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A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Antibiotics in Animal Health".

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 33566

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Prof. Dr. Jie Yin

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College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
Interests: livestock; probiotics; pathogens
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Yingping Xiao

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1. State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, PI, Ningbo, China
2. Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
Interests: Clostridium butyricum; gut microbiota; metabolomics; fat deposition; obesity

Dr. Jie Ma

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College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
Interests: gut micribiota; host; lipid metabolism; obesity

Special Issue Information

Dear Colleagues,

Recent decades have witnessed the development of the gut microbiome via the application of fecal bacterial transplantation, a germ-free model, meta-omics approaches, and novel bioinformatics tools. In livestock, gastrointestinal microbiota has been identified in associations with gut infections, growth performance, the host metabolism, and meat quality, while specific mechanisms are not fully studied. The goal of this Special Issue is, therefore, to collate state-of-the-art research focused on compositions of gastrointestinal microbiota in different livestock and molecular mechanisms in animal economic characters. We welcome the submission of reviews, systematic reviews, mini-reviews, hypothesis and theory, perspectives, clinical trials, and original research articles that allow narrowing existing gaps in the knowledge. Systematic reviews are particularly encouraged. We seek the submission of articles around, but not limited to, the following subtopics:

Screening and isolation of probiotics from livestock;
Identification and pathogenesis of pathogens in livestock;
Gut microbial responses to antibiotic exposures in livestock;
Colonization of probiotics and pathogens in livestock;
Quorum sensing in livestock.

Prof. Dr. Jie Yin
Prof. Dr. Yingping Xiao
Dr. Jie Ma
Guest Editors

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Keywords

livestock
probiotics
pathogens

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Published Papers (10 papers)

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16 pages, 4033 KiB

Open AccessArticle

Dietary Bacitracin Methylene Disalicylate Improves Growth Performance by Mediating the Gut Microbiota in Broilers

by Jingshang Li, Yingping Xiao, Qian Fan, Hua Yang, Caimei Yang, Guolong Zhang and Shengchang Chen

Antibiotics 2022, 11(6), 818; https://doi.org/10.3390/antibiotics11060818 - 17 Jun 2022

Cited by 7 | Viewed by 2666

Abstract

The growth performance of livestock and poultry has always been a concern. However, much work is currently focused on the selection of breeds and diets to improve the growth performance of livestock and poultry. Furthermore, numerous studies have shown that the gut microbiota is closely related to the growth performance of livestock and poultry. At present, there are many reports on the impact of antibiotic intervention on the structure of gut microbiota. However, there are few reports on the influence of antibiotic intervention on the structure of intestinal microbes and the effect of this change on growth performance. Bacitracin methylene disalicylate (BMD) intervention changes the microbial structure in the caecum of broilers at different growth stages, as shown in this study. To further reveal the potential relationship between gut microbiota changes and growth performance caused by BMD intervention, correlation analysis was used for analysis. A total of 144 1-day-old male Cobb-Vantress were randomly divided into two groups. In addition to antibiotic-free starter mash diets, starter mash diets supplemented with 55 mg/kg BMD were also used, called the CON group and the BMD group, and lasted 28 days. (1) These study results showed that adding BMD to the diet had a significant effect on the growth performance of broilers. Compared with the CON group, the body weight of the BMD group increased significantly by 11.08% and 20.13% on Days 14 and 28, respectively (p < 0.05). Similarly, at 0–14, 14–28 and 0–28 days of age, the average daily gain of the BMD group increased significantly by 12.28%, 24.49% and 20.80%, respectively. The average daily feed intake of the BMD group increased significantly by 18.28%, 27.39% and 24.97% (p < 0.05). In addition, at 0–28 days of age, the feed conversion ratio increased significantly by 5.5% (p < 0.05). (2) Alpha diversity results show that BMD intervention has an impact on gut microbiota at different growth stages. (3) The early intervention significantly affected 7 taxa by Day 14, followed by 22 taxa by Day 28, which is similar to the results in the caecal flora. Compared with the CON group, the Christensenellaceae R-7 group had the highest linear discriminant analysis (LDA) score on Day 28. In addition, Pearson’s correlation analysis showed that the Lachnospiraceae FCS020 group was significantly negatively correlated with growth performance. In general, these results indicate that dietary supplementation of BMD has an effect on broiler gut microbiota structure and growth performance. However, changes in growth performance may be caused by the gut microbiota structure. Full article

