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Parzygnat JL, Dunn RR, Koci MD, Crespo R, Harden L, Thakur S. Fluoroquinolone-resistant Campylobacter in backyard and commercial broiler production systems in the United States. JAC Antimicrob Resist 2024; 6:dlae102. [PMID: 38974944 PMCID: PMC11227224 DOI: 10.1093/jacamr/dlae102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 06/13/2024] [Indexed: 07/09/2024] Open
Abstract
Objectives Campylobacter spp. are one of the leading foodborne pathogens in the world, and chickens are a known reservoir. This is significant considering broiler chicken is the top consumed meat worldwide. In the USA, backyard poultry production is increasing, but little research has been done to investigate prevalence and antimicrobial resistance associated with Campylobacter in these environments. Methods Our study encompasses a farm-to-genome approach to identify Campylobacter and investigate its antimicrobial resistance phenotypically and genotypically. We travelled to 10 backyard and 10 integrated commercial broiler farms to follow a flock throughout production. We sampled at days 10, 31 and 52 for backyard and 10, 24 and 38 for commercial farms. Bird faecal (n = 10) and various environmental samples (soil n = 5, litter/compost n = 5, and feeder and waterer swabs n = 6) were collected at each visit and processed for Campylobacter. Results Our results show a higher prevalence of Campylobacter in samples from backyard farms (21.9%) compared to commercial (12.2%). Most of our isolates were identified as C. jejuni (70.8%) and the remainder as C. coli (29.2%). Antimicrobial susceptibility testing reveals phenotypic resistance to ciprofloxacin (40.2%), an important treatment drug for Campylobacter infection, and tetracycline (46.6%). A higher proportion of resistance was found in C. jejuni isolates and commercial farms. Whole-genome sequencing revealed resistance genes, such as tet(O) and gyrA_T86I point mutation, that may confer resistance. Conclusion Overall, our research emphasizes the need for interventions to curb prevalence of resistant Campylobacter spp. on broiler production systems.
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Affiliation(s)
- Jessica L Parzygnat
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Matthew D Koci
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Rocio Crespo
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
| | - Lyndy Harden
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
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2
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Swinkels AF, Berendsen BJA, Fischer EAJ, Zomer AL, Wagenaar JA. Extended period of selection for antimicrobial resistance due to recirculation of persistent antimicrobials in broilers. J Antimicrob Chemother 2024:dkae213. [PMID: 38953288 DOI: 10.1093/jac/dkae213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/31/2024] [Indexed: 07/03/2024] Open
Abstract
OBJECTIVES Antimicrobials can select for antimicrobial-resistant bacteria. After treatment the active compound is excreted through urine and faeces. As some antimicrobials are chemically stable, recirculation of subinhibitory concentrations of antimicrobials may occur due to coprophagic behaviour of animals such as chickens. METHODS The persistence of three antimicrobials over time and their potential effects on antimicrobial resistance were determined in four groups of broilers. Groups were left untreated (control) or were treated with amoxicillin (unstable), doxycycline or enrofloxacin (stable). Antimicrobials were extracted from the faecal samples and were measured by LC-MS/MS. We determined the resistome genotypically using shotgun metagenomics and phenotypically by using Escherichia coli as indicator microorganism. RESULTS Up to 37 days after treatment, doxycycline and enrofloxacin had concentrations in faeces equal to or higher than the minimal selective concentration (MSC), in contrast to the amoxicillin treatment. The amoxicillin treatment showed a significant difference (P ≤ 0.01 and P ≤ 0.0001) in the genotypic resistance only directly after treatment. On the other hand, the doxycycline treatment showed approximately 52% increase in phenotypic resistance and a significant difference (P ≤ 0.05 and P ≤ 0.0001) in genotypic resistance throughout the trial. Furthermore, enrofloxacin treatment resulted in a complete non-WT E. coli population but the quantity of resistance genes was similar to the control group, likely because resistance is mediated by point mutations. CONCLUSIONS Based on our findings, we suggest that persistence of antimicrobials should be taken into consideration in the assessment of priority classification of antimicrobials in livestock.
