The gut microbiome as a virtual endocrine organ with implications for farm and domestic animal endocrinology

Integrating Omics Technologies for a Comprehensive Understanding of the Microbiome and Its Impact on Cattle Production

Ruminant production holds a pivotal position within the global animal production and agricultural sectors. As population growth escalates, posing environmental challenges, a heightened emphasis is directed toward refining ruminant production systems. Recent investigations underscore the connection between the composition and functionality of the rumen microbiome and economically advantageous traits in cattle. Consequently, the development of innovative strategies to enhance cattle feed efficiency, while curbing environmental and financial burdens, becomes imperative. The advent of omics technologies has yielded fresh insights into metabolic health fluctuations in dairy cattle, consequently enhancing nutritional management practices. The pivotal role of the rumen microbiome in augmenting feeding efficiency by transforming low-quality feedstuffs into energy substrates for the host is underscored. This microbial community assumes focal importance within gut microbiome studies, contributing indispensably to plant fiber digestion, as well as influencing production and health variability in ruminants. Instances of compromised animal welfare can substantially modulate the microbiological composition of the rumen, thereby influencing production rates. A comprehensive global approach that targets both cattle and their rumen microbiota is paramount for enhancing feed efficiency and optimizing rumen fermentation processes. This review article underscores the factors that contribute to the establishment or restoration of the rumen microbiome post perturbations and the intricacies of host-microbiome interactions. We accentuate the elements responsible for responsible host-microbiome interactions and practical applications in the domains of animal health and production. Moreover, meticulous scrutiny of the microbiome and its consequential effects on cattle production systems greatly contributes to forging more sustainable and resilient food production systems, thereby mitigating the adverse environmental impact.

The Ketogenic Diet but not Hydroxycitric Acid Keeps Brain Mitochondria Quality Control and mtDNA Integrity Under Focal Stroke

Mitochondrial dysfunction in the ischemic brain is one of the hallmarks of stroke. Dietary interventions such as the ketogenic diet and hydroxycitric acid supplementation (a caloric restriction mimetic) may potentially protect neurons from mitochondrial damage induced by focal stroke in mice. We showed that in control mice, the ketogenic diet and the hydroxycitric acid did not impact significantly on the mtDNA integrity and expression of genes involved in the maintenance of mitochondrial quality control in the brain, liver, and kidney. The ketogenic diet changed the bacterial composition of the gut microbiome, which via the gut-brain axis may affect the increase in anxiety behavior and reduce mice mobility. The hydroxycitric acid causes mortality and suppresses mitochondrial biogenesis in the liver. Focal stroke modelling caused a significant decrease in the mtDNA copy number in both ipsilateral and contralateral brain cortex and increased the levels of mtDNA damage in the ipsilateral hemisphere. These alterations were accompanied by a decrease in the expression of some of the genes involved in maintaining mitochondrial quality control. The ketogenic diet consumption before stroke protects mtDNA in the ipsilateral cortex, probably via activation of the Nrf2 signaling. The hydroxycitric acid, on the contrary, increased stroke-induced injury. Thus, the ketogenic diet is the most preferred variant of dietetic intervention for stroke protection compared with the hydroxycitric acid supplementation. Our data confirm some reports about hydroxycitric acid toxicity, not only for the liver but also for the brain under stroke condition.

Standardized Complex Gut Microbiomes Influence Fetal Growth, Food Intake, and Adult Body Weight in Outbred Mice

Obesity places a tremendous burden on individual health and the healthcare system. The gut microbiome (GM) influences host metabolism and behaviors affecting body weight (BW) such as feeding. The GM of mice varies between suppliers and significantly influences BW. We sought to determine whether GM-associated differences in BW are associated with differences in intake, fecal energy loss, or fetal growth. Pair-housed mice colonized with a low or high microbial richness GM were weighed, and the total and BW-adjusted intake were measured at weaning and adulthood. Pups were weighed at birth to determine the effects of the maternal microbiome on fetal growth. Fecal samples were collected to assess the fecal energy loss and to characterize differences in the microbiome. The results showed that supplier-origin microbiomes were associated with profound differences in fetal growth and excessive BW-adjusted differences in intake during adulthood, with no detected difference in fecal energy loss. Agreement between the features of the maternal microbiome associated with increased birth weight here and in recent human studies supports the value of this model to investigate the mechanisms by which the maternal microbiome regulates offspring growth and food intake.

