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Gut Microbiome of Farm Animals in Health and Disease

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Veterinary Microbiology".

Deadline for manuscript submissions: closed (31 May 2022) | Viewed by 56892

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Dr. Łukasz M. Grześkowiak

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Institute of Animal Nutrition, Freie Universität Berlin, 14195 Berlin, Germany
Interests: microbial ecology; microbiota-host cross-talk; health
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear colleagues,

The role of the gut microbiome in maintaining health in farm animals has been gaining increasing interest. Specifically, gut microbe–host crosstalk has been associated with animal physiology, metabolism and immunity. Early-life microbial succession in newborn offspring is essential for gut maturation and immune development and may play a significant role in animal resilience to pathogens later in life. In addition, some evidence suggests that the maternal microenvironment could play a significant role in early microbial and immune development in young animals. In intensive production systems, animals face significant stress and become more vulnerable to gut dysbiosis and illnesses. Nutrition is a strong modulating factor gut microbial ecosystems in animals. Supplying animals with certain dietary components shows promise for modulating the microbiota and their impact on the host by controlling pathogen colonisation and dissemination, and reducing the risk of diseases. Finally, uncovering the mechanisms by which the microbiome and host interact with each other is crucial for the understanding of homeostasis, to prevent or treat gut dysbiosis and illnesses.

This Special Issue aims to publish recent findings on various aspects of the gut microbiota and its ecological interactions with the animal host through cellular, metabolic, genetic and environmental pathways. Research articles, review articles and short communications on the gut microbiome in farm animals are welcome. We look forward to publishing your work.

Dr. Łukasz M. Grześkowiak
Guest Editor

Manuscript Submission Information

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Keywords

farm animal
microbiome
microbiota
intestine
physiology
infection
diarrhoea
probiotics
antimicrobials

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Published Papers (11 papers)

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Research

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20 pages, 3632 KiB

Open AccessArticle

The Microbiota–Gut–Brain Axis: Gut Microbiota Modulates Conspecific Aggression in Diversely Selected Laying Hens

by Jiaying Hu, Timothy A. Johnson, Huanmin Zhang and Heng-Wei Cheng

Microorganisms 2022, 10(6), 1081; https://doi.org/10.3390/microorganisms10061081 - 24 May 2022

Cited by 14 | Viewed by 3703

Abstract

The gut microbiota plays an important role in regulating brain function, influencing psychological and emotional stability. The correlations between conspecific aggression, gut microbiota, and physiological homeostasis were further studied in inbred laying chicken lines, 6₃ and 7₂, which were diversely selected for Marek’s disease, and they also behave differently in aggression. Ten sixty-week-old hens from each line were sampled for blood, brain, and cecal content. Neurotransmitters, cytokines, corticosterone, and heterophil/lymphocyte ratios were determined. Cecal microbiota compositions were determined by bacterial 16s rRNA sequencing, and functional predictions were performed. Our data showed that the central serotonin and tryptophan levels were higher in line 6₃ compared to line 7₂ (p < 0.05). Plasma corticosterone, heterophil/lymphocyte ratios, and central norepinephrine were lower in line 6₃ (p < 0.05). The level of tumor necrosis factor α tended to be higher in line 6₃. Faecalibacterium, Oscillibacter, Butyricicoccus, and Bacteriodes were enriched in line 6₃ birds, while Clostridiales vadin BB60, Alistipes, Mollicutes RF39 were dominated in line 7₂. From the predicted bacterial functional genes, the kynurenine pathway was upregulated in line 7₂. These results suggested a functional linkage of the line differences in serotonergic activity, stress response, innate immunity, and gut microbiota populations. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease)

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15 pages, 1379 KiB

Open AccessArticle

The Impact of Pre- and Probiotic Product Combinations on Ex vivo Growth of Avian Pathogenic Escherichia coli and Salmonella Enteritidis

by Laura Fuhrmann, Wilfried Vahjen, Jürgen Zentek, Ronald Günther and Eva-Maria Saliu

Microorganisms 2022, 10(1), 121; https://doi.org/10.3390/microorganisms10010121 - 7 Jan 2022