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Affiliation(s)
- Aram F Swinkels
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Bjorn J A Berendsen
- Wageningen Food Safety Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Egil A J Fischer
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Aldert L Zomer
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Jaap A Wagenaar
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
- Wageningen Bioveterinary Research, Wageningen University & Research, Lelystad, The Netherlands
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Aruwa CE, Sabiu S. Interplay of poultry-microbiome interactions - influencing factors and microbes in poultry infections and metabolic disorders. Br Poult Sci 2024:1-15. [PMID: 38920059 DOI: 10.1080/00071668.2024.2356666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/06/2024] [Indexed: 06/27/2024]
Abstract
1. The poultry microbiome and its stability at every point in time, either free range or reared under different farming systems, is affected by several environmental and innate factors. The interaction of the poultry birds with their microbiome, as well as several inherent and extraneous factors contribute to the microbiome dynamics. A poor understanding of this could worsen poultry heath and result in disease/metabolic disorders.2. Many diseased states associated with poultry have been linked to dysbiosis state, where the microbiome experiences some perturbation. Dysbiosis itself is too often downplayed; however, it is considered a disease which could lead to more serious conditions in poultry. The management of interconnected factors by conventional and emerging technologies (sequencing, nanotechnology, robotics, 3D mini-guts) could prove to be indispensable in ensuring poultry health and welfare.3. Findings showed that high-throughput technological advancements enhanced scientific insights into emerging trends surrounding the poultry gut microbiome and ecosystem, the dysbiotic condition, and the dynamic roles of intrinsic and exogenous factors in determining poultry health. Yet, a combination of conventional, -omics based and other techniques further enhance characterisation of key poultry microbiome actors, their mechanisms of action, and roles in maintaining gut homoeostasis and health, in a bid to avert metabolic disorders and infections.4. In conclusion, there is an important interplay of innate, environmental, abiotic and biotic factors impacting on poultry gut microbiome homoeostasis, dysbiosis, and overall health. Associated infections and metabolic disorders can result from the interconnected nature of these factors. Emerging concepts (interkingdom or network signalling and neurotransmitter), and future technologies (mini-gut models, cobots) need to include these interactions to ensure accurate control and outcomes.
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Affiliation(s)
- C E Aruwa
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - S Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
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4
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Nwokorogu VC, Pillai S, San JE, Pillay C, Nyaga MM, Sabiu S. A metagenomic investigation of the faecal RNA virome structure of asymptomatic chickens obtained from a commercial farm in Durban, KwaZulu-Natal province, South Africa. BMC Genomics 2024; 25:629. [PMID: 38914944 PMCID: PMC11194887 DOI: 10.1186/s12864-024-10517-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 06/12/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Virome studies on birds, including chickens are relatively scarce, particularly from the African continent. Despite the continuous evolution of RNA viruses and severe losses recorded in poultry from seasonal viral outbreaks, the information on RNA virome composition is even scantier as a result of their highly unstable nature, genetic diversity, and difficulties associated with characterization. Also, information on factors that may modulate the occurrence of some viruses in birds is limited, particularly for domesticated birds. Viral metagenomics through advancements in sequencing technologies, has enabled the characterization of the entire virome of diverse host species using various samples. METHODS The complex RNA viral constituents present in 27 faecal samples of asymptomatic chickens from a South African farm collected at 3-time points from two independent seasons were determined, and the impact of the chicken's age and collection season on viral abundance and diversity was further investigated. The study utilized the non-invasive faecal sampling method, mRNA viral targeted enrichment steps, a whole transcriptome amplification strategy, Illumina sequencing, and bioinformatics tools. RESULTS The results obtained revealed a total of 48 viral species spanning across 11 orders, 15 families and 21 genera. Viral RNA families such as Coronaviridae, Picornaviridae, Reoviridae, Astroviridae, Caliciviridae, Picorbirnaviridae and Retroviridae were abundant, among which picornaviruses, demonstrated a 100% prevalence across the three age groups (2, 4 and 7 weeks) and two seasons (summer and winter) of the 27 faecal samples investigated. A further probe into the extent of variation between the different chicken groups investigated indicated that viral diversity and abundance were significantly influenced by age (P = 0.01099) and season (P = 0.00099) between chicken groups, while there was no effect on viral shedding within samples in a group (alpha diversity) for age (P = 0.146) and season (P = 0.242). CONCLUSION The presence of an exceedingly varied chicken RNA virome, encompassing avian, mammalian, fungal, and dietary-associated viruses, underscores the complexities inherent in comprehending the causation, dynamics, and interspecies transmission of RNA viruses within the investigated chicken population. Hence, chickens, even in the absence of discernible symptoms, can harbour viruses that may exhibit opportunistic, commensal, or pathogenic characteristics.