Association of gut microbiota and SCFAs with finishing weight of Diannan small ear pigs

Finishing weight is a key economic trait in the domestic pig industry. Evidence has linked the gut microbiota and SCFAs to health and production performance in pigs. Nevertheless, for Diannan small ear (DSE) pigs, a specific pig breed in China, the potential effect of gut microbiota and SCFAs on their finishing weight remains unclear. Herein, based on the data of the 16S ribosomal RNA gene and metagenomic sequencing analysis, we found that 13 OTUs could be potential biomarkers and 19 microbial species were associated with finishing weight. Among these, carbohydrate-decomposing bacteria of the families Streptococcaceae, Lactobacillaceae, and Prevotellaceae were positively related to finishing weight, whereas the microbial taxa associated with intestinal inflammation and damage exhibited opposite effects. In addition, interactions of these microbial species were found to be linked with finishing weight for the first time. Gut microbial functional annotation analysis indicated that CAZymes, such as glucosidase and glucanase could significantly affect finishing weight, given their roles in increasing nutrient absorption efficiency. Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthologies (KOs) and KEGG pathways analysis indicated that glycolysis/gluconeogenesis, phosphotransferase system (PTS), secondary bile acid biosynthesis, ABC transporters, sulfur metabolism, and one carbon pool by folate could act as key factors in regulating finishing weight. Additionally, SCFA levels, especially acetate and butyrate, had pivotal impacts on finishing weight. Finishing weight-associated species Prevotella sp. RS2, Ruminococcus sp. AF31-14BH and Lactobacillus pontis showed positive associations with butyrate concentration, and Paraprevotella xylaniphila and Bacteroides sp. OF04-15BH were positively related to acetate level. Taken together, our study provides essential knowledge for manipulating gut microbiomes to improve finishing weight. The underlying mechanisms of how gut microbiome and SCFAs modulate pigs' finishing weight required further elucidation.

The Role of Gut Microbiota in the Pathogenesis of Alzheimer’s Disease

As a degenerative disease of the central nervous system, Alzheimer’s disease (AD) is featured by mental and behavioral dysfunction, and progressive memory loss, which is the most common type of dementia. The incidence of AD is increasing as life expectancy is prolonged, but the pathogenesis of AD remains largely unknown. Recently, the role of gut microbiota in the pathogenesis of AD has drawn increasing attention. The composition of gut microbiota varies across age groups, and the changes in the microbiota metabolites may influence the central nervous system via the brain-gut axis. So far, it has been confirmed that gut bacteria are involved in various pathogenic mechanisms of AD, including amyloid β-protein deposition, Tau protein hyperphosphorylation, neuroinflammation, oxidative stress injury, increased blood-brain barrier permeability, neurotransmitter imbalance, reduced generation of brain-derived neurotrophic factor, and insulin resistance. An important direction of research is to investigate the regulation of gut microbiota for the prevention and treatment of AD.

An Evaluation of Nutritional and Therapeutic Factors Affecting Pre-Weaned Calf Health and Welfare, and Direct-Fed Microbials as a Potential Alternative for Promoting Performance—A Review

The priority for calf rearing has been to maintain good health and welfare in order to promote and sustain future production. However, there have been numerous reports of undesirable levels of morbidity and mortality amongst pre-weaned calves. This may be mitigated or exacerbated by nutritional management practices. Some areas of concern include colostrum feeding, utilization of waste milk, and restrictive milk feeding regimes. Antibiotics may be prescribed at lethal or sub-inhibitory doses to treat or prevent disease. However, extensive antibiotic use may disrupt the gastrointestinal microbiota and aid in expanding the antibiotic resistant gene pool. In an attempt to reduce the use of antibiotics, there is a demand to find alternative performance enhancers. Direct-fed microbials, also known as probiotics, may comply with this role. A DFM consists of live microorganisms that are biologically active and able to confer health benefits onto the host. Lactic acid bacteria have been the most frequently investigated; however, this field of research has expanded to include spore-forming bacteria and live yeast preparations. This review aims to provide a comprehensive evaluation of the nutritional management strategies that may increase a calf’s susceptibility to morbidity and mortality, the efficacy and sustainability of antibiotics as a tool for managing calf health and welfare, and the potential for DFMs as a supportive strategy for promoting calf wellbeing.