(This article belongs to the Special Issue Gastrointestinal Microbiota of Livestock)

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19 pages, 1522 KiB

Open AccessArticle

The Role of Gut Microbiota in the Skeletal Muscle Development and Fat Deposition in Pigs

by Qi Han, Xingguo Huang, Fuyong Yan, Jie Yin and Yingping Xiao

Antibiotics 2022, 11(6), 793; https://doi.org/10.3390/antibiotics11060793 - 11 Jun 2022

Cited by 12 | Viewed by 3788

Abstract

Pork quality is a factor increasingly considered in consumer preferences for pork. The formation mechanisms determining meat quality are complicated, including endogenous and exogenous factors. Despite a lot of research on meat quality, unexpected variation in meat quality is still a major problem in the meat industry. Currently, gut microbiota and their metabolites have attracted increased attention in the animal breeding industry, and recent research demonstrated their significance in muscle fiber development and fat deposition. The purpose of this paper is to summarize the research on the effects of gut microbiota on pig muscle and fat deposition. The factors affecting gut microbiota composition will also be discussed, including host genetics, dietary composition, antibiotics, prebiotics, and probiotics. We provide an overall understanding of the relationship between gut microbiota and meat quality in pigs, and how manipulation of gut microbiota may contribute to increasing pork quality for human consumption. Full article

(This article belongs to the Special Issue Gastrointestinal Microbiota of Livestock)

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20 pages, 7624 KiB

Open AccessArticle

Could Dietary Supplementation with Different Sources of N-3 Polyunsaturated Fatty Acids Modify the Rabbit Gut Microbiota?

by Giulio Curone, Filippo Biscarini, Elisa Cotozzolo, Laura Menchetti, Alessandro Dal Bosco, Federica Riva, Paola Cremonesi, Stella Agradi, Simona Mattioli, Bianca Castiglioni, Alessia Di Giancamillo, Alice Cartoni Mancinelli, Susanna Draghi, Alda Quattrone, Giulia Collodel, Silvia Clotilde Modina, Cesare Castellini and Gabriele Brecchia

Antibiotics 2022, 11(2), 227; https://doi.org/10.3390/antibiotics11020227 - 10 Feb 2022

Cited by 12 | Viewed by 2953

Abstract

The present study evaluated the effects of feed supplemented with two dietary sources of n-3 polyunsaturated fatty acids (PUFAs; fish oil and extruded flaxseed) on the gut microbiota, caecal fermentations, gastrointestinal histology, and histochemistry in rabbits. Fifteen male New Zealand White rabbits were divided into three groups (n = 5/group) and fed with different diets from weaning (35 days of age) until slaughtering (90 days of age): C group, fed with a commercial diet; F group, supplemented with 10% of extruded flaxseed; and O group, supplemented with 3.5% of fish oil. At slaughter, the content of the stomach, duodenum, jejunum, ileum, caecum, and colon was collected and analyzed by Next Generation 16S rRNA gene sequencing. Tissue samples of the same tracts were evaluated with histological and histochemical analysis. Ammonia and lactic acid in the caecum were also quantified. Twenty-nine operational taxonomic units (OTUs) were significantly different between groups. Groups receiving n-3 PUFAs supplementation showed an increase in Bacteroidetes and Lachnospiraceae in several gastrointestinal tracts, while Bacilli abundance, as well as Firmicutes/Bacteroidetes ratio, were reduced compared to the control group (for all p < 0.05). Caecal ammonia was lower in the F than C group (p < 0.032), whereas no difference was found for lactic acid. Finally, histological evaluations revealed a mild hemorrhagic infiltration and vessels ectasia in the stomach mucosa of both F and O groups, but no effect of nutritional treatment was evidenced by the histochemical analyses. In conclusion, n-3 PUFAs supplementation could modify the rabbit gut microbiota and fermentation. The increase in beneficial bacterial populations may, at least partially, explain the positive effects of n-3 PUFAs diet supplementation on human and animals’ health, although the appropriate dosage should be established. Full article

