The Microbiome: The Trillions of Microorganisms That Maintain Health and Cause Disease in Humans and Companion Animals

Meta-transcriptomic analysis of companion animal infectomes reveals their diversity and potential roles in animal and human disease

Companion animals such as cats and dogs harbor diverse microbial communities that can potentially impact human health due to close and frequent contact. To better characterize their total infectomes and assess zoonotic risks, we characterized the overall infectomes of companion animals (cats and dogs) and evaluated their potential zoonotic risks. Meta-transcriptomic analyses were performed on 239 samples from cats and dogs collected across China, identifying 24 viral species, 270 bacterial genera, and two fungal genera. Differences in the overall microbiome and infectome composition were compared across different animal species (cats or dogs), sampling sites (rectal or oropharyngeal), and health status (healthy or diseased). Diversity analyses revealed that viral abundance was generally higher in diseased animals compared to healthy ones, while differences in microbial composition were mainly driven by sampling site, followed by animal species and health status. Disease association analyses validated the pathogenicity of known pathogens and suggested potential pathogenic roles of previously undescribed bacteria and newly discovered viruses. Cross-species transmission analyses identified seven pathogens shared between cats and dogs, such as alphacoronavirus 1, which was detected in both oropharyngeal and rectal swabs albeit with differential pathogenicity. Further analyses showed that some viruses, like alphacoronavirus 1, harbored multiple lineages exhibiting distinct pathogenicity, tissue, or host preferences. Ultimately, a systematic evolutionary screening identified 27 potential zoonotic pathogens in this sample set, with far more bacterial than viral species, implying potential health threats to humans. Overall, our meta-transcriptomic analysis reveals a landscape of actively transcribing microorganisms in major companion animals, highlighting key pathogens, those with the potential for cross-species transmission, and possible zoonotic threats.

IMPORTANCE

This study provides a comprehensive characterization of the entire community of infectious microbes (viruses, bacteria, and fungi) in companion animals like cats and dogs, termed the "infectome." By analyzing hundreds of samples from across China, the researchers identified numerous known and novel pathogens, including 27 potential zoonotic agents that could pose health risks to both animals and humans. Notably, some of these zoonotic pathogens were detected even in apparently healthy pets, highlighting the importance of surveillance. The study also revealed key microbial factors associated with respiratory and gastrointestinal diseases in pets, as well as potential cross-species transmission events between cats and dogs. Overall, this work sheds light on the complex microbial landscapes of companion animals and their potential impacts on animal and human health, underscoring the need for monitoring and management of these infectious agents.

Microbiota insights into pet ownership and human health

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

Alternative amplicon-PCR protocol for maximizing bacterial and fungal sequencing in low-biomass samples

Determining bacterial and fungal communities from low-biomass samples remains a challenge for high-throughput sequencing. Due to the low microbial load and host contamination, some sites, including the female upper reproductive tract and the lower respiratory tract, were even considered sterile until recent years. Despite efforts to improve sampling and DNA isolation protocols, some samples provide insufficient microbial DNA input for library preparation and sequencing. Herein, we propose an alternative amplicon-PCR protocol to be used in bacterial and fungal sequencing in low-biomass samples, targeting 16S-rDNA and the internal transcribed spacer region (ITS), respectively. Similar to a nested-PCR, we performed two sequential PCR reactions to maximise the target amplicon. We compared metagenomic results from the original Illumina protocol (Protocol 1 - P1) and the alternative one (Protocol 2 - P2), using a mock community and clinical samples with different microbial loads. Our findings showed no significant differences in data generated by P1 and P2, indicating that the second amplification round does not bias the microbiota diversity rates. Thus, the alternative protocol can be applied for low-biomass samples when the original protocol results in spurious output, preventing library preparation and sequencing.

Characterization of the chemical composition of different parts of Dolichos lablab L. and revelation of its anti-ulcerative colitis effects by modulating the gut microbiota and host metabolism

ETHNOPHARMACOLOGICAL RELEVANCE

Ulcerative colitis (UC) is a non-specific inflammatory disease characterized by long duration and easy relapse. Dolichos lablab L. (DLL) belongs to the family Fabaceae, was listed in a famous Chinese medical classic, Compendium of Materia Medic, and described as possessing features that invigorate the spleen, alleviate dampness, provide diarrhea relief, and other effects. The DLL-dried white mature seeds (DS) and dried flower (DF), which hold significant medicinal value in China, were used in clinical prescriptions to prevent and treat UC. DS and DF have appeared in different editions of the Pharmacopoeia of the People's Republic of China from 1977 to 2020. However, their chemical composition, pharmacological effects, and mechanism of treating UC are unclear.

AIM OF THE STUDY

This study aimed to characterize the chemical composition of different parts of DLL (seeds and flowers), further explore their pharmacological effects, and elaborate its underlying mechanism of treating UC.

METHODS

The chemical composition of DS and DF crude polysaccharides (DSP and DFP) and ethanolic extracts (DSE and DFE) were characterized by high-performance anion-exchange chromatography (HPAEC), ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS), and gas chromatography-mass spectrometry (GC-MS). Then, based on the acute UC mice model, the pharmacodynamic effects were investigated by Western blotting, ELISA, and other methods. Finally, the 16S rRNA gene sequencing and metabonomic analysis were used to explore the regulatory effects of DS and DF on intestinal microbiota and host metabolism.

RESULTS

DSE and DFE inhibited the oxidative stress response, reducing proinflammatory factor production and maintaining intestinal barrier integrity in UC mice. The 16S rRNA gene sequencing and metabonomic analysis revealed that DS and DF treated UC by regulating the intestinal microbiota structure and reversing the abnormal metabolism of the host.

CONCLUSION

This study suggested that different parts of DLL (flowers and seeds) may be potential medicines for treating UC, which exert their therapeutic effects through various active ingredients and might contribute significantly to reducing the economic pressures and challenges of UC treatment worldwide.

Gastrointestinal tract pathology of the owl monkey (Aotus spp.)

Owl monkeys are small nocturnal new world primates in the genus Aotus that are most used in biomedical research for malaria. Cardiomyopathy and nephropathy are well-described common diseases contributing to their morbidity and mortality; less is known about lesions affecting the gastrointestinal tract. Records from a 14-year period (2008-2022) at the Keeling Center for Comparative Medicine and Research were queried to identify instances of spontaneous gastrointestinal disease that directly contributed to the cause of death from the 235 adult owl monkeys submitted for necropsy. Of the 235, 10.6% (25/235) had gastrointestinal disease listed as a significant factor that contributed to morbidity and mortality. Diagnoses included candidiasis (3/25), gastric bloat (4/25), and intestinal incarceration and ischemia secondary (11/25), which included intussusception (4/25), mesenteric rent (3/25), strangulating lipoma (2/25), intestinal torsion (1/25), and an inguinal hernia (1/25). Intestinal adenocarcinomas affecting the jejunum (4/25) were the most common neoplasia diagnosis. Oral squamous cell carcinoma (1/25) and intestinal lymphoma (2/25) were also diagnosed. This report provides evidence of spontaneous lesions in the species that contribute to morbidity and mortality.

Analysis of subgingival bacterial and fungal diversity in patients with peri-implantitis based on 16sRNA and internal transcribed spacer sequencing

Aim: To analyze subgingival fungal diversity in peri-implant inflammation patients and their relationship with bacteria. Methods: We collected saliva samples from four groups. 16sRNA and internal transcribed spacer sequencing was performed preceded by quantitative PCR and enzyme-linked immunosorbent assay tests. Analyses were done using R and Cytoscape software. Results: Significant differences were observed in the Abundance-based Coverage Estimator (ACE) index between control and peri-implantitis samples. Basidiomycota was the dominant fungal species, while Firmicutes dominated the bacteria. The most abundant fungal and bacterial species were 's_unclassified g Apiotrichum' and 's_unclassified g Streptococcus', respectively. Dothiorella was strongly associated with immunoglobulin G levels, with positive correlations between specific microorganisms and peri-implantitis in Q-PCR. Conclusion: Our findings have significant clinical implications, suggesting specific fungal and bacterial taxa roles in peri-implant inflammation.

The Role of the Human Microbiome in Epithelial Ovarian Cancer

Ovarian cancer is the fifth-leading cause of cancer deaths among women due to the absence of available screening methods to identify early disease. Thus, prevention and early disease detection investigations are of high priority, surrounding a critical window of opportunity to better understand important pathogenic mechanisms of disease progression. Microorganisms modulate molecular interactions in humans that can influence states of health and disease, including ovarian cancer. While the mechanisms of infectious microbial invasion that trigger the immune-inflammatory axis are well studied in cancer research, the complex interactions that promote the transition of noninfectious healthy microbes to pathobiont expansion are less understood. As traditional research has focused on the influences of infectious pathogens on ovarian cancer development and progression, the impact of noninfectious microbes has gained scientific attention. The objective of this chapter is to summarize current evidence on the role of microbiota in epithelial ovarian cancer throughout disease.