Effects of supplementation with lysophospholipids on performance, nutrient digestibility, and bacterial communities of beef cattle

An experiment was conducted to investigate the influences of supplemental lysophospholipids (LPL) on the growth performance, nutrient digestibility, and fecal bacterial profile, and short-chain fatty acids (SCFAs) of beef cattle. Thirty-six Angus beef cattle [565 ± 10.25 kg body weight (BW)] were grouped by BW and age, and randomly allocated to 1 of 3 treatment groups: (1) control (CON, basal diet); (2) LLPL [CON supplemented with 0.5 g/kg LPL, dry matter (DM) basis]; and (3) HLPL (CON supplemented with 0.75 g/kg, DM basis). The Angus cattle were fed a total mixed ration that consisted of 25% roughage and 75% concentrate (dry matter [DM] basis). The results reveal that LPL inclusion linearly increased the average daily gain (P = 0.02) and the feed efficiency (ADG/feed intake, P = 0.02), while quadratically increasing the final weight (P = 0.02) of the beef cattle. Compared with CON, the total tract digestibilities of DM (P < 0.01), ether extract (P = 0.04) and crude protein (P < 0.01) were increased with LPL supplementation. At the phylum-level, the relative abundance of Firmicutes (P = 0.05) and ratio of Firmicutes: Bacteroidetes (P = 0.04) were linearly increased, while the relative abundances of Bacteroidetes (P = 0.04) and Proteobacteria (P < 0.01) were linearly decreased with increasing LPL inclusion. At the genus-level, the relative abundances of Clostridium (P < 0.01) and Roseburia (P < 0.01) were quadratically increased, and the relative abundances of Ruminococcus was linearly increased (P < 0.01) with LPL supplementation. Additionally, increasing the dose of LPL in diets linearly increased the molar proportion of butyrate (P < 0.01) and total SCFAs (P = 0.01) concentrations. A conclusion was drawn that, as a promising feed additive, LPL promoted growth performance and nutrient digestibility, which may be associated with the change of fecal microbiome and SCFAs.

Effects of early-life cecal microbiota transplantation from divergently selected inbred chicken lines on growth, gut serotonin, and immune parameters in recipient chickens

Recent studies have revealed that fecal microbiota transplantation exerts beneficial effects on modulating stress-related inflammation and gastrointestinal health of the host. The aim of this study was to examine if cecal microbiota transplantation (CMT) presents similar efficiency in improving the health status of egg-laying strain chickens. Chicken lines 6₃ and 7₂ divergently selected for resistance or susceptibility to Marek's disease were used as CMT donors. Eighty-four d-old male recipient chicks (a commercial DeKalb XL layer strain) were randomly assigned into 3 treatments with 7 replicates per treatment and 4 birds per replicate (n = 7): saline (control, CTRL), cecal solution of line 6₃ (6₃-CMT), and cecal solution of line 7₂ (7₂-CMT) for a 16-wk trial. Cecal transplant gavage was conducted once daily from d 1 to d 10, then boosted once weekly from wk 3 to wk 5. The results indicated that 7₂-CMT birds had the highest body weight and ileal villus/crypt ratio among the treatments at wk 5 (P ≤ 0.05); and higher heterophil/lymphocyte ratios than that of 6₃-CMT birds at wk 16 (P < 0.05). 7₂-CMT birds also had higher levels of plasma natural IgG and Interleukin (IL)-6 at wk 16, while 6₃-CMT birds had higher concentrations of ileal mucosal secretory IgA at wk 5 and plasma IL-10 at wk 16 (P < 0.05), with a tendency for lower mRNA abundance of splenic IL-6 and tumor necrosis factor (TNF)-α at wk 16 (P = 0.08 and 0.07, respectively). In addition, 7₂-CMT birds tended to have the lowest serotonin concentrations (P = 0.07) with the highest serotonin turnover in the ileum at wk 5 (P < 0.05). There were no treatment effects on the levels of plasma corticosterone and testosterone at wk 16 (P > 0.05). In conclusion, early postnatal CMT from different donors led to different patterns of growth and health status through the regulation of ileal morphological structures, gut-derived serotonergic activities, peripheral cytokines, and antibody production in recipient chickens.