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Affiliation(s)
- Vivian C Nwokorogu
- Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Santhosh Pillai
- Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - James E San
- Nelson Mandela School of Medicine, KwaZulu-Natal Research Innovation and Sequencing platform unit, University of KwaZulu- Natal, 719 Umbilo Road, Durban, 4001, South Africa
| | - Charlene Pillay
- Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Martin M Nyaga
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa.
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Khan I, Bu R, Ali Z, Iqbal MS, Shi H, Ding L, Hong M. Metagenomics Analysis Reveals the Composition and Functional Differences of Fecal Microbiota in Wild, Farm, and Released Chinese Three-Keeled Pond Turtles ( Mauremys reevesii). Animals (Basel) 2024; 14:1750. [PMID: 38929370 PMCID: PMC11201187 DOI: 10.3390/ani14121750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
The intestine of living organisms harbors different microbiota associated with the biological functioning and health of the host and influences the process of ecological adaptation. Here, we studied the intestinal microbiota's composition and functional differences using 16S rRNA and metagenomic analysis in the wild, farm, and released Chinese three-keeled pond turtle (Mauremys reevesii). At the phylum level, Bacteroidota dominated, followed by Firmicutes, Fusobacteriota, and Actinobacteriota in the wild group, but Chloroflexi was more abundant in the farm and released groups. Moreover, Chryseobacterium, Acinetobacter, Comamonas, Sphingobacterium, and Rhodobacter were abundant in the released and farm cohorts, respectively. Cetobacterium, Paraclostridium, Lysobacter, and Leucobacter showed an abundance in the wild group. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed that the relative abundance of most pathways was significantly higher in the wild turtles (carbohydrate metabolism, lipid metabolism, metabolism of cofactors, and vitamins). The comprehensive antibiotic resistance database (CARD) showed that the antibiotic resistance gene (ARG) subtype macB was the most abundant in the farm turtle group, while tetA was higher in the wild turtles, and srpYmcr was higher in the released group. Our findings shed light on the association between the intestinal microbiota of M. reevesii and its habitats and could be useful for tracking habitats to protect and conserve this endangered species.
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Affiliation(s)
- Ijaz Khan
- Key Laboratory of Tropical Island Ecology, Ministry of Education, Hainan Key Laboratory of Tropical Animal and Plant Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China; (I.K.); (R.B.)
| | - Rongping Bu
- Key Laboratory of Tropical Island Ecology, Ministry of Education, Hainan Key Laboratory of Tropical Animal and Plant Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China; (I.K.); (R.B.)
- College of Marine Science, Guangxi Key Laboratory of Beibu Gulf Biodiversity Conservation, Beibu Gulf University, Qinzhou 535000, China
| | - Zeeshan Ali
- Key Laboratory of Tropical Island Ecology, Ministry of Education, Hainan Key Laboratory of Tropical Animal and Plant Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China; (I.K.); (R.B.)
| | - Muhammad Shahid Iqbal
- Key Laboratory of Tropical Island Ecology, Ministry of Education, Hainan Key Laboratory of Tropical Animal and Plant Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China; (I.K.); (R.B.)
| | - Haitao Shi
- Key Laboratory of Tropical Island Ecology, Ministry of Education, Hainan Key Laboratory of Tropical Animal and Plant Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China; (I.K.); (R.B.)
| | - Li Ding
- Key Laboratory of Tropical Island Ecology, Ministry of Education, Hainan Key Laboratory of Tropical Animal and Plant Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China; (I.K.); (R.B.)
| | - Meiling Hong
- Key Laboratory of Tropical Island Ecology, Ministry of Education, Hainan Key Laboratory of Tropical Animal and Plant Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China; (I.K.); (R.B.)
