Gut Microbiome of Farm Animals in Health and Disease 2.0

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

Deadline for manuscript submissions: closed (15 December 2023) | Viewed by 23104

Special Issue Editors


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Institute of Animal Nutrition, Freie Universität Berlin, 14195 Berlin, Germany
Interests: microbial ecology; microbiota-host cross-talk; health
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Department of Biology, School of Sciences and Technology and MED-Mediterranean Institute for Agriculture, Environment and Development, University of Évora, Évora, Portugal
Interests: medical microbiology; infectious diseases
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
Dr. Elsa Leclerc Duarte
Guest Editors

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Published Papers (14 papers)

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11 pages, 1125 KiB  
Article
Effects of Resistant Starch Infusion, Solely and Mixed with Xylan or Cellulose, on Gut Microbiota Composition in Ileum-Cannulated Pigs
by Yaowen Zhang, Yu Bai, Zhenyu Wang, Hao Ye, Dandan Han, Jinbiao Zhao, Junjun Wang and Defa Li
Microorganisms 2024, 12(2), 356; https://doi.org/10.3390/microorganisms12020356 - 9 Feb 2024
Viewed by 835
Abstract
Fermentation of dietary fiber (DF) is beneficial for gut health, but its prebiotic effects are often impeded in the distal large intestine because of the fast degradation of fermentable substrates. One way to enhance the prebiotic effect of DF is to deliver fibers [...] Read more.
Fermentation of dietary fiber (DF) is beneficial for gut health, but its prebiotic effects are often impeded in the distal large intestine because of the fast degradation of fermentable substrates. One way to enhance the prebiotic effect of DF is to deliver fibers to the lower parts of the gut, which can be achieved by mixing different kinds of fiber. Therefore, in the present study, an ileum-cannulated pig model was employed to investigate the fermentation influence in the large intestine by infusing resistant starch solely (RS, fast fermentable fiber) and mixing with other fibers (xylan or cellulose). Twenty-four ileum-cannulated growing pigs were divided into four groups: one control group receiving saline ileal infusions and three experimental groups infused with RS, RS with xylan, or RS with cellulose. Fecal and plasma samples were analyzed for gut microbiota composition, short-chain fatty acids (SCFAs), and blood biochemistry. Results indicated no significant differences between the RS and control group for the microbiome and SCFA concentration (p > 0.05). However, RS combined with fibers, particularly xylan, resulted in enhanced and prolonged fermentation, marked by an increase in Blautia and higher lactate and acetate production (p < 0.05). In contrast, RS with cellulose infusion enriched bacterial diversity in feces (p < 0.05). Blood biochemistry parameters showed no significant differences across groups (p > 0.05), though a trend of increased glucose levels was noted in the treatment groups (p < 0.1). Overall, RS alone had a limited impact on the distal hindgut microbiota due to rapid fermentation in the proximal gut, whereas combining RS with other fibers notably improved gut microecology by extending the fermentation process. Full article
(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)
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13 pages, 1137 KiB  
Article
Assessment of Potential Anti-Methanogenic and Antimicrobial Activity of Ethyl Nitroacetate, α-Lipoic Acid, Taurine and L-Cysteinesulfinic Acid In Vitro
by Gizem Levent, Aleksandar Božić, Branko T. Petrujkić, Todd R. Callaway, Toni L. Poole, Tawni L. Crippen, Roger B. Harvey, Pedro Ochoa-García, Agustin Corral-Luna, Kathleen M. Yeater and Robin C. Anderson
Microorganisms 2024, 12(1), 34; https://doi.org/10.3390/microorganisms12010034 - 23 Dec 2023
Viewed by 909
Abstract
Livestock producers need new technologies to maintain the optimal health and well-being of their animals while minimizing the risks of propagating and disseminating pathogenic and antimicrobial-resistant bacteria to humans or other animals. Where possible, these interventions should contribute to the efficiency and profitability [...] Read more.