Chinese Yam and Its Active Components Regulate the Structure of Gut Microbiota and Indole-like Metabolites in Anaerobic Fermentation In Vitro

As a medicinal and edible plant, Chinese yam (CY) can promote the enrichment of intestinal probiotics. Mucilage polysaccharides, diosgenin and taxifolin are the dominant components of CY. The purpose of this study was to investigate whether the impact of Chinese yam on gut microbiome structure and metabolism is attributable to its components. In the in vitro gastrointestinal digestion and colon fermentation system, the changes in gut microbiota composition and function were determined by 16S rRNA sequencing, and the levels of bacterial metabolites including short-chain fatty acids (SCFAs) and indole-like metabolites were detected by gas chromatography and an enzyme-linked immunoassay. The results show that CY, mucilage polysaccharides, diosgenin and taxifolin could increase the microbial diversity index. Furthermore, probiotics including Lactobacillus and Bacteroides were significantly increased, while harmful bacteria such as Escherichia and Proteus declined. CY could increase the production of SCFAs including acetic acid and butyric acid. Of note, CY and diosgenin displayed similar impacts on enhancing the abundance of Clostridium and promoting the production of indole-3-lactic acid and lactic acid. These findings provide evidence supporting Chinese yam as a natural food to regulate intestinal health. Diosgenin as a component of CY contributes mostly to the impact on regulating intestinal flora.

Uncovering the promising role of grape pomace as a modulator of the gut microbiome: An in-depth review

Grape pomace is the primary wine coproduct consisting primarily of grape seeds and skins. Grape pomace holds immense potential as a functional ingredient to improve human health while its valorization can be beneficial for industrial sustainability. Pomace contains bioactive compounds, including phenols and oligosaccharides, most of which reach the colon intact, enabling interaction with the gut microbiome. Microbial analysis found that grape pomace selectively promotes the growth of many commensal bacteria strains, while other types of bacteria, including various pathogens, are highly sensitive to the pomace and its components and are inactivated. In vitro studies showed that grape pomace and its extracts inhibit the growth of pathogenic bacteria in Enterobacteriaceae family while increasing the growth and survival of some beneficial bacteria, including Bifidobacterium spp. and Lactobacillus spp. Grape pomace supplementation in mice and rats improves their gut microbiome complexity and decreases diet-induced obesity as well as related illnesses, including insulin resistance, indicating grape pomace could improve human health. A human clinical trial found that pomace, regardless of its phenolic content, had cardioprotective effects, suggesting that dietary fiber induced those health benefits. To shed light on the active components, this review explores the potential prebiotic capacity of select bioactive compounds in grape pomace.

Gut Probiotics and Health of Dogs and Cats: Benefits, Applications, and Underlying Mechanisms

Pets (mostly domestic dogs and cats) play an important role in the daily lives of humans and their health has attracted growing attention from pet owners. The intestinal microbiota, a complex microbial community with barrier-protective, nutritional, metabolic, and immunological functions, is integral to host health. Dysbiosis has been related to a variety of diseases in humans and animals. Probiotics have been used in functional foods and dietary supplements to modulate intestinal microbiota and promote host health, which has been introduced in pet dogs and cats in recent years. Various canine- and feline-derived probiotic strains have been isolated and characterized. The administration of probiotics has shown positive effects on the gut health and can alleviate some intestinal diseases and disorders in dogs and cats, although the underlying mechanisms are largely unresolved. In this review, we summarize the current knowledge on the benefits of probiotics and discuss their possible mechanisms in dogs and cats in order to provide new insights for the further development and application of probiotics in pets.

A microbial causal mediation analytic tool for health disparity and applications in body mass index

BACKGROUND

Emerging evidence suggests the potential mediating role of microbiome in health disparities. However, no analytic framework can be directly used to analyze microbiome as a mediator between health disparity and clinical outcome, due to the non-manipulable nature of the exposure and the unique structure of microbiome data, including high dimensionality, sparsity, and compositionality.

METHODS

Considering the modifiable and quantitative features of the microbiome, we propose a microbial causal mediation model framework, SparseMCMM_HD, to uncover the mediating role of microbiome in health disparities, by depicting a plausible path from a non-manipulable exposure (e.g., ethnicity or region) to the outcome through the microbiome. The proposed SparseMCMM_HD rigorously defines and quantifies the manipulable disparity measure that would be eliminated by equalizing microbiome profiles between comparison and reference groups and innovatively and successfully extends the existing microbial mediation methods, which are originally proposed under potential outcome or counterfactual outcome study design, to address health disparities.

RESULTS

Through three body mass index (BMI) studies selected from the curatedMetagenomicData 3.4.2 package and the American gut project: China vs. USA, China vs. UK, and Asian or Pacific Islander (API) vs. Caucasian, we exhibit the utility of the proposed SparseMCMM_HD framework for investigating the microbiome's contributions in health disparities. Specifically, BMI exhibits disparities and microbial community diversities are significantly distinctive between reference and comparison groups in all three applications. By employing SparseMCMM_HD, we illustrate that microbiome plays a crucial role in explaining the disparities in BMI between ethnicities or regions. 20.63%, 33.09%, and 25.71% of the overall disparity in BMI in China-USA, China-UK, and API-Caucasian comparisons, respectively, would be eliminated if the between-group microbiome profiles were equalized; and 15, 18, and 16 species are identified to play the mediating role respectively.

CONCLUSIONS

The proposed SparseMCMM_HD is an effective and validated tool to elucidate the mediating role of microbiome in health disparity. Three BMI applications shed light on the utility of microbiome in reducing BMI disparity by manipulating microbial profiles. Video Abstract.

Staphylococcal species composition in the skin microbiota of domestic pigeons (Columba livia domestica)

Staphylococci are a natural component of the skin microbiota of many organisms, including humans and birds. As opportunistic pathogens, they can cause a variety of infections in humans. The close contact between domestic pigeons and their owners provide an opportunity for exchange of skin-associated bacteria. In this study, 41 healthy racing pigeons were tested. Staphylococci were detected on the skin of each bird (41/41, 100%). Isolates were identified at the species level using matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). The diversity of the Staphylococcus species was relatively high and coagulase-negative staphylococci (CoNS) were predominantly isolated. In total, ten different staphylococcal species were identified. S. lentus (19/41, 46.3%) was noted most frequently. The pigeon skin was also inhabited by S. xylosus (6/41, 14.6%), S. equorum (4/41, 9.8%), S. hyicus (3/41, 7.3%), S. intermedius (2/41, 4.9%), S. sciuri (2/41, 4.9%), S. vitulinus (2/41, 4.9%), S. lugdunensis (1/41, 2.4%), S. hominis (1/41, 2.4%), and S. auricularis (1/41, 2.4%). Our results indicate that domestic pigeons may carry pathogens with zoonotic potential. All strains were susceptible to 12 antibiotics (ciprofloxacin, clindamycin chloramphenicol, erythromycin, fosfomycin, gentamicin, levofloxacin, norfloxacin, rifampicin, tobramycin, trimethoprim/sulfamethoxazole, vancomycin) representing 8 different classes. None isolate displayed a multidrug-resistant phenotype. Resistance to tetracycline (6/41, 14.6%) and to penicillin (4/41, 9.7%) was shown. The mecA gene was not detected in the examined strains and no methicillin-resistant staphylococci were found on the skin of the healthy pigeons.

Association between Gut Dysbiosis and the Occurrence of SIBO, LIBO, SIFO and IMO

Gut microbiota is the aggregate of all microorganisms in the human digestive system. There are 1014 CFU/mL of such microorganisms in the human body, including bacteria, viruses, fungi, archaea and protozoa. The Firmicutes and Bacteroidetes bacteria phyla comprise 90% of the human gut microbiota. The microbiota support the healthy functioning of the human body by helping with digestion (mainly via short-chain fatty acids and amino acids) and producing short-chain fatty acids. In addition, it exhibits many physiological functions, such as forming the intestinal epithelium, intestinal integrity maintenance, the production of vitamins, and protection against pathogens. An altered composition or the number of microorganisms, known as dysbiosis, disrupts the body's homeostasis and can lead to the development of inflammatory bowel disease, irritable bowel syndrome, and metabolic diseases such as diabetes, obesity and allergies. Several types of disruptions to the gut microbiota have been identified: SIBO (Small Intestinal Bacterial Overgrowth), LIBO (Large Intestinal Bacterial Overgrowth), SIFO (Small Intestinal Fungal Overgrowth), and IMO (Intestinal Methanogen Overgrowth). General gastrointestinal problems such as abdominal pain, bloating, gas, diarrhoea and constipation are the main symptoms of dysbiosis. They lead to malabsorption, nutrient deficiencies, anaemia and hypoproteinaemia. Increased lipopolysaccharide (LPS) permeability, stimulating the inflammatory response and resulting in chronic inflammation, has been identified as the leading cause of microbial overgrowth in the gut. The subject literature is extensive but of limited quality. Despite the recent interest in the gut microbiome and its disorders, more clinical research is needed to determine the pathophysiology, effective treatments, and prevention of small and large intestinal microbiota overgrowth. This review was designed to provide an overview of the available literature on intestinal microbial dysbiosis (SIBO, LIBO, SIFO and IMO) and to determine whether it represents a real threat to human health.