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Panyako PM, Ommeh SC, Kuria SN, Lichoti JK, Musina J, Nair V, Nene V, Munir M, Oyola SO. Metagenomic Characterization of Poultry Cloacal and Oropharyngeal Swabs in Kenya Reveals Bacterial Pathogens and Their Antimicrobial Resistance Genes. Int J Microbiol 2024; 2024:8054338. [PMID: 38374958 PMCID: PMC10876313 DOI: 10.1155/2024/8054338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 11/28/2023] [Accepted: 01/25/2024] [Indexed: 02/21/2024] Open
Abstract
Poultry enteric bacterial diseases are of significant economic importance because they are responsible for production losses due to weight loss, increased morbidity and mortality, and increased cost of production arising from poor feed conversion and treatment. This cross-sectional purposive study characterized enteric bacterial pathogens in poultry from selected agroclimatic regions in Kenya and investigated their antimicrobial resistance gene profiles. Cloacal (n = 563) and oropharyngeal (n = 394) swabs were collected and pooled into 16 and 14 samples, respectively, to characterize bacterial pathogens and their antimicrobial resistance gene profiles. We report that Proteobacteria, Chlamydiae, and Firmicutes are the most dominant phyla present in both cloacal and oropharyngeal swabs of the six poultry species studied, indicating the colonization of the poultry gut by many pathogenic bacteria. Using KEGG and COG databases, some pathways related to metabolism, genetic information, and cellular processing were detected. We also report the abundance of antimicrobial resistance genes that confer resistance to β-lactamases, aminoglycosides, and tetracycline in most of the poultry analyzed, raising concern about the dangers associated with continuous and inappropriate use of these antibiotics in poultry production. The antimicrobial resistance gene data generated in this study provides a valuable indicator of the use of antimicrobials in poultry in Kenya. The information generated is essential for managing bacterial diseases, especially in backyard poultry raised under scavenging conditions.
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Affiliation(s)
- Philip M. Panyako
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Sheila C. Ommeh
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Stephen N. Kuria
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Jacqueline K. Lichoti
- Directorate of Veterinary Services, State Department of Livestock, Ministry of Agriculture, Livestock and Fisheries, Nairobi, Kenya
| | - Johns Musina
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | | | - Vish Nene
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Muhammad Munir
- Department: Biomedical and Life Sciences, Lancaster University, Bailrigg, UK
| | - Samuel O. Oyola
- International Livestock Research Institute (ILRI), Nairobi, Kenya
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7
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Soundararajan S, Selvakumar J, Maria Joseph ZM, Gopinath Y, Saravanan V, Santhanam R. Investigating the modulatory effects of Moringa oleifera on the gut microbiota of chicken model through metagenomic approach. Front Vet Sci 2023; 10:1153769. [PMID: 37323848 PMCID: PMC10267347 DOI: 10.3389/fvets.2023.1153769] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/17/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction This study aimed to assess the effects of supplementing chicken feed with Moringa oleifera leaf powder, a phytobiotic, on the gastrointestinal microbiota. The objective was to examine the microbial changes induced by the supplementation. Methods A total of 40, one-day-old chickens were fed their basal diet for 42 days and then divided into two groups: SG1 (basal diet) and SG2 (basal diet + 10 g/kg Moringa oleifera leaf powder). Metagenomics analysis was conducted to analyze operational taxonomic units (OTUs), species annotation, and biodiversity. Additionally, 16S rRNA sequencing was performed for molecular characterization of isolated gut bacteria, identified as Enterococcus faecium. The isolated bacteria were tested for essential metabolites, demonstrating antibacterial, antioxidant, and anticancer activities. Results and discussion The analysis revealed variations in the microbial composition between the control group (SG1) and the M. oleifera-treated group (SG2). SG2 showed a 47% increase in Bacteroides and a 30% decrease in Firmicutes, Proteobacteria, Actinobacteria, and Tenericutes compared to SG1. TM7 bacteria were observed exclusively in the M. oleifera-treated group. These findings suggest that Moringa oleifera leaf powder acts as a modulator that enhances chicken gut microbiota, promoting the colonization of beneficial bacteria. PICRUSt analysis supported these findings, showing increased carbohydrate and lipid metabolism in the M.oleifera-treated gut microbiota. Conclusion This study indicates that supplementing chicken feed with Moringa oleifera leaf powder as a phytobiotic enhances the gut microbiota in chicken models, potentially improving overall health. The observed changes in bacterial composition, increased presence of Bacteroides, and exclusive presence of TM7 bacteria suggest a positive modulation of microbial balance. The essential metabolites from isolated Enterococcus faecium bacteria further support the potential benefits of Moringa oleifera supplementation.