Gut Microbiota Implications for Health and Welfare in Farm Animals: A Review

Simple Summary

Farm animal health and welfare have been paid increasing concern in the world, which is generally assessed by the measurements of physical health, immune response, behavior, and physiological indicators, such as stress-related hormone, cortisone, and norepinephrine. Gut microbiota as a “forgotten organ” has been reported for its great influence on the host phenotypes through the immune, neural, and endocrine pathways to affect the host health and behavior. In addition, fecal microbiota transplantation as a novel approach is applied to regulating the composition and function of the recipient farm animals. In this review, we summarized recent studies that gut microbiota influenced health, immunity, behavior, and stress response, as well as the progress of fecal microbiota transplantation in farm animals. The review will provide new insights into the measurement of farm animal health and welfare concerning gut microbiota, and the implication of fecal microbiota transplantation to improve productivity, health, and welfare. Above all, this review suggests that gut microbiota is a promising field to evaluate and improve animal welfare.

Abstract

In the past few decades, farm animal health and welfare have been paid increasing concern worldwide. Farm animal health and welfare are generally assessed by the measurements of physical health, immune response, behavior, and physiological indicators. The gut microbiota has been reported to have a great influence on host phenotypes, possibly via the immune processes, neural functions, and endocrine pathways, thereby influencing host phenotypes. However, there are few reviews regarding farm animals’ health and welfare status concerning the gut microbiota. In this point of view, (1) we reviewed recent studies showing that gut microbiota (higher alpha diversity, beneficial composition, and positive functions) effectively influenced health characteristics, immunity, behaviors, and stress response in farm animals (such as pigs, chickens, and cows), which would provide a novel approach to measure and evaluate the health status and welfare of farm animals. In addition, fecal microbiota transplantation (FMT) as one of the methods can modulate the recipient individual’s gut microbiota to realize the expected phenotype. Further, (2) we highlighted the application of FMT on the improvement of the production performance, the reduction in disease and abnormal behavior, as well as the attenuation of stress in farm animals. It is concluded that the gut microbiota can be scientifically used to assess and improve the welfare of farm animals. Moreover, FMT may be a helpful strategy to reduce abnormal behavior and improve stress adaption, as well as the treatment of disease for farm animals. This review suggests that gut microbiota is a promising field to evaluate and improve animal welfare.

Freeze-Thaw Pretreatment Can Improve Efficiency of Bacterial DNA Extraction From Meconium

Although the presence of live microbes in utero remains under debate, newborn gastrointestinal bacteria are undoubtedly important to infant health. Measuring bacteria in meconium is an ideal strategy to understand this issue; however, the low efficiency of bacterial DNA extraction from meconium has limited its utilization. This study aims to improve the efficiency of bacterial DNA extraction from meconium, which generally has low levels of microflora but high levels of PCR inhibitors in the viscous matrix. The research was approved by the ethical committee of the Xiamen Maternity and Child Health Care Hospital, Xiamen, China. All the mothers delivered naturally, and their newborns were healthy. Meconium samples passed by the newborns within 24 h were collected. Each sample was scraped off of a sterile diaper, transferred to a 5-ml sterile tube, and stored at −80°C. For the assay, a freeze-thawing sample preparation protocol was designed, in which a meconium-InhibitEX buffer mixture was intentionally frozen 1–3 times at −20°C, −80°C, and (or) in liquid nitrogen. Then, DNA was extracted using a commercial kit and sequenced by 16S rDNA to verify the enhanced bacterial DNA extraction efficiency. Ultimately, we observed the following: (1) About 30 mg lyophilized meconium was the optimal amount for DNA extraction. (2) Freezing treatment for 6 h improved DNA extraction at −20°C. (3) DNA extraction efficiency was significantly higher with the immediate thaw strategy than with gradient thawing at −20°C, −80°C, and in liquid nitrogen. (4) Among the conditions of −20°C, −80°C, and liquid nitrogen, −20°C was the best freezing condition for both improving DNA extraction efficiency and preserving microbial species diversity in meconium, while liquid nitrogen was the worst condition. (5) Three freeze-thaw cycles could markedly enhance DNA extraction efficiency and preserve the species diversity of meconium microflora. We developed a feasible freeze-thaw pretreatment protocol to improve the extraction of microbial DNA from meconium, which may be beneficial for newborn bacterial colonization studies.