(This article belongs to the Special Issue Gastrointestinal Microbiota of Livestock)

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11 pages, 943 KiB

Open AccessArticle

The Antibiotics Used in Livestock and Their Impact on Resistance in Enterococcus faecium and Enterococcus hirae on Farms in Gabon

by Désiré Otsaghe Ekore, Richard Onanga, Pierre Phillipe Mbehang Nguema, Chloé Lozano and Brice Serge Kumulungui

Antibiotics 2022, 11(2), 224; https://doi.org/10.3390/antibiotics11020224 - 10 Feb 2022

Cited by 7 | Viewed by 2492

Abstract

The emergence of antibiotic resistance is a major concern around the world. The objective of this study was to investigate the antibiotics used in livestock and their impact on resistance in Enterococcus faecium and Enterococcus hirae on farms in Gabon. A structured questionnaire was used to collect information on the farms. Samples were collected from farms (n = 20) tested for Enterococcus by culture and isolation and were identified using a polymerase chain reaction (PCR) and sequencing. Antibiotic susceptibility was determined by the disc diffusion method on Mueller Hinton agar. The 20 farms included laying hens (6), swine (6), sheep (4) and cattle farms (4). Tetracycline was the most used antibiotic family (91%) and the most used prophylactic method (47%) for the treatment of animals. A total of 555 samples were collected and 515 (93%) Enterococcus spp. isolates of the genus were obtained. The prevalence of E. faecium and E. hirae were 10% and 8%, respectively. The isolates from E. faecium and E. hirae we found were related to clinical and human isolates in the NCBI database. E. faecium and E. hirae isolates showed a high resistance to tetracycline (69% and 65%) and rifampicin (39% and 56%). The tet(M) gene was detected in 65 tetracycline-resistant isolates with a large majority in hens (78% (21/27) and 86% (12/14) in E. faecium and E. hirae, respectively). The consumption of antibiotics favours the emergence of antibiotic resistance in animals in Gabon. Full article

(This article belongs to the Special Issue Gastrointestinal Microbiota of Livestock)

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19 pages, 3463 KiB

Open AccessArticle

Chemically Protected Sodium Butyrate Improves Growth Performance and Early Development and Function of Small Intestine in Broilers as One Effective Substitute for Antibiotics

by Huaibao Zhao, Hai Bai, Fuli Deng, Ruqing Zhong, Lei Liu, Liang Chen and Hongfu Zhang

Antibiotics 2022, 11(2), 132; https://doi.org/10.3390/antibiotics11020132 - 20 Jan 2022

Cited by 24 | Viewed by 3428

Abstract

The purpose of this study was to investigate the effects of chemically protected sodium butyrate (CSB) on growth performance and the early development and function of small intestine in broilers as one potential substitute for antibiotics. A total of 192 one-day-old Arbor Acres male broilers were randomly assigned into three dietary treatment groups (eight replicates per treatment): the control (CON) diet; ANT diet, CON diet supplemented with the antibiotics (enramycin, 8 mg/kg and aureomycin, 100 mg/kg); CSB diet, CON diet supplemented with 1000 mg/kg CSB, respectively. The results showed that dietary CSB and antibiotics addition significantly improved the growth performance of broilers by increasing the body weight gain (BWG) and feed conversion ratio (FCR) during different stages (p < 0.05). On day 21, the supplement of CSB in diet improved the structure of small intestine (duodenum, jejunum, and ileum) in broilers by increasing the ratio of villus height to crypt depth (VH/CD) (p < 0.05) and enhanced the butyric acid (BA) (p < 0.05) and total short chain fatty acids (SCFA) concentrations of small intestine (jejunum and ileum) compared with the CON and ANT diets. Besides that, the superoxide dismutase (SOD), total antioxidant capacity (TAC) and TAC to malondialdehyde (TAC/MDA) ratio of the ileal and jejunal mucosa were significantly higher (p < 0.05) in the CSB and ANT than in the CON. In addition, the supplement of CSB in diet markedly significantly enhanced α-amylase, lipase, and trypsin activities of the ileum (p < 0.05) as compared to the ANT diet. 16S rRNA gene sequencing indicated that CSB markedly increased the microbiota diversity of ileum in broilers at 21 days of age as compared to CON and ANT (p < 0.05). Furthermore, we found that Firmicutes was the predominant phyla and Lactobacillus was the major genus in the ileum of broilers. Compared with the ANT diet, the supplement of CSB in diet increased the relative abundance of some genera microbiota (e.g., Candidatus_Arthromitus, Romboutsia) by decreasing the relative abundance of Lactobacillus. Moreover, Akkermansia in the CSB was the highest in comparison to that in the CON and ANT. In addition, Kitasatospora that belongs to the phylum Actinobacteriota was only found in ileum of broilers fed the ANT diet. In summary, the supplement of 1000 mg/kg CSB in the diet improved the growth performance by promoting early development and function of the small intestine, which is associated with the regulation of intestinal flora and reestablishment of micro-ecological balance in broilers. Thus, CSB has great potential value as one of effective substitutes for in-feed antibiotics in the broiler industry. Full article