Livestock producers need new technologies to maintain the optimal health and well-being of their animals while minimizing the risks of propagating and disseminating pathogenic and antimicrobial-resistant bacteria to humans or other animals. Where possible, these interventions should contribute to the efficiency and profitability of animal production to avoid passing costs on to consumers. In this study, we examined the potential of nitroethane, 3-nitro-1-propionate, ethyl nitroacetate, taurine and L-cysteinesulfinic acid to modulate rumen methane production, a digestive inefficiency that results in the loss of up to 12% of the host’s dietary energy intake and a major contributor of methane as a greenhouse gas to the atmosphere. The potential for these compounds to inhibit the foodborne pathogens, Escherichia coli O157:H7 and Salmonella Typhimurium DT104, was also tested. The results from the present study revealed that anaerobically grown O157:H7 and DT104 treated with the methanogenic inhibitor, ethyl nitroacetate, at concentrations of 3 and 9 mM had decreased (p < 0.05) mean specific growth rates of O157:H7 (by 22 to 36%) and of DT104 (by 16 to 26%) when compared to controls (0.823 and 0.886 h−1, respectively). The growth rates of O157:H7 and DT104 were decreased (p < 0.05) from controls by 31 to 73% and by 41 to 78% by α-lipoic acid, which we also found to inhibit in vitro rumen methanogenesis up to 66% (p < 0.05). Ethyl nitroacetate was mainly bacteriostatic, whereas 9 mM α-lipoic acid decreased (p < 0.05) maximal optical densities (measured at 600 nm) of O157:H7 and DT104 by 25 and 42% compared to controls (0.448 and 0.451, respectively). In the present study, the other oxidized nitro and organosulfur compounds were neither antimicrobial nor anti-methanogenic. Full article
(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)
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14 pages, 2134 KiB  
Article
Competitive Analysis of Rumen and Hindgut Microbiota Composition and Fermentation Function in Diarrheic and Non-Diarrheic Postpartum Dairy Cows
by Yangyi Hao, Tong Ouyang, Wei Wang, Yajing Wang, Zhijun Cao, Hongjian Yang, Le Luo Guan and Shengli Li
Microorganisms 2024, 12(1), 23; https://doi.org/10.3390/microorganisms12010023 - 22 Dec 2023
Cited by 1 | Viewed by 811
Abstract
Postpartum dairy cows can develop nutritional diarrhea when their diet is abruptly changed for milk production. However, it is unclear whether nutritional diarrhea develops as a result of gut acidosis and/or dysbiosis. This study aimed to uncover changes in the gastrointestinal microbiota and [...] Read more.
Postpartum dairy cows can develop nutritional diarrhea when their diet is abruptly changed for milk production. However, it is unclear whether nutritional diarrhea develops as a result of gut acidosis and/or dysbiosis. This study aimed to uncover changes in the gastrointestinal microbiota and its fermentation parameters in response to nutritional diarrhea in postpartum dairy cows. Rumen and fecal samples were collected from twenty-four postpartum cows fed with the same diet but with different fecal scores: the low-fecal-score (LFS: diarrheic) group and high-fecal-score (HFS: non-diarrheic) group. A microbiota difference was only observed for fecal microbiota, with the relative abundance of Defluviitaleaceae_UCG-011 and Lachnospiraceae_UCG-001 tending (p < 0.10) to be higher in HFS cows compared to LFS cows, and Frisingicoccus were only detected in HFS cows. The fecal bacterial community in LFS cows had higher robustness (p < 0.05) compared to that in HFS cows, and also had lower negative cohesion (less competitive behaviors) and higher positive cohesion (more cooperative behaviors) (p < 0.05) compared that in to HFS cows. Lower total volatile fatty acids and higher ammonia nitrogen (p < 0.05) were observed in LFS cows’ feces compared to HFS cows. The observed shift in fecal bacterial composition, community networks, and metabolites suggests that hindgut dysbiosis could be related to nutritional diarrhea in postpartum cows. Full article
(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)
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18 pages, 2660 KiB  
Article
Deciphering the Association between Campylobacter Colonization and Microbiota Composition in the Intestine of Commercial Broilers
by Jinji Pang, Torey Looft, Qijing Zhang and Orhan Sahin
Microorganisms 2023, 11(7), 1724; https://doi.org/10.3390/microorganisms11071724 - 30 Jun 2023
Cited by 3 | Viewed by 1605
Abstract
Campylobacter is a major food safety concern and is transmitted mainly via poultry meat. We previously found that some commercial broiler farms consistently produced Campylobacter-negative flocks while others were consistently Campylobacter-positive for consecutive production cycles although the farms operated under similar [...] Read more.