Neutralising Effects of Different Antibodies on Clostridioides difficile Toxins TcdA and TcdB in a Translational Approach

Given the high prevalence of intestinal disease in humans and animals, there is a strong need for clinically relevant models recapitulating gastrointestinal systems, ideally replacing in vivo models in accordance with the principles of the 3R. We established a canine organoid system and analysed the neutralising effects of recombinant versus natural antibodies on Clostridioides difficile toxins A and B in this in vitro system. Sulforhodamine B cytotoxicity assays in 2D and FITC-dextran barrier integrity assays on basal-out and apical-out organoids revealed that recombinant, but not natural antibodies, effectively neutralised C. difficile toxins. Our findings emphasise that canine intestinal organoids can be used to test different components and suggest that they can be further refined to also mirror complex interactions between the intestinal epithelium and other cells.

The gut microbiota: A new perspective for tertiary prevention of hepatobiliary and gallbladder diseases

The gut microbiota is a complex ecosystem that has coevolved with the human body for hundreds of millions of years. In the past 30 years, with the progress of gene sequencing and omics technology, the research related to gut microbiota has developed rapidly especially in the field of digestive system diseases and systemic metabolic diseases. Mechanical, biological, immune, and other factors make the intestinal flora form a close bidirectional connection with the liver and gallbladder, which can be called the "gut-liver-biliary axis." Liver and gallbladder, as internal organs of the peritoneum, suffer from insidious onset, which are not easy to detect. The diagnosis is often made through laboratory chemical tests and imaging methods, and intervention measures are usually taken only when organic lesions have occurred. At this time, some people may have entered the irreversible stage of disease development. We reviewed the literature describing the role of intestinal flora in the pathogenesis and biotherapy of hepatobiliary diseases in the past 3-5 years, including the dynamic changes of intestinal flora at different stages of the disease, as well as the signaling pathways involved in intestinal flora and its metabolites, etc. After summarizing the above contents, we hope to highlight the potential of intestinal flora as a new clinical target for early prevention, early diagnosis, timely treatment and prognosis of hepatobiliary diseases. GRAPHICAL ABSTRACT.

Network-based quantitative trait linkage analysis of microbiome composition in inflammatory bowel disease families

Introduction: Inflammatory bowel disease (IBD) is characterized by a dysbiosis of the gut microbiome that results from the interaction of the constituting taxa with one another, and with the host. At the same time, host genetic variation is associated with both IBD risk and microbiome composition. Methods: In the present study, we defined quantitative traits (QTs) from modules identified in microbial co-occurrence networks to measure the inter-individual consistency of microbial abundance and subjected these QTs to a genome-wide quantitative trait locus (QTL) linkage analysis. Results: Four microbial network modules were consistently identified in two cohorts of healthy individuals, but three of the corresponding QTs differed significantly between IBD patients and unaffected individuals. The QTL linkage analysis was performed in a sub-sample of the Kiel IBD family cohort (IBD-KC), an ongoing study of 256 German families comprising 455 IBD patients and 575 first- and second-degree, non-affected relatives. The analysis revealed five chromosomal regions linked to one of three microbial module QTs, namely on chromosomes 3 (spanning 10.79 cM) and 11 (6.69 cM) for the first module, chr9 (0.13 cM) and chr16 (1.20 cM) for the second module, and chr13 (19.98 cM) for the third module. None of these loci have been implicated in a microbial phenotype before. Discussion: Our study illustrates the benefit of combining network and family-based linkage analysis to identify novel genetic drivers of microbiome composition in a specific disease context.

A microbial causal mediation analytic tool for health disparity and applications in body mass index

Background: Emerging evidence suggests the potential mediating role of microbiome in health disparities. However, no analytic framework is available to analyze microbiome as a mediator between health disparity and clinical outcome, due to the unique structure of microbiome data, including high dimensionality, sparsity, and compositionality. Methods: Considering the modifiable and quantitative features of microbiome, we propose a microbial causal mediation model framework, SparseMCMM_HD, to uncover the mediating role of microbiome in health disparities, by depicting a plausible path from a non-manipulable exposure (e.g. race or region) to a continuous outcome through microbiome. The proposed SparseMCMM_HD rigorously defines and quantifies the manipulable disparity measure that would be eliminated by equalizing microbiome profiles between comparison and reference groups. Moreover, two tests checking the impact of microbiome on health disparity are proposed. Results: Through three body mass index (BMI) studies selected from the curatedMetagenomicData 3.4.2 package and the American gut project: China vs. USA, China vs. UK, and Asian or Pacific Islander (API) vs. Caucasian, we exhibit the utility of the proposed SparseMCMM_HD framework for investigating microbiome’s contributions in health disparities. Specifically, BMI exhibits disparities and microbial community diversities are significantly distinctive between the reference and comparison groups in all three applications. By employing SparseMCMM_HD, we illustrate that microbiome plays a crucial role in explaining the disparities in BMI between races or regions. 11.99%, 12.90%, and 7.4% of the overall disparity in BMI in China-USA, China-UK, and API-Caucasian comparisons, respectively, would be eliminated if the between-group microbiome profiles were equalized; and 15, 21, and 12 species are identified to play the mediating role respectively. Conclusions: The proposed SparseMCMM_HD is an effective and validated tool to elucidate the mediating role of microbiome in health disparity. Three BMI applications shed light on the utility of microbiome in reducing BMI disparity by manipulating microbial profiles.

Evaluation of high-protein diets differing in protein source in healthy adult dogs

Given the dynamic market for protein-based ingredients in the pet food industry, demand continues to increase for both plant- and animal-based options. Protein sources contain different amino acid (AA) profiles and vary in digestibility, affecting protein quality. The objective of this study was to evaluate the apparent total tract digestibility (ATTD) of canine diets differing in protein source and test their effects on serum metabolites and fecal characteristics, metabolites, and microbiota of healthy adult dogs consuming them. Four extruded diets were formulated to be isonitrogenous and meet the nutrient needs for adult dogs at maintenance, with the primary difference being protein source: 1) fresh deboned, dried, and spray-dried chicken (DC), 2) chicken by-product meal (CBPM), 3) wheat gluten meal (WGM), and 4) corn gluten meal (CGM). Twelve adult spayed female beagles (body weight [BW] = 9.9 ± 1.0 kg; age = 6.3 ± 1.1 yr) were used in a replicated 4 × 4 Latin square design (n = 12/treatment). Each period consisted of a 22-d adaptation phase, 5 d for fecal collection, and 1 d for blood collection. Fecal microbiota data were analyzed using QIIME 2.2020.8. All other data were analyzed using the Mixed Models procedure of SAS version 9.4. Fecal scores were higher (P < 0.05; looser stools) in dogs fed DC or CBPM than those fed WGM or CGM, but all remained within an appropriate range. Dry matter ATTD was lower (P < 0.05) in dogs fed CBPM or CGM than those fed DC or WGM. Crude protein ATTD was lower (P < 0.05) in dogs fed DC or CGM than those fed WGM. Dogs fed CBPM had lower (P < 0.05) organic matter, crude protein, and energy ATTD than those fed the other diets. Fecal indole was higher (P < 0.05) in dogs fed CBPM than those fed WGM. Fecal short-chain fatty acids were higher (P < 0.05) in dogs fed DC than those fed CGM. Fecal branched-chain fatty acids were higher (P < 0.05) in dogs fed DC or CBPM than those fed WGM. Fecal ammonia was higher (P < 0.05) in dogs fed DC or CBPM than those fed WGM or CGM. The relative abundances of three bacterial phyla and nine bacterial genera were shifted among treatment groups (P < 0.05). Considering AA profiles and digestibility data, the DC diet protein sources provided the highest quality protein without additional AA supplementation, but the animal-based protein diets resulted in higher fecal proteolytic metabolites. Further studies evaluating moderate dietary protein concentrations are needed to better compare plant- and animal-based protein sources.