The microbiota-gut-brain axis: A novel nutritional therapeutic target for growth retardation

Growth retardation (GR), which commonly occurs in childhood, is a major health concern globally. However, the specific mechanism remains unclear. It has been increasingly recognized that changes in the gut microbiota may lead to GR through affecting the microbiota-gut-brain axis. Microbiota interacts with multiple factors such as birth to affect the growth of individuals. Microbiota communicates with the nerve system through chemical signaling (direct entry into the circulation system or stimulation of enteroendocrine cells) and nervous signaling (interaction with enteric nerve system and vagus nerve), which modulates appetite and immune response. Besides, they may also influence the function of enteric glial cells or lymphocytes and levels of systemic inflammatory cytokines. Environmental stress may cause leaky gut through perturbing the hypothalamic-pituitary-adrenal axis to further result in GR. Nutritional therapies involving probiotics and pre-/postbiotics are being investigated for helping the patients to overcome GR. In this review, we summarize the role of microbiota in GR with human and animal models. Then, existing and potential regulatory mechanisms are reviewed, especially the effect of microbiota-gut-brain axis. Finally, we propose nutritional therapeutic strategies for GR by the intervention of microbiota-gut-brain axis, which may provide novel perspectives for the treatment of GR in humans and animals.

Impact of selected environmental factors on microbiome of the digestive tract of ruminants

Ruminants are an important part of world animal production. The main factors affecting their production rates are age, diet, physiological condition and welfare. Disorders related to low level of welfare can significantly affect the microbiological composition of the digestive system, which is essential to maintain high production rates. The microbiology of the ruminant gastrointestinal tract may be significantly affected by inappropriate keeping system (especially in juveniles), psychological stress (e.g. transport), or heat stress. This results in an increased risk of metabolic diseases, reduced fertility and systemic diseases. Therefore, the paper focuses on selected disorders i.e., aforementioned inappropriate maintenance system, psychological stress, heat stress and their effects on the microbiome of the digestive system.

Development of the equine hindgut microbiome in semi-feral and domestic conventionally-managed foals

Background

Early development of the gut microbiome is an essential part of neonate health in animals. It is unclear whether the acquisition of gut microbes is different between domesticated animals and their wild counterparts. In this study, fecal samples from ten domestic conventionally managed (DCM) Standardbred and ten semi-feral managed (SFM) Shetland-type pony foals and dams were compared using 16S rRNA sequencing to identify differences in the development of the foal hindgut microbiome related to time and management.

Results

Gut microbiome diversity of dams was lower than foals overall and within groups, and foals from both groups at Week 1 had less diverse gut microbiomes than subsequent weeks. The core microbiomes of SFM dams and foals had more taxa overall, and greater numbers of taxa within species groups when compared to DCM dams and foals. The gut microbiomes of SFM foals demonstrated enhanced diversity of key groups: Verrucomicrobia (RFP12), Ruminococcaceae, Fusobacterium spp., and Bacteroides spp., based on age and management. Lactic acid bacteria Lactobacillus spp. and other Lactobacillaceae genera were enriched only in DCM foals, specifically during their second and third week of life. Predicted microbiome functions estimated computationally suggested that SFM foals had higher mean sequence counts for taxa contributing to the digestion of lipids, simple and complex carbohydrates, and protein. DCM foal microbiomes were more similar to their dams in week five and six than were SFM foals at the same age.

Conclusions

This study demonstrates the impact of management on the development of the foal gut microbiome in the first 6 weeks of life. The higher numbers of taxa within and between bacterial groups found in SFM dams and foals suggests more diversity and functional redundancy in their gut microbiomes, which could lend greater stability and resiliency to these communities. The colonization of lactic acid bacteria in the early life of DCM foals suggests enrichment in response to the availability of dams’ feed. Thus, management type is an important driver of gut microbiome establishment on horses, and we may look to semi-feral horses for guidance in defining a healthy gut microbiome for domestic horses.

Supplementary Information

Supplementary information accompanies this paper at 10.1186/s42523-020-00060-6.