Campylobacter is a major food safety concern and is transmitted mainly via poultry meat. We previously found that some commercial broiler farms consistently produced Campylobacter-negative flocks while others were consistently Campylobacter-positive for consecutive production cycles although the farms operated under similar management practices. We hypothesized that this difference in Campylobacter colonization might be associated with the gut microbiota composition. To address this, six commercial broiler farms were selected based on their Campylobacter status (three negative and three positive) to evaluate the microbiota differences between each farm category. For each farm on each production cycle (2–3 cycles), 40 ceca collected from five-week-old broilers were processed for microbiota analysis via 16S rRNA gene sequencing. Cecal microbiota species richness, phylogenetic diversity, community structure, and composition of Campylobacter-positive farms were noticeably different from those of Campylobacter-negative farms. Rikenella, Methanocorpusculum, Barnesiella, Parasutterella, and Helicobacter were significantly more abundant among Campylobacter-positive farms. In contrast, Ruminococcaceae, Streptococcus, Escherichia, Eggerthellaceae, Lactobacillus, Monoglobus, and Blausia were more abundant in Campylobacter-negative farms. Eggerthellaceae, Clostridia, Lachnospiraceae, Lactobacillus, Monoglobus, and Parabacteroides were significantly negatively correlated with Campylobacter abundance. These findings suggest that specific members of cecal microbiota may influence Campylobacter colonization in commercial broilers and may be further explored to control Campylobacter in poultry. Full article
(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)
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22 pages, 6893 KiB  
Article
Microbiome of Ceca from Broiler Chicken Vaccinated or Not against Coccidiosis and Fed Berry Pomaces
by Chongwu Yang, Quail Das, Muhammad A. Rehman, Xianhua Yin, Julie Shay, Martin Gauthier, Calvin Ho-Fung Lau, Kelly Ross and Moussa S. Diarra
Microorganisms 2023, 11(5), 1184; https://doi.org/10.3390/microorganisms11051184 - 30 Apr 2023
Cited by 1 | Viewed by 2045
Abstract
American cranberry (Vaccinium macrocarpon) and lowbush/wild blueberry (V. angustifolium) pomace are polyphenol-rich products having potentially beneficial effects in broiler chickens. This study investigated the cecal microbiome of broiler-vaccinated or non-vaccinated birds against coccidiosis. Birds in each of the two [...] Read more.
American cranberry (Vaccinium macrocarpon) and lowbush/wild blueberry (V. angustifolium) pomace are polyphenol-rich products having potentially beneficial effects in broiler chickens. This study investigated the cecal microbiome of broiler-vaccinated or non-vaccinated birds against coccidiosis. Birds in each of the two groups (vaccinated or non-vaccinated) were fed a basal non-supplemented diet (NC), a basal diet supplemented with bacitracin (BAC), American cranberry (CP), and lowbush blueberry (BP) pomace alone or in combination (CP + BP). At 21 days of age, cecal DNA samples were extracted and analyzed using both whole-metagenome shotgun sequencing and targeted-resistome sequencing approaches. Ceca from vaccinated birds showed a lower abundance of Lactobacillus and a higher abundance of Escherichia coli than non-vaccinated birds (p < 0.05). The highest and lowest abundance of L. crispatus and E. coli, respectively, were observed in birds fed CP, BP, and CP + BP compared to those from NC or BAC treatments (p < 0.05). Coccidiosis vaccination affected the abundance of virulence genes (VGs) related to adherence, flagella, iron utilization, and secretion system. Toxin-related genes were observed in vaccinated birds (p < 0.05) in general, with less prevalence in birds fed CP, BP, and CP + BP than NC and BAC (p < 0.05). More