Exposure to glyphosate in the United States: Data from the 2013-2014 National Health and Nutrition Examination Survey

BACKGROUND

Exposure to glyphosate, the most used herbicide in the United States, is not well characterized. We assessed glyphosate exposure in a representative sample of the U.S. population ≥ 6 years from the 2013-2014 National Health and Nutrition Examination Survey.

METHODS

We quantified glyphosate in urine (N = 2,310) by ion chromatography isotope-dilution tandem mass spectrometry. We conducted univariate analysis using log-transformed creatinine-corrected glyphosate concentrations with demographic and lifestyle covariates we hypothesized could affect glyphosate exposure based on published data including race/ethnicity, sex, age group, family income to poverty ratio, fasting time, sample collection season, consumption of food categories (including cereal consumption) and having used weed killer products. We used multiple logistic regression to examine the likelihood of glyphosate concentrations being above the 95th percentile and age-stratified multiple linear regression to evaluate associations between glyphosate concentrations and statistically significant covariates from the univariate analysis: race/ethnicity, sex, age group, fasting time, cereal consumption, soft drink consumption, sample collection season, and urinary creatinine.

RESULTS

Glyphosate weighted detection frequency was 81.2 % (median (interquartile range): 0.392 (0.263-0.656) μg/L; 0.450 (0.266-0.753) μg/g creatinine). Glyphosate concentration decreased from age 6-11 until age 20-59 and increased at 60+ years in univariate analyses. Children/adolescents and adults who fasted > 8 h had significantly lower model-adjusted geometric means (0.43 (0.37-0.51) μg/L and 0.37 (0.33-0.39) μg/L) than those fasting ≤ 8 h (0.51 (0.46-0.56) μg/L and 0.44 (0.41-0.48) μg/L), respectively. The likelihood (odds ratio (95 % CI)) of glyphosate concentrations being > 95th percentile was 1.94 (1.06-3.54) times higher in people who fasted ≤ 8 h than people fasting > 8 h (P = 0.0318).

CONCLUSIONS

These first nationally representative data suggest that over four-fifths of the U.S. general population ≥ 6 years experienced recent exposure to glyphosate. Variation in glyphosate concentration by food consumption habits may reflect diet or lifestyle differences.

The role of the gut microbiota in health and cardiovascular diseases

The gut microbiota is critical to human health, such as digesting nutrients, forming the intestinal epithelial barrier, regulating immune function, producing vitamins and hormones, and producing metabolites to interact with the host. Meanwhile, increasing evidence indicates that the gut microbiota has a strong correlation with the occurrence, progression and treatment of cardiovascular diseases (CVDs). In patients with CVDs and corresponding risk factors, the composition and ratio of gut microbiota have significant differences compared with their healthy counterparts. Therefore, gut microbiota dysbiosis, gut microbiota-generated metabolites, and the related signaling pathway may serve as explanations for some of the mechanisms about the occurrence and development of CVDs. Several studies have also demonstrated that many traditional and latest therapeutic treatments of CVDs are associated with the gut microbiota and its generated metabolites and related signaling pathways. Given that information, we summarized the latest advances in the current research regarding the effect of gut microbiota on health, the main cardiovascular risk factors, and CVDs, highlighted the roles and mechanisms of several metabolites, and introduced corresponding promising treatments for CVDs regarding the gut microbiota. Therefore, this review mainly focuses on exploring the role of gut microbiota related metabolites and their therapeutic potential in CVDs, which may eventually provide better solutions in the development of therapeutic treatment as well as the prevention of CVDs.

The World of Organoids: Gastrointestinal Disease Modelling in the Age of 3R and One Health with Specific Relevance to Dogs and Cats

One Health describes the importance of considering humans, animals, and the environment in health research. One Health and the 3R concept, i.e., the replacement, reduction, and refinement of animal experimentation, shape today’s research more and more. The development of organoids from many different organs and animals led to the development of highly sophisticated model systems trying to replace animal experiments. Organoids may be used for disease modelling in various ways elucidating the manifold host–pathogen interactions. This review provides an overview of disease modelling approaches using organoids of different kinds with a special focus on animal organoids and gastrointestinal diseases. We also provide an outlook on how the research field of organoids might develop in the coming years and what opportunities organoids hold for in-depth disease modelling and therapeutic interventions.

Marine-Bioinspired Nanoparticles as Potential Drugs for Multiple Biological Roles

The increased interest in nanomedicine and its applicability for a wide range of biological functions demands the search for raw materials to create nanomaterials. Recent trends have focused on the use of green chemistry to synthesize metal and metal-oxide nanoparticles. Bioactive chemicals have been found in a variety of marine organisms, including invertebrates, marine mammals, fish, algae, plankton, fungi, and bacteria. These marine-derived active chemicals have been widely used for various biological properties. Marine-derived materials, either whole extracts or pure components, are employed in the synthesis of nanoparticles due to their ease of availability, low cost of production, biocompatibility, and low cytotoxicity toward eukaryotic cells. These marine-derived nanomaterials have been employed to treat infectious diseases caused by bacteria, fungi, and viruses as well as treat non-infectious diseases, such as tumors, cancer, inflammatory responses, and diabetes, and support wound healing. Furthermore, several polymeric materials derived from the marine, such as chitosan and alginate, are exploited as nanocarriers in drug delivery. Moreover, a variety of pure bioactive compounds have been loaded onto polymeric nanocarriers and employed to treat infectious and non-infectious diseases. The current review is focused on a thorough overview of nanoparticle synthesis and its biological applications made from their entire extracts or pure chemicals derived from marine sources.

Microbial risk score for capturing microbial characteristics, integrating multi-omics data, and predicting disease risk

BACKGROUND

With the rapid accumulation of microbiome-wide association studies, a great amount of microbiome data are available to study the microbiome's role in human disease and advance the microbiome's potential use for disease prediction. However, the unique features of microbiome data hinder its utility for disease prediction.

METHODS

Motivated from the polygenic risk score framework, we propose a microbial risk score (MRS) framework to aggregate the complicated microbial profile into a summarized risk score that can be used to measure and predict disease susceptibility. Specifically, the MRS algorithm involves two steps: (1) identifying a sub-community consisting of the signature microbial taxa associated with disease and (2) integrating the identified microbial taxa into a continuous score. The first step is carried out using the existing sophisticated microbial association tests and pruning and thresholding method in the discovery samples. The second step constructs a community-based MRS by calculating alpha diversity on the identified sub-community in the validation samples. Moreover, we propose a multi-omics data integration method by jointly modeling the proposed MRS and other risk scores constructed from other omics data in disease prediction.

RESULTS

Through three comprehensive real-data analyses using the NYU Langone Health COVID-19 cohort, the gut microbiome health index (GMHI) multi-study cohort, and a large type 1 diabetes cohort separately, we exhibit and evaluate the utility of the proposed MRS framework for disease prediction and multi-omics data integration. In addition, the disease-specific MRSs for colorectal adenoma, colorectal cancer, Crohn's disease, and rheumatoid arthritis based on the relative abundances of 5, 6, 12, and 6 microbial taxa, respectively, are created and validated using the GMHI multi-study cohort. Especially, Crohn's disease MRS achieves AUCs of 0.88 (0.85-0.91) and 0.86 (0.78-0.95) in the discovery and validation cohorts, respectively.

CONCLUSIONS

The proposed MRS framework sheds light on the utility of the microbiome data for disease prediction and multi-omics integration and provides a great potential in understanding the microbiome's role in disease diagnosis and prognosis. Video Abstract.

Probiotics: A gut response to the COVID-19 pandemic but what does the evidence show?

Since the global outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), research has focused on understanding the etiology of coronavirus disease 2019 (COVID-19). Identifying and developing prophylactic and therapeutics strategies to manage the pandemic is still of critical importance. Among potential targets, the role of the gut and lung microbiomes in COVID-19 has been questioned. Consequently, probiotics were touted as potential prophylactics and therapeutics for COVID-19. In this review we highlight the role of the gut and lung microbiome in COVID-19 and potential mechanisms of action of probiotics. We also discuss the progress of ongoing clinical trials for COVID-19 that aim to modulate the microbiome using probiotics in an effort to develop prophylactic and therapeutic strategies. To date, despite the large interest in this area of research, there is promising but limited evidence to suggest that probiotics are an effective prophylactic or treatment strategy for COVID-19. However, the role of the microbiome in pathogenesis and as a potential target for therapeutics of COVID-19 cannot be discounted.