Cited by 7 | Viewed by 2965

Abstract

Due to the global spread of antibiotic resistance, there is a strong demand to replace antimicrobial growth promotors in livestock. To identify suitable additives that inhibit the growth of avian pathogenic Escherichia coli O1/O18 and Salmonella enterica serotype Enteritidis strains, an ex vivo screening was performed. Inulin and fructooligosaccharides (FOS) were investigated as prebiotics. Enterococcus faecium and Bacillus coagulans served as probiotic strains. Firstly, the pathogen was anaerobically incubated in caecal digesta from different broiler breeder flocks with the addition of feed additives. Secondly, subsamples of these suspensions were incubated in an antibiotic medium for selective growth of the pathogen. During this step, turbidity was recorded, and lag times were calculated for each pathogen as readout of growth inhibition. Combinations of E. faecium with inulin or FOS significantly extended the lag time for E. coli compared to control. Moreover, older age was a significant factor to enhance this inhibitory effect. In contrast, the combination of FOS and B. coagulans showed shorter lag times for S. Enteritidis. Our results indicate that the E. faecium strain with prebiotics may inhibit the pathogen proliferation in the studied poultry flocks. Furthermore, our results suggest that prophylactic treatments should be assigned by feed additive, age and animal origin. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease)

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10 pages, 1341 KiB

Open AccessCommunication

The Impact of Pre-Slaughter Fasting on the Ruminal Microbial Population of Commercial Angus Steers

by Christina Breanne Welch, Jeferson M. Lourenco, Darren S. Seidel, Taylor Rae Krause, Michael J. Rothrock, T. Dean Pringle and Todd R. Callaway

Microorganisms 2021, 9(12), 2625; https://doi.org/10.3390/microorganisms9122625 - 19 Dec 2021

Cited by 8 | Viewed by 3092

Abstract

Diet impacts the composition of the ruminal microbiota; however, prior to slaughter, cattle are fasted, which may change the ruminal microbial ecosystem structure and lead to dysbiosis. The objective of this study was to determine changes occurring in the rumen after pre-slaughter fasting, which can allow harmful pathogens an opportunity to establish in the rumen. Ruminal samples were collected before and after pre-slaughter fasting from seventeen commercial Angus steers. DNA extraction and 16S rRNA gene sequencing were performed to determine the ruminal microbiota, as well as volatile fatty acid (VFA) concentrations. Microbial richness (Chao 1 index), evenness, and Shannon diversity index all increased after fasting (p ≤ 0.040). During fasting, the two predominant families Prevotellaceae and Ruminococcaceae decreased (p ≤ 0.029), whereas the remaining minor families increased (p < 0.001). Fasting increased Blautia and Methanosphaera (p ≤ 0.003), while Campylobacter and Treponema tended to increase (p ≤ 0.086). Butyrate concentration tended to decrease (p = 0.068) after fasting. The present findings support that fasting causes ruminal nutrient depletion resulting in dysbiosis, allowing opportunistic pathogens to exploit the void in the ruminal ecological niche. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease)

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14 pages, 2205 KiB

Open AccessCommunication

Insights into the Oral Bacterial Microbiota of Sows

by Jasmine Hattab, Giuseppe Marruchella, Alberto Pallavicini, Fabrizia Gionechetti, Francesco Mosca, Abigail Rose Trachtman, Laura Lanci, Luigino Gabrielli and Pietro Giorgio Tiscar

Microorganisms 2021, 9(11), 2314; https://doi.org/10.3390/microorganisms9112314 - 9 Nov 2021

Cited by 3 | Viewed by 2330

Abstract

The investigation of bacterial microbiota represents a developing research field in veterinary medicine intended to look for correlations between animal health and the balance within bacterial populations. The aim of the present work was to define the bacterial microbiota of the oral cavity of healthy sows, which had not been thoroughly described so far. In total, 22 samples of oral fluid were collected and analyzed by 16S-rRNA gene sequencing. CLC Genomics Workbench 20.0 (QIAGEN Digital Insights, Aarhus, Denmark) was then used to examine the results. The predominant orders were Lactobacillales, Clostridiales, and Corynebacteriales. Lactobacillaceae, Corynebacteriaceae, Moraxellaceae, Aerococcaceae, and Staphylococcaceae were the most represented families. As regards the most abundant genera, Lactobacillus, Corynebacterium, Acinetobacter, Staphylococcus, Rothia, Aerococcus, and Clostridium can be pointed out as the bacterial core microbiota. Sows were also divided into “gestating” and “lactating” groups, and mild differences were found between pregnant and lactating sows. The data herein described represent an original contribution to the knowledge of the porcine bacterial microbiota. Moreover, the choice of sows as experimental animals was strategic for identifying the adult microbial community. These data provide a basis for further studies on the oral bacterial microbiota of pigs. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease)