than 75 antimicrobial resistance genes (ARGs) detected by the shotgun metagenomics sequencing were impacted by vaccination. Ceca from birds fed CP, BP, and CP + BP showed the lowest (p < 0.05) abundances of ARGs related to multi-drug efflux pumps, modifying/hydrolyzing enzyme and target-mediated mutation, when compared to ceca from birds fed BAC. Targeted metagenomics showed that resistome from BP treatment was distant to other groups for antimicrobials, such as aminoglycosides (p < 0.05). Significant differences in the richness were observed between the vaccinated and non-vaccinated groups for aminoglycosides, β-lactams, lincosamides, and trimethoprim resistance genes (p < 0.05). Overall, this study demonstrated that dietary berry pomaces and coccidiosis vaccination significantly impacted cecal microbiota, virulome, resistome, and metabolic pathways in broiler chickens. Full article
(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)
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17 pages, 2352 KiB  
Article
Exploring the Bacterial Community in Aged Fecal Sources from Dairy Cows: Impacts on Fecal Source Tracking
by Megan L. Devane, William Taylor, Pierre-Yves Dupont, Bridget Armstrong, Louise Weaver and Brent J. Gilpin
Microorganisms 2023, 11(5), 1161; https://doi.org/10.3390/microorganisms11051161 - 28 Apr 2023
Viewed by 1269
Abstract
(1) Background: This paper discusses the impact of agricultural activities on stream health, particularly in relation to dairy cow fecal pollution. The study explores the fecal microbiome of cattle and the potential ecological implications of aging fecal pollution on waterways. (2) Methods: The [...] Read more.
(1) Background: This paper discusses the impact of agricultural activities on stream health, particularly in relation to dairy cow fecal pollution. The study explores the fecal microbiome of cattle and the potential ecological implications of aging fecal pollution on waterways. (2) Methods: The study examines changes in the bacterial community available for mobilization from in-situ decomposing cowpats and the effects of simulated rainfall. The microbiome of individual cowpats was monitored over 5.5 months. We used 16S rRNA metagenomics and machine learning software, FEAST (Fast Expectation-mAximization for microbial Source Tracking), for bacterial and fecal source assignments. (3) Results: The phyla Bacillota and Bacteroidota are dominant in the fecal microbiota of fresh cow feces but shift to Pseudomonodota, Actinomycetota, and environmental Bacteroidota in aged cowpats. Potential impacts of these bacterial community shifts on inputs to local agricultural streams are discussed in relation to water quality monitoring and aging sources of fecal contamination. We identified taxon orders that are potential indicators of fresh cattle sources (Oscillospirales and Bacteroidales) and aged sources (Peptostreptococcales-Tissierellales) in water bodies. (4) The paper highlights that bacterial metagenomic profiling can inform our understanding of the ecology of microbial communities in aquatic environments and the potential impacts of agricultural activities on ecosystem health. Full article
(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)
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11 pages, 21233 KiB  
Article
The Gut Microbiota of Broilers Reared with and without Antibiotic Treatment
by Genevieve Greene, Leonard Koolman, Paul Whyte, Catherine Burgess and Declan Bolton
Microorganisms 2023, 11(4), 876; https://doi.org/10.3390/microorganisms11040876 - 29 Mar 2023
Cited by 1 | Viewed by 1665
Abstract
The aim of this study was to examine the microbiota in broilers reared with and without antibiotics and to investigate differences between the upper, middle and lower sections of the gastrointestinal tract (GIT). One of two commercial flocks was treated with an antibiotic [...] Read more.