Microbial Risk Score for Capturing Microbial Characteristics, Integrating Multi-omics Data, and Predicting Disease Risk

Background:

With the rapid accumulation of microbiome-wide association studies, a great amount of microbiome data are available to study the microbiome’s role in human disease and advance the microbiome’s potential use for disease prediction. However, the unique features of microbiome data hinder its utility for disease prediction.

Methods:

Motivated from the polygenic risk score framework, we propose a microbial risk score (MRS) framework to aggregate the complicated microbial profile into a summarized risk score that can be used to measure and predict disease susceptibility. Specifically, the MRS algorithm involves two steps: 1) identifying a sub-community consisting of the signature microbial taxa associated with disease, and 2) integrating the identified microbial taxa into a continuous score. The first step is carried out using the existing sophisticated microbial association tests and pruning and thresholding method in the discovery samples. The second step constructs a community-based MRS by calculating alpha diversity on the identified sub-community in the validation samples. Moreover, we propose a multi-omics data integration method by jointly modeling the proposed MRS and other risk scores constructed from other omics data in disease prediction.

Results:

Through three comprehensive real data analyses using the NYU Langone Health COVID-19 cohort, the gut microbiome health index (GMHI) multi-study cohort, and a large type 1 diabetes cohort separately, we exhibit and evaluate the utility of the proposed MRS framework for disease prediction and multi-omics data integration. In addition, the disease-specific MRSs for colorectal adenoma, colorectal cancer, Crohn’s disease, and rheumatoid arthritis based on the relative abundances of 5, 6, 12, and 6 microbial taxa respectively are created and validated using the GMHI multi-study cohort. Especially, Crohn’s disease MRS achieves AUCs of 0.88 ([0.85–0.91]) and 0.86 ([0.78–0.95]) in the discovery and validation cohorts, respectively.

Conclusions:

The proposed MRS framework sheds light on the utility of the microbiome data for disease prediction and multi-omics integration, and provides great potential in understanding the microbiome’s role in disease diagnosis and prognosis.

Protective effects of glycine against lipopolysaccharide-induced intestinal apoptosis and inflammation

Intestinal dysfunction is commonly observed in humans and animals. Glycine (Gly) is a functional amino acid with anti-inflammatory and anti-apoptotic properties. The objective of this study was to test the protective effects of Gly against lipopolysaccharide (LPS)-induced intestinal injury. 28 C57BL/6 mice with a body weight (BW) of 18 ± 2 g were randomly assigned into four groups: CON (control), GLY (orally administered Gly, 5 g/kg BW/day for 6 days), LPS (5 mg/kg BW on day 7, i. p.), and GLY + LPS (Gly pretreatment and LPS administration). Histological alterations, inflammatory responses, epithelial cell apoptosis, and changes of the intestinal microbiota were analyzed. Results showed that, compared with the CON group, mice in the LPS treatment group showed decreased villus height, increased crypt depth, and decreased ratio of villus height to crypt depth, which were significantly attenuated by Gly. Neither LPS nor Gly treatment altered morphology of the distal colon tissues. LPS increased the apoptosis of jejunum and colon epithelial cells and protein abundance of cleaved caspase3 in the jejunum, which were markedly abrogated by Gly. LPS also elevated the mRNA levels of Toll-like receptor 4 (TLR4), myeloid differentiation factor 88 (MYD88), pro-inflammatory cytokines, and chemokines in the jejunum and colon. These alterations were significantly suppressed by Gly. In addition, Gly supplementation attenuated infiltration of CD4+, CD8+ T-lymphocytes, CD11b+ and F4/80+ macrophages in the colon. Furthermore, Gly increased the relative abundance of Mucispirillum, Lachnospiraceae-NK4A136-group, Anaerotruncus, Faecalibaculum, Ruminococcaceae-UCG-014, and decreased the abundance of Bacteroides at genus level. Supplementation with Gly might be a nutritional strategy to ameliorate LPS-induced intestinal injury in mice.

Effects of Zinc Source and Enzyme Addition on the Fecal Microbiota of Dogs

Supplemental zinc from organic sources has been suggested to be more bioavailable than inorganic ones for dog foods. However, the bioavailability of zinc might be affected by dietary constituents such as phytates. The present study aimed to evaluate the effects of two zinc sources (zinc sulfate and zinc proteinate) and the addition of a multi-enzymatic complex from the solid-state fermentation of Aspergillus niger on end-products of fecal fermentation and fecal microbiota of adult Beagles fed a high-phytate diet. The experimental design consisted of three 4 × 4 Latin Squares with a 2 × 2 factorial arrangement of treatments (n = 12 Beagles), with four periods and four diets: zinc sulfate without (IZ) or with (IZ +) enzyme addition, and zinc proteinate without (OZ) or with (OZ +) enzyme addition. Enzyme addition significantly affected Faith’s phylogenetic diversity index, whereas zinc source did not affect either beta or alpha diversity measures. Linear discriminant analysis effect size detected nine taxa as markers for organic zinc, 18 for inorganic source, and none for enzyme addition. However, with the use of a negative binomial generalized linear model, further effects were observed. Organic zinc was associated with a significantly higher abundance of Firmicutes and lower Proteobacteria and Bacteroidetes, although at a genus level, the response varied. The DNA abundance of Clostridium cluster I, Clostridium cluster XIV, Campylobacter spp., Ruminococcaceae, Turicibacter, and Blautia was significantly higher in dogs fed IZ and IZ + diets. Higher abundance of genus Lactobacillus was observed in dogs fed enzyme-supplemented diets. End-products of fecal fermentation were not affected by zinc source or enzymes. An increase in some taxa of the phyla Actinobacteria and Firmicutes was observed in feces of dogs fed organic zinc with enzyme addition but not with inorganic zinc. This study fills a gap in knowledge regarding the effect of zinc source and enzyme addition on the fecal microbiota of dogs. An association of zinc bioavailability and bacteria abundance is suggested, but the implications for the host (dog) are not clear. Further studies are required to unveil the effects of the interaction between zinc sources and enzyme addition on the fecal microbial community.

Microbial trend analysis for common dynamic trend, group comparison, and classification in longitudinal microbiome study

BACKGROUND

The human microbiome is inherently dynamic and its dynamic nature plays a critical role in maintaining health and driving disease. With an increasing number of longitudinal microbiome studies, scientists are eager to learn the comprehensive characterization of microbial dynamics and their implications to the health and disease-related phenotypes. However, due to the challenging structure of longitudinal microbiome data, few analytic methods are available to characterize the microbial dynamics over time.

RESULTS

We propose a microbial trend analysis (MTA) framework for the high-dimensional and phylogenetically-based longitudinal microbiome data. In particular, MTA can perform three tasks: 1) capture the common microbial dynamic trends for a group of subjects at the community level and identify the dominant taxa; 2) examine whether or not the microbial overall dynamic trends are significantly different between groups; 3) classify an individual subject based on its longitudinal microbial profiling. Our extensive simulations demonstrate that the proposed MTA framework is robust and powerful in hypothesis testing, taxon identification, and subject classification. Our real data analyses further illustrate the utility of MTA through a longitudinal study in mice.

CONCLUSIONS

The proposed MTA framework is an attractive and effective tool in investigating dynamic microbial pattern from longitudinal microbiome studies.

Glycine Attenuates Citrobacter rodentium-Induced Colitis by Regulating ATF6-Mediated Endoplasmic Reticulum Stress in Mice

SCOPE

Inflammatory bowel disease (IBD) is an inflammatory gastrointestinal disorder in which endoplasmic reticulum (ER) stress and dysbiosis of the intestinal microbiota are implicated. Glycine supplementation is reported to reduce inflammatory responses in experimental colitis. However, the underlying mechanisms responsible for the beneficial effects remain unclear.

METHODS AND RESULTS

Female C57BL/6 mice are orally administered with glycine (3.5 or 5.2 g kg-1 body weight) for 14 continuous days. On day 8 post-glycine supplementation, the mice are orally inoculated with 2 × 109 CFU Citrobacter rodentium (C. rodentium). The results show that glycine alleviates C. rodentium-induced body weight loss, increased disease activity index and spleen weight, colon length shortening, and colonic hyperplasia. Glycine suppresses the activation and infiltration of inflammatory cells, and secretion of pro-inflammatory cytokines in the colon tissues. The apoptosis of colon epithelial cells is also abrogated by glycine, which is associated with the inactivation of activating transcription factor 6α (ATF6α)-C/EBP homologous protein (CHOP) signaling. In addition, glycine administration increases α diversity, restores β diversity, and abolishes the reduction in Lactobacillus, Bifidobacterium, Alistipes, Turicibacter, and Alloprevotella in the colon.