Effects of Gut Microbiome and Short-Chain Fatty Acids (SCFAs) on Finishing Weight of Meat Rabbits

Understanding how the gut microbiome and short-chain fatty acids (SCFAs) affect finishing weight is beneficial to improve meat production in the meat rabbit industry. In this study, we identified 15 OTUs and 23 microbial species associated with finishing weight using 16S rRNA gene and metagenomic sequencing analysis, respectively. Among these, butyrate-producing bacteria of the family Ruminococcaceae were positively associated with finishing weight, whereas the microbial taxa related to intestinal damage and inflammation showed opposite effects. Furthermore, interactions of these microbial taxa were firstly found to be associated with finishing weight. Gut microbial functional capacity analysis revealed that CAZymes, such as galactosidase, xylanase, and glucosidase, could significantly affect finishing weight, given their roles in regulating nutrient digestibility. GOs related to the metabolism of several carbohydrates and amino acids also showed important effects on finishing weight. Additionally, both KOs and KEGG pathways related to the membrane transportation system and involved in aminoacyl-tRNA biosynthesis and butanoate metabolism could act as key factors in modulating finishing weight. Importantly, gut microbiome explained nearly 11% of the variation in finishing weight, and our findings revealed that a subset of metagenomic species could act as predictors of finishing weight. SCFAs levels, especially butyrate level, had critical impacts on finishing weight, and several finishing weight-associated species were potentially contributed to the shift in butyrate level. Thus, our results should give deep insights into how gut microbiome and SCFAs influence finishing weight of meat rabbits and provide essential knowledge for improving finishing weight by manipulating gut microbiome.

Regulation of endocrine systems by the microbiome: Perspectives from comparative animal models

The microbiome regulates endocrine systems and influences many aspects of hormone signaling. Using examples from different animal taxa, we highlight the state of the science in microbiome research as it relates to endocrinology and endocrine disruption research. Using a comparative approach discussing fish, birds, and mammals, we demonstrate the bidirectional interaction between microbiota and hormone systems, presenting concepts that include (1) gastrointestinal microbiome regulation of the neuroendocrine feeding axis; (2) stress hormones and microbial communities; (3) the role of site-specific microbiota in animal reproduction; (4) microbiome effects on the neuroendocrine systems and behavior; and (5) novel mechanisms of endocrine disruption through the microbiome. This mini-review demonstrates that hormones can directly affect the richness and diversity of microbiota and conversely, microbiota can influence hormone production and mediate their functions in animals. In addition, microbiota can influence the action of a diverse range of neurotransmitters and neuropeptides in the central nervous system, which can lead to behavioral disruptions. As many animals have species-specific reproductive behaviors, it is important to understand how shifts in the microbiota relate to these complex interactions between sexes. This is especially important for captive animals on specialized diets, and there are significant implications for microbiome research in conservation and reproductive biology. For example, microbial metabolites may modify motility of gametes or modulate hormone-receptor interactions in reproductive tissues. Thus, efforts to incorporate metabolomics into the science of microbiome-endocrine relationships, both those produced by the host and those generated from microbial metabolism, are increasingly needed. These concepts have fostered an exciting emerging era in comparative endocrinology.

Factors Influencing Equine Gut Microbiota: Current Knowledge

Gastrointestinal microbiota play a crucial role in nutrient digestion, maintaining animal health and welfare. Various factors may affect microbial balance often leading to disturbances that may result in debilitating conditions such as colic and laminitis. The invention of next-generation sequencing technologies and bioinformatics has provided valuable information on the effects of factors influencing equine gut microbiota. Among those factors are nutrition and management (e.g., diet, supplements, exercise), medical substances (e.g., antimicrobials, anthelmintics, anesthetics), animal-related factors (breed and age), various pathological conditions (colitis, diarrhea, colic, laminitis, equine gastric ulcer syndrome), as well as stress-related factors (transportation and weaning). The aim of this review is to assimilate current knowledge on equine microbiome studies, focusing on the effect of factors influencing equine gastrointestinal microbiota. Decrease in microbial diversity and richness leading to decrease in stability; decrease in Lachnospiraceae and Ruminococcaceae family members, which contribute to gut homeostasis; increase in Lactobacillus and Streptococcus; decrease in lactic acid utilizing bacteria; decrease in butyrate-producing bacteria that have anti-inflammatory properties may all be considered as a negative change in equine gut microbiota. Shifts in Firmicutes and Bacteroidetes have often been observed in the literature in response to certain treatments or when describing healthy and unhealthy animals; however, these shifts are inconsistent. It is time to move forward and use the knowledge now acquired to start manipulating the microbiota of horses.