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18 pages, 3690 KiB

Open AccessArticle

Characterizing the Cattle Gut Microbiome in Farms with a High and Low Prevalence of Shiga Toxin Producing Escherichia coli

by Karla Vasco, Brian Nohomovich, Pallavi Singh, Cristina Venegas-Vargas, Rebekah E. Mosci, Steven Rust, Paul Bartlett, Bo Norby, Daniel Grooms, Lixin Zhang and Shannon D. Manning

Microorganisms 2021, 9(8), 1737; https://doi.org/10.3390/microorganisms9081737 - 14 Aug 2021

Cited by 13 | Viewed by 4357

Abstract

Cattle are the main reservoirs of Shiga toxin producing Escherichia coli (STEC), a major foodborne pathogen associated with acute enteric disease and hemolytic–uremic syndrome in humans. A total of 397 beef and dairy cattle from 5 farms were included in this study, of which 660 samples were collected for 16S rRNA gene sequencing. The microbiota of farms with a high-STEC prevalence (HSP) had greater richness compared to those of farms with a low-STEC prevalence (LSP). Longitudinal analyses showed STEC-shedders from LSP farms had higher microbiome diversity; meanwhile, changes in the microbiome composition in HSP farms were independent of the STEC shedding status. Most of the bacterial genera associated with STEC shedding in dairy farms were also correlated with differences in the percentage of forage in diet and risk factors of STEC carriage such as days in milk, number of lactations, and warm temperatures. Identifying factors that alter the gut microbiota and enable STEC colonization in livestock could lead to novel strategies to prevent fecal shedding and the subsequent transmission to humans. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease)

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26 pages, 4050 KiB

Open AccessArticle

Effect of Methionine Supplementation on Rumen Microbiota, Fermentation, and Amino Acid Metabolism in In Vitro Cultures Containing Nitrate

by Faiz-ul Hassan, Yanxia Guo, Mengwei Li, Zhenhua Tang, Lijuan Peng, Xin Liang and Chengjian Yang

Microorganisms 2021, 9(8), 1717; https://doi.org/10.3390/microorganisms9081717 - 12 Aug 2021

Cited by 19 | Viewed by 3849

Abstract

This study evaluated the effect of methionine on in vitro methane (CH₄) production, rumen fermentation, amino acid (AA) metabolism, and rumen microbiota in a low protein diet. We evaluated three levels of methionine (M0, 0%; M1, 0.28%; and M2, 1.12%) of in the presence of sodium nitrate (1%) in a diet containing elephant grass (90%) and concentrate (10%). We used an in vitro batch culture technique by using rumen fluid from cannulated buffaloes. Total gas and CH₄ production were measured in each fermentation bottle at 3, 6, 9, 12, 24, 48, 72 h of incubation. Results revealed that M0 decreased (p < 0.001) the total gas and CH₄ production, but methionine exhibited no effect on these parameters. M0 decreased (p < 0.05) the individual and total volatile fatty acids (VFAs), while increasing (p < 0.05) the ruminal pH, acetate to propionate ratio, and microbial protein content. Methionine did not affect ruminal AA contents except asparagine, which substantially increased (p = 0.003). M2 increased the protozoa counts, but both M0 and M1 decreased (p < 0.05) the relative abundance of Firmicutes while increasing (p < 0.05) the Campilobacterota and Proteobacteria. However, Prevotella and γ-Proteobacteria were identified as biomarkers in the nitrate group. Our findings indicate that methionine can increase ruminal asparagine content and the population of Compylobactor. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease)

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15 pages, 2123 KiB

Open AccessArticle

Evolution of Pig Fecal Microbiota Composition and Diversity in Response to Enterotoxigenic Escherichia coli Infection and Colistin Treatment in Weaned Piglets

by Mohamed Rhouma, Charlotte Braley, William Thériault, Alexandre Thibodeau, Sylvain Quessy and Philippe Fravalo

Microorganisms 2021, 9(7), 1459; https://doi.org/10.3390/microorganisms9071459 - 7 Jul 2021