(This article belongs to the Special Issue Gastrointestinal Microbiota of Livestock)

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17 pages, 2851 KiB

Open AccessArticle

Effects of Clostridium butyricum and a Bacteriophage Cocktail on Growth Performance, Serum Biochemistry, Digestive Enzyme Activities, Intestinal Morphology, Immune Responses, and the Intestinal Microbiota in Rabbits

by Pan Huang, Xuemei Cui, Zhipeng Wang, Chenwen Xiao, Quanan Ji, Qiang Wei, Yee Huang, Guolian Bao and Yan Liu

Antibiotics 2021, 10(11), 1347; https://doi.org/10.3390/antibiotics10111347 - 4 Nov 2021

Cited by 20 | Viewed by 2747

Abstract

The objective of this study was to assess the effects of dietary supplementation with Clostridium butyricum (CB) and a bacteriophage cocktail (BP) on growth performance, serum biochemical parameters, intestinal digestive and oxidase enzymes, intestinal morphology, immune responses, and the cecum microbiota in rabbits. In total, 108 New Zealand rabbits (5 weeks old) were randomly and equally allotted into three dietary treatment groups (four replicates per treatment, n = 36/treatment): (1) the control (CN) group—rabbits fed the basal diet; (2) CB group—rabbits fed the basal diet supplemented with 100 mg/kg diet Clostridium butyricum; and (3) BP group—rabbits fed the basal diet supplemented with 200 mg/kg diet BP cocktail, respectively, for 6 weeks. Compared with the CN diet, dietary CB and BP inclusion increased the average daily gain (ADG) and average daily feed intake (ADFI) and decreased the feed/gain (F/G) ratio of rabbits. Furthermore, CB increased the digestive enzyme activity (α-amylase and trypsin in the ileum); the chymotrypsin activity was also significantly increased in the duodenum and jejunum. Supplementation with CB significantly enhanced antioxidant capacity (SOD and GSH-Px) in the jejunum and ileum and reduced MDA levels. Additionally, rabbits fed CB had significantly elevated villus height (V) and (V/C) ratios but reduced crypt depth (C). Moreover, dietary CB supplementation markedly increased the ileal expression of tight junction proteins (occludin, ZO-1, and claudin-1) and increased secretory immunoglobulin A (sIgA) production. High-throughput sequencing indicated that the microbiota in the rabbit intestine was altered by CB and BP. Venn diagrams and heatmap plots revealed that the gut microbial community composition varied obviously among rabbits fed different diets. Specifically, CB increased the relative abundance of beneficial bacteria to maintain intestinal barrier homeostasis, whereas BP decreased the relative abundance of Gammaproteobacteria, which included a plenty of pathogenic bacteria. Full article

(This article belongs to the Special Issue Gastrointestinal Microbiota of Livestock)