The aim of this study was to examine the microbiota in broilers reared with and without antibiotics and to investigate differences between the upper, middle and lower sections of the gastrointestinal tract (GIT). One of two commercial flocks was treated with an antibiotic (T) (20 mg trimethoprim and 100 mg sulfamethoxazole per ml in the drinking water for 3 days) and the other was left untreated (UT). The GIT contents of 51 treated and untreated birds were aseptically removed from the upper (U), middle (M) and lower (L) sections. These were pooled in triplicate (n = 17 per section per flock), the DNA extracted and purified, 16S amplicon metagenomic sequencing performed and the resultant data analysed using a range of bioinformatics software. There were significant differences in the microbiota of the upper, middle and lower GIT, and treatment with the antibiotic significantly affected the microbiota in each of these sections. This study provides new data on broiler GIT microbiota and suggests that GIT location is a more important determinant of the constituent bacterial flora rather than the use or otherwise of antimicrobial treatments, at least when applied early in the production cycle. Full article
(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)
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16 pages, 5384 KiB  
Article
Evaluation of Effectiveness of a Novel Multicomponent Mycotoxins Detoxification Agent in the Presence of AFB1 and T-2 Toxin on Broiler Chicks
by Darko Stefanović, Darko Marinković, Saša Trailović, Marko Vasiljević, Hunor Farkaš, Jog Raj, Nataša Tolimir, Stamen Radulović, Vladimir Nešić, Jelena Nedeljković Trailović and Branko Petrujkić
Microorganisms 2023, 11(3), 574; https://doi.org/10.3390/microorganisms11030574 - 24 Feb 2023
Cited by 3 | Viewed by 1356
Abstract
This experimental study was conducted to determine the ability of a novel mycotoxins detoxification agent (MR) at a concentration of 0.2% to reduce the toxicity of aflatoxin B1 (AFB1) or T-2 toxin, alone or in combination, and to examine its effect on performance, [...] Read more.
This experimental study was conducted to determine the ability of a novel mycotoxins detoxification agent (MR) at a concentration of 0.2% to reduce the toxicity of aflatoxin B1 (AFB1) or T-2 toxin, alone or in combination, and to examine its effect on performance, pathohistological changes (PH) and the residue of these toxins in the tissues of broiler chicks. A total of 96 broiler chicks were divided into eight equal groups: group C, which served as control (without any additives); group MR, which received the novel detoxification agent (supplemented with 0.2%); group E-I (0.1 mg AFB1/kg of diet); group E-II (0.1 mg AFB1/kg of diet + MR 0.2%); group E-III (0.5 mg T-2 toxin/kg of diet); group E-IV (0.5 mg T-2 toxin/kg of diet + 0.2% MR); group E-V (combination of 0.1 mg AFB1/kg, 0.5 mg T-2 toxin/kg of diet); and group E-VI (combination of 0.1 mg AFB1/kg, 0.5 mg T-2 toxin + 0.2% MR). Results indicate that feeds containing AFB1 and T-2 toxin, alone or in combination, adversely affected the health and performance of poultry. However, the addition of MR to diets containing AFB1 and T-2 toxin singly and in combination exerted a positive effect on body weight, feed intake, weight gain, feed efficiency and microscopic lesions in visceral organs. Residual concentration of AFB1 in liver samples was significantly (p < 0.05) decreased when chicks were fed diets supplemented with 0.2% of MR. Full article
(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)
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21 pages, 3377 KiB  
Article
Dietary Supplementation with Botanical Blends Modified Intestinal Microbiota and Metabolomics of Weaned Pigs Experimentally Infected with Enterotoxigenic Escherichia coli
by Cynthia Jinno, Kwangwook Kim, Braden Wong, Emma Wall, Ravichandran Sripathy and Yanhong Liu
Microorganisms 2023, 11(2), 320; https://doi.org/10.3390/microorganisms11020320 - 27 Jan 2023
Cited by 1 | Viewed by 1508
Abstract
The objective of this study was to investigate supplementation of botanical blends (BB) comprised of 0.3% capsicum oleoresin and 12% garlic oil on gut microbiota and metabolomic profiles in serum and ileal mucosa of Escherichia coli infected pigs. Sixty weaned pigs were assigned [...] Read more.