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Affiliation(s)
- Sowmiya Soundararajan
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Affiliated With Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Jasmine Selvakumar
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Affiliated With Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Zion Mercy Maria Joseph
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Affiliated With Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Yuvapriya Gopinath
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Affiliated With Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Vaishali Saravanan
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Affiliated With Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Rameshkumar Santhanam
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
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8
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Chen Q, Wang Z, Shao D, Shi S. Effects of heat stress on the intestinal microorganisms in poultry and its nutritional regulations: a review. WORLD POULTRY SCI J 2022. [DOI: 10.1080/00439339.2022.2106344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Qingyi Chen
- Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou, China
- Huanan Agricultural University, Guangzhou, China
| | - Zhenxin Wang
- Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou, China
| | - Dan Shao
- Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou, China
| | - Shourong Shi
- Poultry Institute, Chinese Academy of Agricultural Science, Yangzhou, China
- Center of Effective Evaluation of Feed and Feed Additive (Poultry Institute) Ministry of Agriculture, Yangzhou, China
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Kang K, Zhou N, Peng W, Peng F, Ma M, Li L, Fu F, Xiang S, Zhang H, He X, Song Z. Multi-Omics Analysis of the Microbiome and Metabolome Reveals the Relationship Between the Gut Microbiota and Wooden Breast Myopathy in Broilers. Front Vet Sci 2022; 9:922516. [PMID: 35812872 PMCID: PMC9260154 DOI: 10.3389/fvets.2022.922516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/23/2022] [Indexed: 11/19/2022] Open
Abstract
Wooden breast (WB) is a widely prevalent myopathy in broiler chickens. However, the role of the gut microbiota in this myopathy remains largely unknown, in particular the regulatory effect of gut microbiota in the modulation of muscle metabolism. Totally, 300 1-day-old Arbor Acres broilers were raised until 49 days and euthanized, and the breast filets were classified as normal (NORM), mild (MILD), or severe wooden breast (SEV). Birds with WB comprised 27.02% of the individuals. Severe WB filets had a greater L* value, a* value, and dripping loss but a lower pH (P < 0.05). WB filets had abundant myofiber fragmentation, with a lower average myofiber caliber and more fibers with a diameter of <20 μm (P < 0.05). The diversity of the intestinal microflora was decreased in birds with severe WB, with decreases in Chao 1, and observed species indices. At the phylum level, birds with severe WB had a lower Firmicutes/Bacteroidetes ratio (P = 0.098) and a decreased abundance of Verrucomicrobia (P < 0.05). At the species level, gut microbiota were positively correlated with 131 digesta metabolites in pathways of glutamine and glutamate metabolism and arginine biosynthesis but were negatively correlated with 30 metabolites in the pathway of tyrosine metabolism. In plasma, WB induced five differentially expressed metabolites (DEMs), including anserine and choline, which were related to the severity of the WB lesion. The microbial-derived metabolites, including guanidoacetic acid, antiarol, and (2E)-decenoyl-ACP, which entered into plasma were related to meat quality traits and myofiber traits. In summary, WB filets differed in gut microbiota, digesta, and plasma metabolites. Gut microbiota respond to the wooden breast myopathy by driving dynamic changes in digesta metabolites that eventually enter the plasma.