Cited by 16 | Viewed by 4048

Abstract

The intestinal microbiota plays several important roles in pig health and growth. The aim of the current study was to characterize the changes in the fecal microbiota diversity and composition of weaned piglets following an oral challenge with an ETEC: F4 strain and/or a treatment with colistin sulfate (CS). Twenty-eight piglets were used in this experiment and were divided into four groups: challenged untreated, challenged treated, unchallenged treated, and unchallenged untreated. Rectal swab samples were collected at five sampling times throughout the study. Total genomic DNA was used to assess the fecal microbiota diversity and composition using the V4 region of the 16S rRNA gene. The relative abundance, the composition, and the community structure of piglet fecal microbiota was highly affected by the ETEC: F4 challenge throughout the experiment, while the oral treatment with CS, a narrow spectrum antibiotic, resulted in a significant decrease of E. coli/Shigella populations during the treatment period only. This study was the first to identify some gut microbiota subgroups (e.g., Streptococcus, Lachnospiraceae) that are associated with healthy piglets as compared to ETEC: F4 challenged animals. These key findings might contribute to the development of alternative strategies to reduce the use of antimicrobials in the control of post-weaning diarrhea in pigs. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease)

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24 pages, 7688 KiB

Open AccessArticle

Taxonomic and Functional Characteristics of the Gill and Gastrointestinal Microbiota and Its Correlation with Intestinal Metabolites in NEW GIFT Strain of Farmed Adult Nile Tilapia (Oreochromis niloticus)

by Zhenbing Wu, Qianqian Zhang, Yaoyao Lin, Jingwen Hao, Shuyi Wang, Jingyong Zhang and Aihua Li

Microorganisms 2021, 9(3), 617; https://doi.org/10.3390/microorganisms9030617 - 17 Mar 2021

Cited by 38 | Viewed by 3934

Abstract

The gill and gastrointestinal tract are primary entry routes for pathogens. The symbiotic microbiota are essential to the health, nutrition and disease of fish. Though the intestinal microbiota of Nile tilapia (Oreochromis niloticus) has been extensively studied, information on the mucosa-associated microbiota of this species, especially the gill and gastrointestinal mucosa-associated microbiota, is lacking. This study aimed to characterize the gill and gastrointestinal mucosa- and digesta-associated microbiota, as well as the intestinal metabolite profiles in the New Genetically Improved Farmed Tilapia (NEW GIFT) strain of farmed adult Nile tilapia by high-throughput sequencing and gas chromatography/mass spectrometry metabolomics. The diversity, structure, composition, and predicted function of gastrointestinal microbiota were significantly different across gastrointestinal regions and sample types (Welch t-test; p < 0.05). By comparing the mucosa- and digesta-associated microbiota, linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that Pelomonas, Ralstoniapickettii, Comamonadaceae, and Staphylococcus were significantly enriched in the mucosa-associated microbiota, whereas many bacterial taxa were significantly enriched in the digesta-associated microbiota, including Chitinophagaceae, Cetobacterium, CandidatusCompetibacter, Methyloparacoccus, and chloroplast (LDA score > 3.5). Furthermore, Undibacterium, Escherichia-Shigella, Paeniclostridium, and Cetobacterium were dominant in the intestinal contents and mucosae, whereas Sphingomonasaquatilis and Roseomonasgilardii were commonly found in the gill and stomach mucosae. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) analysis revealed that the predictive function of digesta-associated microbiota significantly differed from that of mucosa-associated microbiota (R = 0.8152, p = 0.0001). In addition, our results showed a significant interdependence between specific intestinal microbes and metabolites. Notably, the relative abundance values of several potentially beneficial microbes, including Undibacterium, Crenothrix, and Cetobacterium, were positively correlated with most intestinal metabolites, whereas the relative abundance values of some potential opportunistic pathogens, including Acinetobacter, Mycobacterium, Escherichia-Shigella, Paeniclostridium, Aeromonas, and Clostridiumsensustricto 1, were negatively correlated with most intestinal metabolites. This study revealed the characteristics of gill and gastrointestinal mucosa-associated and digesta-associated microbiota of farmed Nile tilapia and identified a close correlation between intestinal microbes and metabolites. The results serve as a basis for the effective application of targeted probiotics or prebiotics in the diet to regulate the nutrition and health of farmed tilapia. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease)

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Review

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19 pages, 697 KiB

Open AccessReview

Influence of the Gut Microbiome on Feed Intake of Farm Animals

by Anna Grete Wessels

Microorganisms 2022, 10(7), 1305; https://doi.org/10.3390/microorganisms10071305 - 27 Jun 2022