The objective of this study was to investigate supplementation of botanical blends (BB) comprised of 0.3% capsicum oleoresin and 12% garlic oil on gut microbiota and metabolomic profiles in serum and ileal mucosa of Escherichia coli infected pigs. Sixty weaned pigs were assigned to one of five treatments: negative control (CON−), positive control (CON+), dietary supplementation of 100 ppm BB1, 50 or 100 ppm BB2. All pigs, except CON−, were orally inoculated with 1010 CFU F18 ETEC/3-mL dose for 3 consecutive days after 7 d adaption. Feces, ileal digesta and cecal content were collected for 16S rRNA amplicon sequencing. Serum and ileal mucosa underwent primary metabolomics analysis. Supplementing 100 ppm BB1 increased (p < 0.05) relative abundances of Enterobacteriaceae and Escherichia–Shigella in ileum, and the relative abundances of Bacteroidota and Prevotellaceae in cecum than CON+ on d 5 post-inoculation (PI). Supplementing 100 ppm BB2 upregulated serum pinitol on d 4 PI and serum cholesterol and aminomalonic acids on d 21 PI, while supplementing 50 ppm BB2 reduced asparagine in ileal mucosa on d 5 PI than CON+. Supplementation with botanical blends modulated ileal and cecal microbiota and serum metabolomics profiles in weaned pigs under Escherichia coli challenge. Full article
(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)
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16 pages, 3778 KiB  
Article
Effects of Dietary Isoleucine Supplementation on the Production Performance, Health Status and Cecal Microbiota of Arbor Acre Broiler Chickens
by Hengchen Liu, Jianli Sun, Shuzhen Jiang, Ning Jiao, Libo Huang, Xuejun Yuan, Qinglin Guan, Yang Li and Weiren Yang
Microorganisms 2023, 11(2), 236; https://doi.org/10.3390/microorganisms11020236 - 17 Jan 2023
Cited by 5 | Viewed by 2679
Abstract
A total of 24,000 healthy 1-day-old Arbor Acres broilers with similar initial weights were used in this study and fed a basal diet supplemented with 0, 400 and 800 mg/kg isoleucine (Ile), denoted CON, ILE400 and ILE800, respectively. Results revealed that the final [...] Read more.
A total of 24,000 healthy 1-day-old Arbor Acres broilers with similar initial weights were used in this study and fed a basal diet supplemented with 0, 400 and 800 mg/kg isoleucine (Ile), denoted CON, ILE400 and ILE800, respectively. Results revealed that the final body weight, average daily weight gain, and eviscerated carcass rate, of broiler chickens in the ILE400 group were significantly higher than in other groups (p < 0.05). In addition, the ILE400 and ILE800 groups had a lower feed conversion rate and a higher survival rate and breast muscle rate (p < 0.05), while the abdominal fat rate was significantly lower than the CON group (p < 0.05). There were significantly lower serum concentrations of UREA, glucose (GLU) and total cholesterol (TCHO) in the ILE400 and ILE800 groups than in the CON group (p < 0.05); glutathione peroxidase (GSH-Px) activity was significantly higher in the ILE400 group than in the other groups, and tumor necrosis factor-alpha (TNF-α) concentration was considerably lower than in other groups (p < 0.05). Moreover, interleukin (IL)-10 concentration in the ILE800 group was significantly higher than in the other groups (p < 0.05). The ILE400 group significantly down-regulated the mRNA expressions of fatty-acid synthase (FASN) and solid alcohol regulatory element binding protein 1c (SREBP1c), and significantly up-regulated the mRNA expressions of adipose triglyceride lipase (ATGL), hormone-sensitive lipase (HSL), lipoprotein lipase (LPL) and sirtuin1 (Sirt1) (p < 0.05). The ILE400 group had significantly higher intestinal villus height than the CON and ILE800 groups, while the ILE800 group had significantly lower intestinal villus height/crypt depth (p < 0.05). Furthermore, high-throughput sequencing showed that the Shannon index, and Verrucomicrobiota, Colidextribacter and Bacteroides abundances were significantly higher in the ILE400 group than in the CON group (p < 0.05). Interestingly, the ILE800 group reduced the Simpson index, phylum Firmicutes and Bacteroidota abundances (including genera Colidextribacter, Butyricicoccus, [Ruminococcus]_torques_group, Bacteroides, Alistipes, Barnesiella and Butyricimonas), and increased Proteobacteria and Cyanobacteria (including genera Dyella, Devosia, unidentified_Chloroplast and Hyphomicrobium) (p < 0.05). Overall, our study showed that adding 400 mg/kg Ile to the diet (diets total Ile levels at 1.01%, 0.90% and 0.87% during the starter, grower and finisher phases, respectively) increased production performance and improved the health status in broiler chickens. Full article
(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)
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14 pages, 2018 KiB  
Article
Bacterial Profiles of Brain in Downer Cattle with Unknown Etiology
by Yeong-Jun Park, Gi-Ung Kang, Minsoo Jeong, Vineet Singh, Jongho Kim, Kyunghyun Lee, Eun-Jin Choi, Heui-Jin Kim, Seungjun Lee, Sook-Young Lee, Jae-Ku Oem and Jae-Ho Shin
Microorganisms 2023, 11(1), 98; https://doi.org/10.3390/microorganisms11010098 - 30 Dec 2022
Cited by 1 | Viewed by 2336
Abstract
Downer cow can be caused by muscular paralysis, neurological damage, metabolic disorder, and/or the complication of microbial infection. However, downer cow with unknown etiology is issued because of the non-detection of its bacterial etiological agent. In this study, differences in the bacterial community [...] Read more.