Reproductive Microbiomes in Wild Animal Species: A New Dimension in Conservation Biology

Communities of microbes have coevolved in animal organisms and are found in almost every part of the body. Compositions of those communities (microbiota) as well as their genomes and genes (microbiomes) are critical for functional regulations of the body organ systems-the digestive or 'gut' microbiome being the most described so far. Based on extensive research in humans, microbiomes in the reproductive tract may play a role in reproductive functions and pregnancy. However, in wild animal species, those microbiomes have been poorly studied, and as a result, little is known about their involvement in fertility or parental/offspring health. This emerging research area is highly relevant to conservation biology from captive breeding management to successful reintroduction or maintenance of wild populations. The objective of this chapter is to review current knowledge about reproductive microbiomes in healthy wild animal species. While recognizing the current technical limits of microbial identification in all animal species, we also explore the link between microbial communities (within female or male reproductive systems) and fertility, from conception to birth outcome. In addition, it is critical to understanding how reproductive microbiomes are affected by environmental factors (including captivity, contact with other individuals, or changes in the ecosystem) to optimize conservation efforts. Thus, reproductive microbiomes represent a novel dimension in conservation biology that will likely gain importance in the future.

Obesity: A New Adverse Effect of Antibiotics?

Since the introduction of antibiotics, they have been used freely, with their prescription occurring almost always when they were not necessary. The other major form of contact between humans and antibiotics, now unintentionally, is with the large amount of these drugs in the environment and in our food. The relationship between antibiotic use and the development of obesity has become increasingly evident and apparent in humans, with some authors clearly establishing the relationship between the large-scale use of antibiotics in the past 70 years and the “epidemic” of obesity that has occurred in parallel, almost as an adverse epidemiological effect. In the research effort entertained herein, a correlation between the use and abuse of antibiotics and the onset of obesity was investigated.

Raw meat based diet influences faecal microbiome and end products of fermentation in healthy dogs

BACKGROUND

Dietary intervention studies are required to deeper understand the variability of gut microbial ecosystem in healthy dogs under different feeding conditions and to improve diet formulations. The aim of the study was to investigate in dogs the influence of a raw based diet supplemented with vegetable foods on faecal microbiome in comparison with extruded food.

METHODS

Eight healthy adult Boxer dogs were recruited and randomly divided in two experimental blocks of 4 individuals. Dogs were regularly fed a commercial extruded diet (RD) and starting from the beginning of the trial, one group received the raw based diet (MD) and the other group continued to be fed with the RD diet (CD) for a fortnight. After 14 days, the two groups were inverted, the CD group shifted to the MD and the MD shifted to the CD, for the next 14 days. Faeces were collected at the beginning of the study (T0), after 14 days (T14) before the change of diet and at the end of experimental period (T28) for DNA extraction and analysis of metagenome by sequencing 16SrRNA V3 and V4 regions, short chain fatty acids (SCFA), lactate and faecal score.

RESULTS

A decreased proportion of Lactobacillus, Paralactobacillus (P < 0.01) and Prevotella (P < 0.05) genera was observed in the MD group while Shannon biodiversity Index significantly increased (3.31 ± 0.15) in comparison to the RD group (2.92 ± 0.31; P < 0.05). The MD diet significantly (P < 0.05) decreased the Faecal Score and increased the lactic acid concentration in the feces in comparison to the RD treatment (P < 0.01). Faecal acetate was negatively correlated with Escherichia/Shigella and Megamonas (P < 0.01), whilst butyrate was positively correlated with Blautia and Peptococcus (P < 0.05). Positive correlations were found between lactate and Megamonas (P < 0.05), Escherichia/Shigella (P < 0.01) and Lactococcus (P < 0.01).

CONCLUSION

These results suggest that the diet composition modifies faecal microbial composition and end products of fermentation. The administration of MD diet promoted a more balanced growth of bacterial communities and a positive change in the readouts of healthy gut functions in comparison to RD diet.