions were found between fungal and bacterial members of the porcine gut ecosystem. In this study, we performed a longitudinal assessment of the fecal bacteriome and mycobiome of piglets from birth through the weaning transition. Piglet feces in this study showed a dramatic shift over time in the bacterial and fungal communities, as well as an increase in network connectivity between the two kingdoms. The piglet fecal bacteriome showed a relatively stable and predictable pattern of development from Bacteroidaceae to Prevotellaceae, as seen in other studies, while the mycobiome demonstrated a loss in diversity over time with a post-weaning population dominated by Saccharomycetaceae. The mycobiome demonstrated a more transient community that is likely driven by factors such as diet or environmental exposure rather than an organized pattern of colonization and succession evidenced by fecal sample taxonomic clustering with nursey feed samples post-weaning. Due to the potential tractability of the community, the mycobiome may be a viable candidate for potential microbial interventions that will alter piglet health and growth during the weaning transition.

Investigating the relationship between vaginal microbiota and host genetics and their impact on immune response and farrowing traits in commercial gilts

Our objectives were to evaluate the interaction between host genetics and vaginal microbiota and their relationships with antibody (Ab) response to porcine reproductive and respiratory syndrome virus (PRRSV) vaccination and farrowing performance in commercial gilts. The farrowing performance traits were number born alive, number weaning (NW), total number born, number born dead, stillborn, mummies and preweaning mortality (PWM). The vaginal microbiota was collected on days 4 (D4) and 52 (D52) after vaccination for PRRSV. Blood samples were collected on D52 for Ab measurement. Actinobacteria, Bacterioidetes, Firmicutes, Proteobacteria and Tenericutes were the most abundant Phyla identified in the vaginal microbiota. Heritability ranged from ~0 to 0.60 (Fusobacterium) on D4 and from ~0 to 0.63 (Terrisporobacter) on D52, with 43 operational taxonomic units (OTUs) presenting moderate to high heritability. One major QTL on chromosome 12 was identified for 5 OTUs (Clostridiales, Acinetobacter, Ruminococcaceae, Campylobacter and Anaerococcus), among other 19 QTL. The microbiability for Ab response to PRRSV vaccination was low for both days (<0.07). For farrowing performance, microbiability varied from <0.001 to 0.15 (NW on D4). For NW and PWM, the microbiability was greater than the heritability estimates. Actinobacillus, Streptococcus, Campylobacter, Anaerococcus, Mollicutes, Peptostreptococcus, Treponema and Fusobacterium showed different abundance between low and high Ab responders. Finally, canonical discriminant analyses revealed that vaginal microbiota was able to classify gilts in high and low Ab responders to PRRSV vaccination with a misclassification rate of <0.02. Although the microbiota explained limited variation in Ab response and farrowing performance traits, there is still potential to explore the use of vaginal microbiota to explain variation in traits such as NW and PWM. In addition, these results revealed that there is a partial control of host genetic over vaginal microbiota, suggesting a possibility for genetic selection on the vaginal microbiota.