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Affiliation(s)
- Kelang Kang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Ministry of Education Engineering Research Center of Feed Safety and Efficient Use, Changsha, China
| | - Nanxuan Zhou
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Ministry of Education Engineering Research Center of Feed Safety and Efficient Use, Changsha, China
| | - Weishi Peng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Ministry of Education Engineering Research Center of Feed Safety and Efficient Use, Changsha, China
| | - Fang Peng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Ministry of Education Engineering Research Center of Feed Safety and Efficient Use, Changsha, China
| | - Mengmeng Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Ministry of Education Engineering Research Center of Feed Safety and Efficient Use, Changsha, China
| | - Liwei Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Ministry of Education Engineering Research Center of Feed Safety and Efficient Use, Changsha, China
| | - Fuyi Fu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Ministry of Education Engineering Research Center of Feed Safety and Efficient Use, Changsha, China
| | - Shuhan Xiang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Ministry of Education Engineering Research Center of Feed Safety and Efficient Use, Changsha, China
| | - Haihan Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Ministry of Education Engineering Research Center of Feed Safety and Efficient Use, Changsha, China
- Hunan Engineering Research Center of Poultry Production Safety, Changsha, China
| | - Xi He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Ministry of Education Engineering Research Center of Feed Safety and Efficient Use, Changsha, China
- Hunan Engineering Research Center of Poultry Production Safety, Changsha, China
- Hunan Co-Innovation Center of Animal Production Safety, Changsha, China
| | - Zehe Song
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Ministry of Education Engineering Research Center of Feed Safety and Efficient Use, Changsha, China
- Hunan Engineering Research Center of Poultry Production Safety, Changsha, China
- Hunan Co-Innovation Center of Animal Production Safety, Changsha, China
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10
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Adenaike AS, Akpan U, Awopejo OO, Oloye OS, Alli-Balogun AO, Agbaje M, Ikeobi CON. Characterization of the cecal microbiome composition of Nigerian indigenous chickens. Trop Anim Health Prod 2022; 54:211. [PMID: 35687206 DOI: 10.1007/s11250-022-03191-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/30/2022] [Indexed: 02/07/2023]
Abstract
Poultry cecum microbes are dynamic and complex. They play important roles in disease prevention, detoxification of harmful substances, nutrient processing, and ingestion harvesting. It may be possible to increase poultry productivity by better understanding and controlling the microbial population. We analyzed the composition and function of Nigerian hens' cecal microbiota using high-throughput sequencing methods. Using high-throughput sequencing of the 16S rRNA genes (V1-V9) hypervariable regions, the cecal microbiota of three Nigerian indigenous chicken genotypes (Naked neck, Frizzle, and Normal feather) was described and compared. A total of two phyla were represented among the three genotypes (Firmicutes and Proteobacteria). Microbiological diversity was found in the community, with naked neck having the most evenness, followed by normal feather, which had the least. There were a lot of similarities between the naked neck and frizzle feather chicken groups when it came to genetic diversity between them. For example, the bacterial cecal microbiota of the naked neck chickens was more diverse, with a higher concentration of motility proteins, two-component systems, bacterial secretion systems, and the formation and breakdown of secondary metabolites. More understanding on gut microbiota roles and interactions will help Nigerian poultry farmers improve their methods and give valuable data for the study of bacteria in the chicken gut.
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Affiliation(s)
- A S Adenaike
- Department of Animal Breeding and Genetics, Federal University of Agriculture, P.M.B 2240, Alabata Road, Abeokuta, Ogun, Nigeria.