Downer cow can be caused by muscular paralysis, neurological damage, metabolic disorder, and/or the complication of microbial infection. However, downer cow with unknown etiology is issued because of the non-detection of its bacterial etiological agent. In this study, differences in the bacterial community in brain tissues between downer cattle with unknown etiology and healthy slaughtered cattle are investigated. Bacterial diversity and representative genera between downer and normal cattle were significantly different (p < 0.05). There are significant differences in representative genera of downer and normal cattle, especially the significance, fold change, and area under the receiver operating characteristic curve score (p < 0.05). Furthermore, the prediction of functional genes in brain microbiota between the downer and normal cattle revealed differences in the cluster of orthologous gene categories, such as lipid transport and metabolism, secondary metabolite biosynthesis, and signal transduction (p < 0.05). This study revealed a significant difference in microbiota between the downer and normal cattle. Thus, we demonstrate that representative genera from downer cattle through 16S rRNA gene amplicon sequencing and microbiota analysis have the potential as candidates for bacterial etiological agents for downer cow. Full article
(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)
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20 pages, 5290 KiB  
Article
Effects of Oral Glutamine Supplementation, Birthweight and Age on Colonic Morphology and Microbiome Development in Male Suckling Piglets
by Johannes Schulze Holthausen, Johannes Schregel, Quentin L. Sciascia, Zeyang Li, Armin Tuchscherer, Wilfried Vahjen, Cornelia C. Metges and Jürgen Zentek
Microorganisms 2022, 10(10), 1899; https://doi.org/10.3390/microorganisms10101899 - 25 Sep 2022
Cited by 4 | Viewed by 1725
Abstract
Mortality, impaired development and metabolic dysfunctions of suckling low-birthweight piglets may be influenced by modulating the intestinal microbiome through glutamine supplementation. Therefore, this study examined whether glutamine supplementation may affect the colonic development and microbiome composition of male low- and normal-birthweight piglets at [...] Read more.
Mortality, impaired development and metabolic dysfunctions of suckling low-birthweight piglets may be influenced by modulating the intestinal microbiome through glutamine supplementation. Therefore, this study examined whether glutamine supplementation may affect the colonic development and microbiome composition of male low- and normal-birthweight piglets at 5 and 12 days of age. Suckling piglets were supplemented orally with glutamine or alanine. Colonic digesta samples were obtained for 16S rDNA sequencing, determination of bacterial metabolites and histomorphological tissue analyses. Glutamine-supplemented piglets had lower concentrations of cadaverine and spermidine in the colonic digesta (p < 0.05) and a higher number of CD3+ colonic intraepithelial lymphocytes compared to alanine-supplemented piglets (p < 0.05). Low-birthweight piglets were characterised by a lower relative abundance of Firmicutes, the genera Negativibacillus and Faecalibacterium and a higher abundance of Alistipes (p < 0.05). Concentrations of cadaverine and total biogenic amines (p < 0.05) and CD3+ intraepithelial lymphocytes (p < 0.05) were lower in low- compared with normal-birthweight piglets. In comparison to the factor age, glutamine supplementation and birthweight were associated with minor changes in microbial and histological characteristics of the colon, indicating that ontogenetic factors play a more important role in intestinal development. Full article
(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)
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Review

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17 pages, 388 KiB  
Review
The Prevalence of Aliarcobacter Species in the Fecal Microbiota of Farm Animals and Potential Effective Agents for Their Treatment: A Review of the Past Decade
by Cansu Çelik, Orhan Pınar and Nisa Sipahi
Microorganisms 2022, 10(12), 2430; https://doi.org/10.3390/microorganisms10122430 - 8 Dec 2022
Cited by 6 | Viewed by 1690
Abstract
There is an endless demand for livestock-originated food, so it is necessary to elucidate the hazard points for livestock breeding. Pathogens are one of the hazard points that threaten the biosecurity of farm-animal breeding and public health. As a potential foodborne pathogen, Aliarcobacter [...] Read more.