Cited by 13 | Viewed by 3941

Abstract

With the advancement of microbiome research, the requirement to consider the intestinal microbiome as the “last organ” of an animal emerged. Through the production of metabolites and/or the stimulation of the host’s hormone and neurotransmitter synthesis, the gut microbiota can potentially affect the host’s eating behavior both long and short-term. Based on current evidence, the major mediators appear to be short-chain fatty acids (SCFA), peptide hormones such as peptide YY (PYY) and glucagon-like peptide-1 (GLP-1), as well as the amino acid tryptophan with the associated neurotransmitter serotonin, dopamine and γ-Aminobutyrate (GABA). The influence appears to extend into central neuronal networks and the expression of taste receptors. An interconnection of metabolic processes with mechanisms of taste sensation suggests that the gut microbiota may even influence the sensations of their host. This review provides a summary of the current status of microbiome research in farm animals with respect to general appetite regulation and microbiota-related observations made on the influence on feed intake. This is briefly contrasted with the existing findings from research with rodent models in order to identify future research needs. Increasing our understanding of appetite regulation could improve the management of feed intake, feed frustration and anorexia related to unhealthy conditions in farm animals. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease)

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21 pages, 386 KiB

Open AccessReview

Porcine and Chicken Intestinal Epithelial Cell Models for Screening Phytogenic Feed Additives—Chances and Limitations in Use as Alternatives to Feeding Trials

by Hannah Marks, Łukasz Grześkowiak, Beatriz Martinez-Vallespin, Heiko Dietz and Jürgen Zentek

Microorganisms 2022, 10(3), 629; https://doi.org/10.3390/microorganisms10030629 - 16 Mar 2022

Cited by 9 | Viewed by 3961

Abstract

Numerous bioactive plant additives have shown various positive effects in pigs and chickens. The demand for feed additives of natural origin has increased rapidly in recent years to support the health of farm animals and thus minimize the need for antibiotics and other drugs. Although only in vivo experiments can fully represent their effect on the organism, the establishment of reliable in vitro methods is becoming increasingly important in the goal of reducing the use of animals in experiments. The use of cell models requires strict control of the experimental conditions so that reliability and reproducibility can be achieved. In particular, the intestinal porcine epithelial cell line IPEC-J2 represents a promising model for the development of new additives. It offers the possibility to investigate antioxidative, antimicrobial, anti- or pro-proliferative and antiviral effects. However, the use of IPEC-J2 is limited due to its purely epithelial origin and some differences in its morphology and functionality compared to the in vivo situation. With regard to chickens, the development of a reliable intestinal epithelial cell model has attracted the attention of researchers in recent years. Although a promising model was presented lately, further studies are needed to enable the standardized use of a chicken cell line for testing phytogenic feed additives. Finally, co-cultivation of the currently available cell lines with other cell lines and the development of organoids will open up further application possibilities. Special emphasis was given to the IPEC-J2 cell model. Therefore, all publications that investigated plant derived compounds in this cell line were considered. The section on chicken cell lines is based on publications describing the development of chicken intestinal epithelial cell models. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease)

34 pages, 4306 KiB

Open AccessReview

Probiotics, Prebiotics, and Phytogenic Substances for Optimizing Gut Health in Poultry

by Awad A. Shehata, Sakine Yalçın, Juan D. Latorre, Shereen Basiouni, Youssef A. Attia, Amr Abd El-Wahab, Christian Visscher, Hesham R. El-Seedi, Claudia Huber, Hafez M. Hafez, Wolfgang Eisenreich and Guillermo Tellez-Isaias

Microorganisms 2022, 10(2), 395; https://doi.org/10.3390/microorganisms10020395 - 8 Feb 2022

Cited by 107 | Viewed by 17341

Abstract

The gut microbiota has been designated as a hidden metabolic ‘organ’ because of its enormous impact on host metabolism, physiology, nutrition, and immune function. The connection between the intestinal microbiota and their respective host animals is dynamic and, in general, mutually beneficial. This complicated interaction is seen as a determinant of health and disease; thus, intestinal dysbiosis is linked with several metabolic diseases. Therefore, tractable strategies targeting the regulation of intestinal microbiota can control several diseases that are closely related to inflammatory and metabolic disorders. As a result, animal health and performance are improved. One of these strategies is related to dietary supplementation with prebiotics, probiotics, and phytogenic substances. These supplements exert their effects indirectly through manipulation of gut microbiota quality and improvement in intestinal epithelial barrier. Several phytogenic substances, such as berberine, resveratrol, curcumin, carvacrol, thymol, isoflavones and hydrolyzed fibers, have been identified as potential supplements that may also act as welcome means to reduce the usage of antibiotics in feedstock, including poultry farming, through manipulation of the gut microbiome. In addition, these compounds may improve the integrity of tight junctions by controlling tight junction-related proteins and inflammatory signaling pathways in the host animals. In this review, we discuss the role of probiotics, prebiotics, and phytogenic substances in optimizing gut function in poultry. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease)

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