| | - U Akpan
- Department of Animal Breeding and Genetics, Federal University of Agriculture, P.M.B 2240, Alabata Road, Abeokuta, Ogun, Nigeria
| | - O O Awopejo
- Department of Animal Breeding and Genetics, Federal University of Agriculture, P.M.B 2240, Alabata Road, Abeokuta, Ogun, Nigeria
| | - O S Oloye
- Department of Animal Breeding and Genetics, Federal University of Agriculture, P.M.B 2240, Alabata Road, Abeokuta, Ogun, Nigeria
| | - A O Alli-Balogun
- Department of Animal Breeding and Genetics, Federal University of Agriculture, P.M.B 2240, Alabata Road, Abeokuta, Ogun, Nigeria
| | - M Agbaje
- Department of Veterinary Microbiology, Federal University of Agriculture, Abeokuta, Nigeria
| | - C O N Ikeobi
- Department of Animal Breeding and Genetics, Federal University of Agriculture, P.M.B 2240, Alabata Road, Abeokuta, Ogun, Nigeria
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11
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Zhang J, Geng X, Zhang Y, Zhao X, Zhang P, Sun G, Li W, Li D, Han R, Li G, Tian Y, Liu X, Kang X, Jiang R. Interaction Between Cecal Metabolites and Liver Lipid Metabolism Pathways During Induced Molting in Laying Hens. Front Physiol 2022; 13:862721. [PMID: 35677092 PMCID: PMC9169092 DOI: 10.3389/fphys.2022.862721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/23/2022] [Indexed: 11/23/2022] Open
Abstract
Moult is a normal physiological phenomenon in poultry. Induced molting (IM) is the most widely used and economical molting technique. By inducing moult, the laying hens can grow new feathers during the next laying cycle and improve laying performance. However, the lack of energy supply has a huge impact on both the liver and intestines and acts on the intestines and liver through the “gut-liver axis”. More importantly, lipid metabolism in the liver is closely related to the laying performance of laying hens. Therefore, in this study, cecal metabolites and liver transcriptome data during IM of laying hens at the late stage of laying (stop feeding method) were analyzed together to reveal the regulatory mechanism of “gut-liver axis” affecting the laying performance of laying hens from the perspective of lipid metabolism. Transcriptome analysis revealed that 4,796 genes were obtained, among which 2,784 genes had significant differences (p < 0.05). Forty-nine genes were associated with lipid metabolism, and five core genes (AGPAT2, SGPL1, SPTLC1, PISD, and CYP51A1) were identified by WGCNA. Most of these differential genes are enriched in steroid biosynthesis, cholesterol metabolism, drug metabolism—cytochrome P450, synthesis and degradation of ketone bodies, PPAR signaling pathway, and bile secretion. A total of 96 differential metabolites were obtained by correlating them with metabolome data. Induced moult affects laying performance by regulating genes related to lipid metabolism, and the cecal metabolites associated with these genes are likely to regulate the expression of these genes through the “enterohepatic circulation”. This experiment enriched the theoretical basis of induced moult and provided the basis for prolonging the feeding cycle of laying hens.
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Affiliation(s)
- Jun Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Xiaoqing Geng
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Yihui Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Xinlong Zhao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Pengwei Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Guirong Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Wenting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Donghua Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Ruirui Jiang,
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12
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Kogut MH. Role of diet-microbiota interactions in precision nutrition of the chicken: facts, gaps, and new concepts. Poult Sci 2022; 101:101673. [PMID: 35104729 PMCID: PMC8814386 DOI: 10.1016/j.psj.2021.101673] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022] Open
Abstract
In the intestine, host-derived factors are genetically hardwired and difficult to modulate. However, the intestinal microbiome is more plastic and can be readily modulated by dietary factors. Further, it is becoming more apparent that the microbiome can potentially impact poultry physiology by participating in digestion, the absorption of nutrients, shaping of the mucosal immune response, energy homeostasis, and the synthesis or modulation of several potential bioactive metabolites. These activities are dependent on the quantity and quality of the microbiota alongside its metabolic potential, which are dictated in large part by diet. Thus, diet-induced microbiota alterations may be harnessed to induce changes in host physiology, including disease development and progression. In this regard, the gut microbiome is malleable and renders the gut microbiome a candidate 'organ' for the possibility of precision nutrition to induce precision microbiomics-the use of the gut microbiome as a biomarker to predict responsiveness to specific dietary constituents to generate precision diets and interventions for optimal poultry performance and health. However, it is vital to identify the causal relationships and mechanisms by which dietary components and additives affect the gut microbiome which then ultimately influence avian physiology. Further, an improved understanding of the spatial and functional relationships between the different sections of the avian gut and their regional microbiota will provide a better understanding of the role of the diet in regulating the intestinal microbiome.
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Affiliation(s)
- Michael H Kogut
- Southern Plains Agricultural Research Center, USDA-ARS, College Station, TX 77845, USA.