There is an endless demand for livestock-originated food, so it is necessary to elucidate the hazard points for livestock breeding. Pathogens are one of the hazard points that threaten the biosecurity of farm-animal breeding and public health. As a potential foodborne pathogen, Aliarcobacter is a member of the intestinal microbiota of farm animals with and without diarrhea. Aliarcobacter spp. are capable of colonizing livestock intestines and are transmitted through the feces. Hence, they endanger slaughterhouses and milk products with fecal contamination. They also have other, rarer, vertical and horizontal transmission routes, including the offspring that abort in farm animals. Gastrointestinal symptoms and abort cases demonstrate potential financial losses to the industry. Viewed from this perspective, the global circulation of farm-animal products is a significant route for zoonotic agents, including Aliarcobacter. In the last decade, worldwide prevalence of Aliarcobacter in fecal samples has ranged from 0.8% in Italy to 100% in Turkey. Furthermore, antibiotic resistance is recognized as a new type of environmental pollutant and has become a hot topic in animal breeding and the food industry. Increasing antibiotic resistance has become a significant problem impacting productivity. The increase in antimicrobial resistance rates in Aliarcobacter is caused by the misuse of antimicrobial drugs in livestock animals, leading to the acquiring of resistance genes from other bacteria, as well as mutations in current resistance genes. The most resistant strains are A. butzleri, A. cryaerophilus, and A. skirrowii. This review analyzes recent findings from the past decade on the prevalence of Aliarcobacter in the intestinal microbiota and the current effective antibiotics against Aliarcobacter. The paper also highlights that A. cryaerophilus and A. skirrowii are found frequently in diarrheal feces, indicating that Aliarcobacter should be studied further in livestock diarrheal diseases. Moreover, Aliarcobacter-infected farm animals can be treated with only a limited number of antibiotics, such as enrofloxacin, doxycycline, oxytetracycline, and gentamicin. Full article
(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)

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21 pages, 979 KiB  
Systematic Review
Effects of Major Families of Modulators on Performances and Gastrointestinal Microbiota of Poultry, Pigs and Ruminants: A Systematic Approach
by Cyrielle Payen, Annaëlle Kerouanton, Jorge Novoa, Florencio Pazos, Carlos Benito, Martine Denis, Muriel Guyard, F. Javier Moreno and Marianne Chemaly
Microorganisms 2023, 11(6), 1464; https://doi.org/10.3390/microorganisms11061464 - 31 May 2023
Cited by 2 | Viewed by 1146
Abstract
Considering the ban on the use of antibiotics as growth stimulators in the livestock industry, the use of microbiota modulators appears to be an alternative solution to improve animal performance. This review aims to describe the effect of different families of modulators on [...] Read more.
Considering the ban on the use of antibiotics as growth stimulators in the livestock industry, the use of microbiota modulators appears to be an alternative solution to improve animal performance. This review aims to describe the effect of different families of modulators on the gastrointestinal microbiota of poultry, pigs and ruminants and their consequences on host physiology. To this end, 65, 32 and 4 controlled trials or systematic reviews were selected from PubMed for poultry, pigs and ruminants, respectively. Microorganisms and their derivatives were the most studied modulator family in poultry, while in pigs, the micronutrient family was the most investigated. With only four controlled trials selected for ruminants, it was difficult to conclude on the modulators of interest for this species. For some modulators, most studies showed a beneficial effect on both the phenotype and the microbiota. This was the case for probiotics and plants in poultry and minerals and probiotics in pigs. These modulators seem to be a good way for improving animal performance. Full article
(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)
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