CONCLUSIONS

Glycine supplementation is a nutritional strategy that may ameliorate C. rodentium-induced colitis by regulating ATF6α-CHOP-mediated ER stress and enhancing the abundance of Lactobacillus.

Predictors of Vaccine Hesitancy: Implications for COVID-19 Public Health Messaging

Objectives: Successful immunization programs require strategic communication to increase confidence among individuals who are vaccine-hesitant. This paper reviews research on determinants of vaccine hesitancy with the objective of informing public health responses to COVID-19. Method: A literature review was conducted using a broad search strategy. Articles were included if they were published in English and relevant to the topic of demographic and individual factors associated with vaccine hesitancy. Results and Discussion: Demographic determinants of vaccine hesitancy that emerged in the literature review were age, income, educational attainment, health literacy, rurality, and parental status. Individual difference factors included mistrust in authority, disgust sensitivity, and risk aversion. Conclusion: Meeting target immunization rates will require robust public health campaigns that speak to individuals who are vaccine-hesitant in their attitudes and behaviours. Based on the assortment of demographic and individual difference factors that contribute to vaccine hesitancy, public health communications must pursue a range of strategies to increase public confidence in available COVID-19 vaccines.

Effects of Differences in Resistant Starch Content of Rice on Intestinal Microbial Composition

The aim of this study was to evaluate the effects of resistant starch (RS) and fat levels on the gut microbiome in C57BL/6 mice. Three levels of RS from three varieties of rice were the major source of carbohydrates and fat levels were low (10%) and high (39%). We confirmed that RS decreased the Firmicutes to Bacteroidetes ratio, increased SCFA production by higher Bacteroidaceae and S24-7 abundance, and enriched predicted gene families of glycosidases and functional pathways associated with carbohydrate and glycan metabolism. We also found correlations between microbial taxa and tissue gene expression related to carbohydrate and lipid metabolism. Moreover, increasing RS levels resulted in a molecular ecological network with enhanced modularity and interspecific synergy, which is less sensitive to high fat intervention. Overall, RS as low as 0.44% from cooked rice can modulate gut microbiome in mice, which correlated to a protective effect against deleterious effects of an obesogenic diet.

Investigating the origin of the fetal gut and placenta microbiome in twins

OBJECTIVE

It is widely accepted that the microbiota is critical for human well-being; however, the origin of microbiota in the newborn is not well understood. In this study, we hypothesized that within a maternal-twin dyad (MTD) the meconium microbiome will be similar to the placenta microbiome and the meconium microbiome of within MTD will be similar to one another.

METHODS

Prospectively, meconium (proxy for fetal gut), placenta and maternal buccal, skin, vaginal, stool samples were collected from a cohort of MTDs at time of delivery hospitalization. We performed gene sequencing using the V4 region of 16S rRNA with rigorous negative controls. Alpha and beta diversity indices were computed to characterize the microbial community of MTD samples. A p value of <.05 was considered significant.

RESULTS

From 17 MTD, 87/132 samples were successfully sequenced. The alpha diversity of the microbiome collected from all the body sites were different (p ≤ .001). The meconium samples when compared to other samples in the MTD microbial community were different (p = .009) and the Bray-Curtis dissimilarity was greater than 0.95 for all of the comparisons (beta diversity). The MTD within-twin placenta microbiome samples were also different, confirmed by Bray-Curtis pairwise dissimilarity distance, 0.83.

CONCLUSION

The fetal gut microbiome is different from placenta and maternal buccal, skin, vaginal and stool microbiome. We clearly identified a distinct placenta microbiome. Furthermore, placentas in the same MTD have distinct microbiomes, suggesting that fetal gut and placenta origin is complex and remains unclear.

Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution

Neo-Darwinism presumes that biological variation is a product of random genetic replication errors and natural selection. Cognition-Based Evolution (CBE) asserts a comprehensive alternative approach to phenotypic variation and the generation of biological novelty. In CBE, evolutionary variation is the product of natural cellular engineering that permits purposive genetic adjustments as cellular problem-solving. CBE upholds that the cornerstone of biology is the intelligent measuring cell. Since all biological information that is available to cells is ambiguous, multicellularity arises from the cellular requirement to maximize the validity of available environmental information. This is best accomplished through collective measurement purposed towards maintaining and optimizing individual cellular states of homeorhesis as dynamic flux that sustains cellular equipoise. The collective action of the multicellular measurement and assessment of information and its collaborative communication is natural cellular engineering. Its yield is linked cellular ecologies and mutualized niche constructions that comprise biofilms and holobionts. In this context, biological variation is the product of collective differential assessment of ambiguous environmental cues by networking intelligent cells. Such concerted action is enabled by non-random natural genomic editing in response to epigenetic impacts and environmental stresses. Random genetic activity can be either constrained or deployed as a 'harnessing of stochasticity'. Therefore, genes are cellular tools. Selection filters cellular solutions to environmental stresses to assure continuous cellular-organismal-environmental complementarity. Since all multicellular eukaryotes are holobionts as vast assemblages of participants of each of the three cellular domains (Prokaryota, Archaea, Eukaryota) and the virome, multicellular variation is necessarily a product of co-engineering among them.

White and Red Sorghum as Primary Carbohydrate Sources in Extruded Diets of Felines

The research objectives were to evaluate the effect of dietary supplementation of white (WSH) and red (RSH) sorghum grains on gastrointestinal health of felines through the determination of apparent total tract macronutrient digestibility (ATTD), fecal characteristics, fermentative end-products, and microbiota, compared with a traditional corn-based diet. We hypothesize that inclusion of RSH and WSH, respectively, would be well-accepted by cats, and the RSH and WSH diets would be comparable to corn when added as the main carbohydrate source in extruded diets. Three diets containing 30% corn, 30% WSH, or 30% RSH were formulated to meet or exceed the AAFCO (2018) nutrient profiles for cats during growth. Nine male cats (0.8 ± 0.00 yr) were randomly assigned to one of the three dietary treatments using a triplicated 3 × 3 Latin square design. Experimental periods consisted of 14 d (10 d of diet adaption and 4 d of total and fresh fecal collections). The ATTD of dry matter (DM) did not differ amongst treatments, organic matter was greatest (P < 0.05) for both sorghum diets (86.4%) and lowest for the corn diet (84.2%), crude protein was comparable among diets ranging from 84.5 to 86.6%, acid hydrolyzed fat was high among diets varying between 91.4 and 92.8%, and total dietary fiber was greatest (P < 0.05) for the WSH diet (56.0%) with the corn diet being lowest (44.7%). Digestible energy was greatest (P < 0.05) for the WSH diet (4.66 kcal/g) and lowest for the corn diet (4.54 kcal/g), with the RSH diet being intermediate (4.64; P > 0.05). Fecal pH (6.3–6.5) and most fecal metabolites did not differ among diets except for phenol/indole concentrations that were significantly lower (P < 0.05) in cats fed the RSH diet (1.5 μmole/g DM) than for cats fed the corn diet (2.1 μmole/g DM). Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria were the major phyla observed in the microbiota of feces of cats fed the three experimental diets, with no differences seen amongst all treatments. Data indicate that dietary supplementation of these varieties of WSH and RSH as carbohydrate sources were well-tolerated by the cat.

Understanding the role of gut microbiota in the pathogenesis of schizophrenia

Schizophrenia is a chronic mental disorder with marked symptoms of hallucination, delusion, and impaired cognitive behaviors. Although multidimensional factors have been associated with the development of schizophrenia, the principal cause of the disorder remains debatable. Microbiome involvement in the etiology of schizophrenia has been widely researched due to the advancement in sequencing technologies. This review describes the contribution of the gut microbiome in the development of schizophrenia that is facilitated by the gut-brain axis. The gut microbiota is connected to the gut-brain axis via several pathways and mechanisms, that are discussed in this review. The role of the oral microbiota, probiotics and prebiotics in shaping the gut microbiota are also highlighted. Lastly, future perspectives for microbiome research in schizophrenia are addressed.

The Fecal Bacterial Microbiota in Horses with Equine Recurrent Uveitis

The objective of this study was to describe and compare the fecal bacterial microbiota of horses with equine recurrent uveitis (ERU) and healthy horses using next-generation sequencing techniques. Fecal samples were collected from 15 client-owned horses previously diagnosed with ERU on complete ophthalmic examination. For each fecal sample obtained from a horse with ERU, a sample was collected from an environmentally matched healthy control with no evidence of ocular disease. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. The relative abundance of predominant taxa, and alpha and beta diversity indices were calculated and compared between groups. The phyla Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria predominated in both ERU and control horses, accounting for greater than 60% of sequences. Based on linear discriminant analysis effect size (LEfSe), no taxa were found to be enriched in either group. No significant differences were observed in alpha and beta diversity indices between groups (p > 0.05 for all tests). Equine recurrent uveitis is not associated with alteration of the gastrointestinal bacterial microbiota when compared with healthy controls.