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13
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Zhang B, Liu N, Hao M, Zhou J, Xie Y, He Z. Plant-Derived Polysaccharides Regulated Immune Status, Gut Health and Microbiota of Broilers: A Review. Front Vet Sci 2022; 8:791371. [PMID: 35155646 PMCID: PMC8831899 DOI: 10.3389/fvets.2021.791371] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/06/2021] [Indexed: 12/22/2022] Open
Abstract
In modern intensive breeding system, broilers are exposed to various challenges, such as diet changes and pathological environment, which may cause the increase in the incidence rate and even death. It is necessary to take measures to prevent diseases and maintain optimal health and productivity of broilers. With the forbidden use of antibiotics in animal feed, polysaccharides from plants have attracted much attention owing to their lower toxicity, lower drug resistance, fewer side effects, and broad-spectrum antibacterial activity. It had been demonstrated that polysaccharides derived from plant exerted various functions, such as growth promotion, anti-inflammation, maintaining the integrity of intestinal mucosa, and regulation of intestinal microbiota. Therefore, the current review aimed to provide an overview of the recent advances in the impacts of plant-derived polysaccharides on anti-inflammation, gut health, and intestinal microbiota community of broilers in order to provide a reference for further study on maintaining the integrity of intestinal structure and function, and the related mechanism involved in the polysaccharide administration intervention.
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14
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Horizontal Gene Transfer Is the Main Driver of Antimicrobial Resistance in Broiler Chicks Infected with Salmonella enterica Serovar Heidelberg. mSystems 2021; 6:e0072921. [PMID: 34427525 PMCID: PMC8409728 DOI: 10.1128/msystems.00729-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The overuse and misuse of antibiotics in clinical settings and in food production have been linked to the increased prevalence and spread of antimicrobial resistance (AR). Consequently, public health and consumer concerns have resulted in a remarkable reduction in antibiotics used for food animal production. However, there are no data on the effectiveness of antibiotic removal in reducing AR shared through horizontal gene transfer (HGT). In this study, we used neonatal broiler chicks and Salmonella enterica serovar Heidelberg, a model food pathogen, to test if chicks raised antibiotic free harbor transferable AR. We challenged chicks with an antibiotic-susceptible S. Heidelberg strain using various routes of inoculation and determined if S. Heidelberg isolates recovered carried plasmids conferring AR. We used antimicrobial susceptibility testing and whole-genome sequencing (WGS) to show that chicks grown without antibiotics harbored an antimicrobial resistant S. Heidelberg population at 14 days after challenge and chicks challenged orally acquired AR at a higher rate than chicks inoculated via the cloaca. Using 16S rRNA gene sequencing, we found that S. Heidelberg infection perturbed the microbiota of broiler chicks, and we used metagenomics and WGS to confirm that a commensal Escherichia coli population was the main reservoir of an IncI1 plasmid acquired by S. Heidelberg. The carriage of this IncI1 plasmid posed no fitness cost to S. Heidelberg but increased its fitness when exposed to acidic pH in vitro. These results suggest that HGT of plasmids carrying AR shaped the evolution of S. Heidelberg and that antibiotic use reduction alone is insufficient to limit antibiotic resistance transfer from commensal bacteria to Salmonella enterica. IMPORTANCE The reported increase in antibiotic-resistant bacteria in humans has resulted in a major shift away from antibiotic use in food animal production. This shift has been driven by the assumption that removing antibiotics will select for antibiotic susceptible bacterial taxa, which in turn will allow the currently available antibiotic arsenal to be more effective. This change in practice has highlighted new questions that need to be answered to assess the effectiveness of antibiotic removal in reducing the spread of antibiotic resistance bacteria. This research demonstrates that antibiotic-susceptible Salmonella enterica serovar Heidelberg strains can acquire multidrug resistance from commensal bacteria present in the gut of neonatal broiler chicks, even in the absence of antibiotic selection. We demonstrate that exposure to acidic pH drove the horizontal transfer of antimicrobial resistance plasmids and suggest that simply removing antibiotics from food animal production might not be sufficient to limit the spread of antimicrobial resistance.
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