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12 pages, 5018 KiB

Open AccessArticle

Effects of Rhamnolipids on Growth Performance, Immune Function, and Cecal Microflora in Linnan Yellow Broilers Challenged with Lipopolysaccharides

by Haoran Zhang, Xiaorong Yu, Qing Li, Guangtian Cao, Jie Feng, Yuanyuan Shen and Caimei Yang

Antibiotics 2021, 10(8), 905; https://doi.org/10.3390/antibiotics10080905 - 24 Jul 2021

Cited by 11 | Viewed by 2337

Abstract

This present study aimed to investigate the effects of rhamnolipids (RLS) on the growth performance, intestinal morphology, immune function, short-chain fatty acid content, and microflora community in broiler chickens challenged with lipopolysaccharides (LPS). A total of 450 broiler chickens were randomly allocated into three groups: basal diet with no supplement (NCO), basal diet with bacitracin (ANT), and basal diet with rhamnolipids (RLS). After 56 d of feeding, 20 healthy broilers were selected from each group, with half being intraperitoneally injected with lipopolysaccharides (LPS) and the other half with normal saline. Treatments with LPS were labelled LPS-NCO, LPS-ANT, and LPS-RLS, whereas treatments with normal saline were labelled NS-NCO, NS-ANT, and NS-RLS. LPS-challenged birds had lower jejunal villus height and higher crypt depth than unchallenged birds. LPS-RLS broilers had increased jejunal villus height and villus height/crypt depth ratio (V/C) but lower crypt depth than LPS-NCO. Dietary supplementation with RLS reduced the LPS-induced immunological stress. Compared with LPS-NCO, birds in LPS-RLS had lower concentrations of IL-1β, IL-6, and TNF-α. In LPS-challenged broilers, RLS and ANT increased the concentrations of IgA, IgM, and IgY compared with LPS-NCO. In LPS treatments, RLS enhanced the contents of acetic acid, butyrate, isobutyric acid, isovalerate, and valerate more than LPS-NCO birds. High-throughput sequencing indicated that RLS supplementation led to changes in the cecal microbial community of broilers. At the species level, Clostridium-sp-Marseille-p3244 was more abundant in NS-RLS than in NS-NCO broilers. In summary, RLS improved the growth performance and relative abundance of cecal microbiota and reduced the LPS-induced immunological stress in broiler chickens. Full article

(This article belongs to the Special Issue Gastrointestinal Microbiota of Livestock)

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15 pages, 3858 KiB

Open AccessArticle

Modulation of the Intestinal Microbiota by the Early Intervention with Clostridium Butyricum in Muscovy Ducks

by Xingning Xiao, Zixian Fu, Na Li, Hua Yang, Wen Wang and Wentao Lyu

Antibiotics 2021, 10(7), 826; https://doi.org/10.3390/antibiotics10070826 - 7 Jul 2021

Cited by 7 | Viewed by 2262

Abstract

This study evaluated the effects of early intervention with Clostridium butyricum (C. butyricum) on shaping the intestinal microbiota of Muscovy ducklings. A total of 160 1-day-old male ducks were randomly divided into two groups: the CB group was administered with 1 mL of C. butyricum (2 × 10⁹ CFU/mL), while the C group was given 1 mL of saline. The administration lasted for 3 days. We found that C. butyricum had no significant effect on growth performance. The results indicated that inoculation with C. butyricum could significantly increase the abundance of genera Bacteroides, Lachnospiraceae_uncultured, and Ruminococcaceae on Day 14 and reduce the abundance of Escherichia–Shigella and Klebsiella on Days 1 and 3. Moreover, the CB group ducks had higher concentrations of acetic, propionic, and butyrate in the cecum than the C group. Overall, these results suggest that early intervention with C. butyricum could have positive effects on Muscovy ducks’ intestinal health, which might be attributed to the modulation in the intestinal microbial composition and the increased concentrations of short-chain fatty acids (SCFAs). C. butyricum might even have the potential to help the colonization of beneficial bacteria in the intestine microbiota in Muscovy ducks in poultry and other livestock. Full article

(This article belongs to the Special Issue Gastrointestinal Microbiota of Livestock)