Collection and storage of DNA-containing biomaterial and isolated DNA

The advances of biomedicine include the new technologies, diagnosis and treatment techniques, as well as the practical use of new types of biological targets, in particular, nucleic acids. Genomic deoxyribonucleic acid (DNA), extracellular DNA (exDNA) and microbiome DNA obtained from different types of samples (tissues, blood and its derivatives, feces, etc.) are used as objects of genetic research. The use of new technologies for DNA analysis required the development of standardized methods for processing biological samples in order to obtain high-quality DNA samples. The research uses various methods for collecting, preparing samples and storing various DNA-containing biomaterials and isolated DNA, as well as methods for assessing the quality of samples and biobank standards. It is obvious that the use of uniform standards will allow large-scale genetic research on the basis of biobanks and research laboratories. Specialists from professional organizations such as International Society for Biological and Environmental Repositories (ISBER), Biobanking and BioMolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC), European, Middle Eastern & African Society for Biopreservationa and Biobanking (ESBB) and the Russian National Association of Biobanks and Biobanking Professionals.

Past, Present, and Future of Gastrointestinal Microbiota Research in Cats

The relationship between microbial community and host has profound effects on the health of animals. A balanced gastrointestinal (GI) microbial population provides nutritional and metabolic benefits to its host, regulates the immune system and various signaling molecules, protects the intestine from pathogen invasion, and promotes a healthy intestinal structure and an optimal intestinal function. With the fast development of next-generation sequencing, molecular techniques have become standard tools for microbiota research, having been used to demonstrate the complex intestinal ecosystem. Similarly to other mammals, the vast majority of GI microbiota in cats (over 99%) is composed of the predominant bacterial phyla Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Many nutritional and clinical studies have shown that cats' microbiota can be affected by several different factors including body condition, age, diet, and inflammatory diseases. All these factors have different size effects, and some of these may be very minor, and it is currently unknown how important these are. Further research is needed to determine the functional variations in the microbiome in disease states and in response to environmental and/or dietary modulations. Additionally, further studies are also needed to explain the intricate relationship between GI microbiota and the genetics and immunity of its host. This review summarizes past and present knowledge of the feline GI microbiota and looks into the future possibilities and challenges of the field.

The Effects of Nutrition on the Gastrointestinal Microbiome of Cats and Dogs: Impact on Health and Disease

The gastrointestinal (GI) microbiome of cats and dogs is increasingly recognized as a metabolically active organ inextricably linked to pet health. Food serves as a substrate for the GI microbiome of cats and dogs and plays a significant role in defining the composition and metabolism of the GI microbiome. The microbiome, in turn, facilitates the host's nutrient digestion and the production of postbiotics, which are bacterially derived compounds that can influence pet health. Consequently, pet owners have a role in shaping the microbiome of cats and dogs through the food they choose to provide. Yet, a clear understanding of the impact these food choices have on the microbiome, and thus on the overall health of the pet, is lacking. Pet foods are formulated to contain the typical nutritional building blocks of carbohydrates, proteins, and fats, but increasingly include microbiome-targeted ingredients, such as prebiotics and probiotics. Each of these categories, as well as their relative proportions in food, can affect the composition and/or function of the microbiome. Accumulating evidence suggests that dietary components may impact not only GI disease, but also allergies, oral health, weight management, diabetes, and kidney disease through changes in the GI microbiome. Until recently, the focus of microbiome research was to characterize alterations in microbiome composition in disease states, while less research effort has been devoted to understanding how changes in nutrition can influence pet health by modifying the microbiome function. This review summarizes the impact of pet food nutritional components on the composition and function of the microbiome and examines evidence for the role of nutrition in impacting host health through the microbiome in a variety of disease states. Understanding how nutrition can modulate GI microbiome composition and function may reveal new avenues for enhancing the health and resilience of cats and dogs.

Potential role of the skin microbiota in Inflammatory skin diseases

BACKGROUND

Inflammatory skin diseases include a variety of skin diseases, such as seborrheic dermatitis, acne, atopic dermatitis, psoriasis and so on, which are more common and tend to have a significant impact on patients' quality of life. Inflammatory skin diseases often result in physical or psychological distress; however, the pathogenesis of these diseases have not been clearly elucidated. Many factors are involved in the pathogenesis of inflammatory skin diseases, including heredity, environment, immunity, epidermal barrier, mental disorders, infection and so on. In recent years, skin microbiota has been shown to play an important role in inflammatory skin diseases.

AIMS

To elaborate on the specific mechanisms of inflammatory skin diseases induced by microbiota dysbiosis.

METHODS

We introduce the function and influence of skin microbiota in inflammatory skin diseases from the following aspects: Immunity, epigenetics, epidermal barrier and treatment.

RESULTS

Skin microbiota can affect many aspects of the host, such as Immunity, epigenetics, epidermal barrier, and it plays an important role in the pathogenesis of inflammatory skin diseases.

CONCLUSION

Skin microbiota is extremely important for maintaining the health of skin and the dysbiosis of skin microbiota is an important pathogenesis of inflammatory skin diseases.

The Bacterial Microbiota of Gastrointestinal Cancers: Role in Cancer Pathogenesis and Therapeutic Perspectives

The microbiota has an essential role in the pathogenesis of many gastrointestinal diseases including cancer. This effect is mediated through different mechanisms such as damaging DNA, activation of oncogenic pathways, production of carcinogenic metabolites, stimulation of chronic inflammation, and inhibition of antitumor immunity. Recently, the concept of "pharmacomicrobiomics" has emerged as a new field concerned with exploring the interplay between drugs and microbes. Mounting evidence indicates that the microbiota and their metabolites have a major impact on the pharmacodynamics and therapeutic responses toward anticancer drugs including conventional chemotherapy and molecular-targeted therapeutics. In addition, microbiota appears as an attractive target for cancer prevention and treatment. In this review, we discuss the role of bacterial microbiota in the pathogenesis of different cancer types affecting the gastrointestinal tract system. We also scrutinize the evidence regarding the role of microbiota in anticancer drug responses. Further, we discuss the use of probiotics, fecal microbiota transplantation, and antibiotics, either alone or in combination with anticancer drugs for prevention and treatment of gastrointestinal tract cancers.

The Life Cycle of Corporate Social Responsibility in Agri-Food: Value Creation Models

This paper contributes to the theoretical debate in agri-food economics focusing on corporate social responsibility. Specifically, it aims to define an interpretative model of the processes of social responsibility and value creation in the food industry. An empirical investigation was conducted using an analysis of case studies—representative of sustainable innovation and social responsibility models—as well as in-depth interviews and focus groups with managers of food industries and the sector’s experts. The paper focuses on a topic that has yet to be analysed in agri-food economics literature: corporate social responsibility as a value-creating strategy. Further, it proposes a life cycle model of social responsibility in business processes. The study findings reveal that corporate social responsibility actions may affect the agri-food process and/or the product. Specifically, the investigated case studies reveal that the production sector in which a company operates strongly influences its orientation towards one or more corporate social responsibility dimensions. This study’s results contribute to the debate on the topic and provide useful insights for practitioners and policy-makers.

Evaluation of the effects of anthelmintic administration on the fecal microbiome of healthy dogs with and without subclinical Giardia spp. and Cryptosporidium canis infections

BACKGROUND

The gastrointestinal microbiome plays an important role in host health and there is increasing concern regarding the deleterious effects of pharmaceuticals on the fecal microbiome. The effect of anthelmintic therapy on the fecal microbiome in dogs has not yet been evaluated. The purpose of this study was to evaluate the effect of anthelmintic administration on the fecal microbiome of dogs with and without subclinical Giardia species and Cryptosporidium canis infections.

METHODOLOGY/PRINCIPAL FINDINGS

Part 1: 6 healthy adult research beagles with subclinical giardiasis and cryptosporidiosis were administered a commercially available preparation of febantel combined with pyrantel and praziquantel (FPP) orally daily for three days. Part 2: 19 healthy staff-owned dogs without giardiasis or cryptosporidiosis were divided into a treatment group (n = 9) that was administered fenbendazole orally daily for five days and an untreated control group (n = 10). For both parts of the study, feces were collected at multiple time points before and after anthelmintic (FPP or fenbendazole) administration. Fecal DNA was extracted for Illumina sequencing of the bacterial 16S rRNA gene and qPCR assays. Neither FPP nor fenbendazole treatment caused a significant change in alpha or beta diversity or the relative abundance of bacterial species. Upon univariate statistical analysis neither FPP or fenbendazole caused minimal changes in the fecal microbiota.