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11 pages, 3293 KiB

Open AccessArticle

Core Altered Microorganisms in Colitis Mouse Model: A Comprehensive Time-Point and Fecal Microbiota Transplantation Analysis

by Lijun Shang, Hongbin Liu, Haitao Yu, Meixia Chen, Tianren Yang, Xiangfang Zeng and Shiyan Qiao

Antibiotics 2021, 10(6), 643; https://doi.org/10.3390/antibiotics10060643 - 28 May 2021

Cited by 84 | Viewed by 5495

Abstract

Inflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), is characterized by chronic and relapsing inflammation within the gastrointestinal tract. Antibiotics have been used to treat IBD, primarily utilizing metronidazole. Although there does seem to be a treatment effect, the broad-spectrum antibiotics that have been used to date are crude tools and have many adverse effects. Available evidence suggests that the host microbiome is implicated in the pathogenesis of IBD, though the key bacteria remain unknown. If the bacterial population can be modified appropriately, the use of antibiotics will have a better therapeutic effect. In this study, mice were fed dextran sodium sulfate (DSS) solution for 5 days, followed by 5 days of normal drinking water, to investigate the gut microbiota response to colitis and the initial alteration of microbiota in recovery phase. Day 0 was considered the normal control, while day 5 and day 10 were considered the colitis mouse model progressive phase and recovery phase, respectively. Results showed that inflammation could induce proportional changes in the gut microbiota. Furthermore, transplanting the microbiota in progressive phase to antibiotic-induced microbiota-depleted mice could induce inflammation similar to colitis, which proves the importance of initial alteration of the microbiota for IBD recovery and the potential of the microbiota as a target for the treatment of IBD. Meanwhile, we have also identified three possible target microorganisms in the development of colitis, namely genera Muribaculaceae (negative correlation), Turicibacter (positive correlation) and Lachnospiraceae (negative correlation) in inflammation status through comprehensive analysis. Full article

(This article belongs to the Special Issue Gastrointestinal Microbiota of Livestock)

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13 pages, 2569 KiB

Open AccessArticle

Effects of Clostridium butyricum- and Bacillus spp.-Based Potential Probiotics on the Growth Performance, Intestinal Morphology, Immune Responses, and Caecal Microbiota in Broilers

by Xinfu Zeng, Qing Li, Caimei Yang, Yang Yu, Zixian Fu, Huixian Wang, Xiaoyan Fan, Min Yue and Yinglei Xu

Antibiotics 2021, 10(6), 624; https://doi.org/10.3390/antibiotics10060624 - 24 May 2021

Cited by 27 | Viewed by 3910

Abstract

We aimed to investigate the effects of Clostridium butyricum-, Bacillus subtilis-, and Bacillus licheniformis-based potential probiotics on the growth performance, intestinal morphology, immune responses, and caecal short chain fatty acids (SCFAs) and microbial structure in broiler chickens. Three treatment groups containing a total of 1200 one-day-old AA broilers were included: birds fed with a basal diet only (Con), birds fed with added 10¹⁰ probiotics cfu/kg (ProL), and birds fed with added 10¹¹ probiotics cfu/kg (ProH). The dietary probiotics significantly improved the final and average body weights and serum immunoglobulins A, M, and Y. The probiotics also enhanced the ileal morphology and improved the caecal acetate, butyrate, and propionate contents. Furthermore, 16S rRNA sequencing revealed that dietary compound probiotics modulated the caecal microflora composition as follows: (1) all birds shared 2794 observed taxonomic units; (2) treatment groups were well separated in the PCA and PCoA analysis; (3) the relative abundance of Parabacteroides, Ruminococcaceae_UCG-014, Barnesiella, Odoribacter, [Eubacterium_coprostanoligenes_group], [Ruminococcus]_torques_group, and Butyricimonas significantly varied between treatments. The compound probiotics improved the growth performance, serum immune responses, the ratio of ileal villus height to crypt depth, and major caecal SCFAs in broiler chickens. The dietary C. butyricum-, B. subtilis-, and B. licheniformis-based probiotics improved overall broiler health and would benefit the poultry industry. Full article

(This article belongs to the Special Issue Gastrointestinal Microbiota of Livestock)

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