CONCLUSION

FPP administration was associated with minimal alterations of the fecal microbiome of healthy research beagles with subclinical giardiasis and cryptosporidiosis. Fenbendazole administration was associated with minimal alterations of the fecal microbiome of healthy staff owned dogs.

Proposed grading scheme for inflammatory bowel disease in ferrets and correlation with clinical signs

Inflammatory bowel disease (IBD) is an idiopathic, chronic, inflammatory disease of the gastrointestinal tract of companion animals, including ferrets (Mustela putorius furo). Clinical signs of IBD are nonspecific, and intestinal biopsies are necessary for a definitive diagnosis. A grading scheme has not been established for ferrets. Additionally, the association between histologic severity and clinical signs in ferrets is unknown. We evaluated enteric samples from ferrets diagnosed with IBD, compared histologic grading schemes, and correlated the results with the severity of clinical signs. Enteric sections from 23 ferrets with IBD were analyzed using grading schemes for intestinal inflammation in cats and dogs, and a correlation with clinical signs was evaluated. After dividing the histologic samples into groups based on the severity of clinical signs, main histologic differences were identified. Age and sex were also assessed for correlation with clinical signs. No significant correlation was found between the 2 grading schemes and clinical signs (rho = 0.02, p = 0.89; rho = 0.26, p = 0.18, respectively). Degree of villus fusion, hemorrhage and/or fibrin, epithelial damage, inflammation density, and crypt abscess formation were used retrospectively to create a ferret IBD grading scheme, which was significantly correlated with the severity of clinical signs (rho = 0.48, p = 0.01). A positive correlation was observed between age (p = 0.04) and females (p = 0.007) with severity of clinical signs. Our ferret grading scheme may have clinical utility in providing a more objective, consistent evaluation of IBD in ferrets.

Potential Applications of Non-thermal Plasma in Animal Husbandry to Improve Infrastructure

Infrastructure in animal husbandry refers to fundamental facilities and services necessary for better living conditions of animals and its economy to function through better productivity. Mainly, infrastructure can be divided into two categories: hard infrastructure and soft infrastructure. Physical infrastructure, such as buildings, roads, and water supplying systems, belongs to hard infrastructure. Soft infrastructure includes services which are required to maintain economic, health, cultural and social standards of animal husbandry. Therefore, the proper management of infrastructure in animal husbandry is necessary for animal welfare and its economy. Among various technologies to improve the quality of infrastructure, non-thermal plasma (NTP) technology is an effectively applicable technology in different stages of animal husbandry. NTP is mainly helpful in maintaining better health conditions of animals in several ways via decontamination from microorganisms present in air, water, food, instruments and surfaces of animal farming systems. Furthermore, NTP is used in the treatment of waste water, vaccine production, wound healing in animals, odor-free ventilation, and packaging of animal food or animal products. This review summarizes the recent studies of NTP which can be related to the infrastructure in animal husbandry.

Reappraising the exteriorization of the mammalian testes through evolutionary physiology

A number of theories have been proposed to explain the exteriorization of the testicles in most mammalian species. None of these provide a consistent account for the wide variety of testicular locations found across the animal kingdom. It is proposed that testicular location is the result of coordinate action of testicular tissue ecologies to sustain preferential states of homeostatic equipoise throughout evolutionary development in response to the advent of endothermy.

Compounds from Olea europaea and Pistacia lentiscus inhibit oral microbial growth

BACKGROUND

In view of the increasing antibiotic resistance, the introduction of natural anti-infective agents has brought a new era in the treatment of bacterially derived oral diseases.

METHODS

The aim of this study was to investigate the antimicrobial potential of five natural constituents of Olea europaea (oleuropein, maslinic acid, hydroxytyrosol, oleocanthal, oleacein) and three compounds of Pistacia lentiscus (24Z-isomasticadienolic acid, oleanolic acid, oleanonic aldehyde) against ten representative oral bacterial species and a Candida albicans strain. After the isolation and quality control of natural compounds, the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) assay were performed.

RESULTS

Among all O. europaea-derived constituents, maslinic acid was the most active (MIC = 4.9-312 μg mL^- 1, MBC = 9.8-25 μg mL^- 1) one against oral streptococci and anaerobic pathogenic bacteria (Porphyromonas gingivalis, Fusobacterium nucleatum, Parvimonas micra), while oleuropein, hydroxytyrosol, oleocanthal and oleacein showed milder, yet significant effects against P. gingivalis and F. nucleatum. Among all P. lentiscus compounds, oleanolic acid was the most effective one against almost all microorganisms with MIC values ranging from 9.8 μg mL^- 1 (P. gingivalis) to 625 μg mL^- 1 (F. nucleatum, P. micra). In the presence of 24Z-isomasticadienolic acid, a mean inhibitory concentration range of 2.4 μg mL^- 1 to 625 μg mL^- 1 was observed for strict anaerobia. The MIC value for 24Z-isomasticadienolic acid was estimated between 39 μg mL^- 1 (Streptococcus sobrinus, Streptococcus oralis) and 78 μg mL^- 1 (Streptococcus mutans). All tested compounds showed no effects against Prevotella intermedia.

CONCLUSIONS

Overall, maslinic acid and oleanolic acid exerted the most significant inhibitory activity against the tested oral pathogens, especially streptococci and anaerobic oral microorganisms.

Effects of Intraoperative Vagal Nerve Stimulation on the Gastrointestinal Microbiome in a Mouse Model of Amyotrophic Lateral Sclerosis

The gastrointestinal microbiota (GM) plays a fundamental role in health and disease and contributes to the bidirectional signaling between the gastrointestinal system and brain. The direct line of communication between these organ systems is through the vagus nerve. Therefore, vagal nerve stimulation (VNS), a commonly used technique for multiple disorders, has potential to modulate the enteric microbiota, enabling investigation and possibly treatment of numerous neurologic disorders in which the microbiota has been linked with disease. Here we investigate the effect of VNS in a mouse model of amyotrophic lateral sclerosis (ALS). B6SJL-Tg(SOD1*G93A)^dl1Gur (SOD1^dl) and wildtype mice underwent ventral neck surgery to access the vagus nerve. During surgery, the experimental group received 1 h of VNS, whereas the sham group underwent 1 h of sham treatment. The third (control) group did not undergo any surgical manipulation. Fecal samples were collected before surgery and at 8 d after the initial collection. Microbial DNA was sequenced to determine the GM profiles at both time points. GM profiles did not differ between genotypes at either the initial or end point. In addition, VNS did not alter GM populations, according to the parameters chosen in this study, indicating that this short intraoperative treatment is safe and has no lasting effects on the GM. Future studies are warranted to determine whether different stimulation parameters or chronic use of VNS affect GM profiles.

Novel association of Psychrobacter and Pseudomonas with malodour in bloodhound dogs, and the effects of a topical product composed of essential oils and plant-derived essential fatty acids in a randomized, blinded, placebo-controlled study

BACKGROUND

The pathogenesis and treatment of cutaneous malodour in dogs have not been investigated previously. Staphylococcus and Corynebacterium spp. are associated with human axillary malodour.

HYPOTHESIS

Staphylococcus and Corynebacterium spp. are associated with cutaneous malodour in dogs, and treatment with a topical essential oil-based product will improve malodour and reduce the abundance of odour-causing bacteria.

ANIMALS

Twenty seven bloodhound dogs from a south Texas boarding facility were enrolled in this study.

METHODS AND MATERIALS

Skin swabs were taken from the axilla and dorsum of 27 dogs at initiation of the study. Mean malodour scores were used to assign dogs to control or malodour groups. The malodourous dogs were randomly assigned to a treatment or placebo group, received four weekly topical applications of the spot-on or placebo, and samples were recollected. Next-generation sequencing (NGS) and real-time quantitative PCR (qPCR) were performed on all swabs.

RESULTS

Psychrobacter and Pseudomonas spp. were significantly more abundant (P < 0.001, P = 0.006; respectively), and overall bacterial diversity was reduced (P = 0.0384) on the skin of malodourous dogs. Staphylococcus and Corynebacterium spp. were not associated with malodour. The topical essential oil-based product significantly (P = 0.0078) improved malodour in the treatment group and shifted their bacterial community structure.

CONCLUSIONS AND CLINICAL IMPORTANCE

A novel association of bacterial genera with malodour in bloodhound dogs, identified by NGS, highlights future targets for odour control. The topical treatment significantly reduced malodour. The interaction between the topical treatment and cutaneous microbiota should be further investigated and may be useful in other dermatological conditions involving microbiota.