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Horyanto D, Bajagai YS, von Hellens J, Chen X, Van TTH, Dunlop MW, Stanley D. The Association between Broiler Litter Microbiota and the Supplementation of Bacillus Probiotics in a Leaky Gut Model. Animals (Basel) 2024; 14:1758. [PMID: 38929376 PMCID: PMC11200599 DOI: 10.3390/ani14121758] [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: 05/27/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Probiotics provided from hatch have a major influence on microbiota development, and together with environmental and bedding microbiota, shape the microbial community of the litter. We investigated the influence of probiotic supplementation and a leaky gut challenge induced using dexamethasone (DEX) on the litter microbial community and litter parameters. The probiotic product was a mix of three Bacillus amyloliquefaciens strains. The litter microbiota were compared to the microbial communities from other gut sections. The litter samples had higher microbial diversity compared to the caecum, gizzard, jejunum, and jejunal mucosa. The high similarity between the litter phylum-level microbiota and gizzard microbiota detected in our study could be a consequence of ingested feed and litter passing through the gizzard. Moreover, the litter microbial community is fundamentally distinct from the intestinal microbiota, as evidenced by the number of genera present in the litter but absent from all the intestinal sections and vice versa. Furthermore, LEfSe analysis identified distinct microbial taxa across different groups, with specific genera associated with different treatments. In terms of litter quality, the birds in the DEX groups had a significantly higher moisture content, indicating successful leaky gut challenge, while probiotic supplementation did not significantly affect the moisture levels. These findings provide comprehensive insights into the distinct microbiota characteristics of litter.
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Affiliation(s)
- Darwin Horyanto
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD 4701, Australia; (D.H.); (Y.S.B.)
- Bioproton Pty Ltd., Brisbane, QLD 4110, Australia; (J.v.H.)
| | - Yadav S. Bajagai
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD 4701, Australia; (D.H.); (Y.S.B.)
| | | | - Xiaojing Chen
- Bioproton Pty Ltd., Brisbane, QLD 4110, Australia; (J.v.H.)
| | - Thi Thu Hao Van
- School of Science, RMIT University, Melbourne, VIC 3083, Australia;
| | - Mark W. Dunlop
- Department of Agriculture and Fisheries, Queensland Government, Toowoomba, QLD 4350, Australia;
| | - Dragana Stanley
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD 4701, Australia; (D.H.); (Y.S.B.)
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Campos PM, Miska KB, Jenkins MC, Yan X, Proszkowiec-Weglarz M. Effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the cecum and ileum in broiler chickens. Sci Rep 2024; 14:10702. [PMID: 38729976 PMCID: PMC11087572 DOI: 10.1038/s41598-024-61299-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/02/2024] [Indexed: 05/12/2024] Open
Abstract
Coccidiosis, an intestinal disease caused by Eimeria parasites, is responsible for major losses in the poultry industry by impacting chicken health. The gut microbiota is associated with health factors, such as nutrient exchange and immune system modulation, requiring understanding on the effects of Eimeria infection on the gut microbiota. This study aimed to determine the effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the cecum (CeL and CeM) and ileum (IlL and IlM) at multiple time points (days 3, 5, 7, 10, and 14) post-infection. E. acervulina infection decreased evenness in CeL microbiota at day 10, increased richness in CeM microbiota at day 3 before decreasing richness at day 14, and decreased richness in IlL microbiota from day 3 to 10. CeL, CeM, and IlL microbiota differed between infected and control birds based on beta diversity at varying time points. Infection reduced relative abundance of bacterial taxa and some predicted metabolic pathways known for short-chain fatty acid production in CeL, CeM, and IlL microbiota, but further understanding of metabolic function is required. Despite E. acervulina primarily targeting the duodenum, our findings demonstrate the infection can impact bacterial diversity and abundance in the cecal and ileal microbiota.
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Affiliation(s)
- Philip M Campos
- Oak Ridge Institute for Science and Education (ORISE), USDA-ARS Research Participation Program, Oak Ridge, TN, USA
- USDA-ARS, NEA Bioinformatics, Beltsville, MD, USA
- USDA-ARS, NEA, Beltsville Agricultural Research Center, Animal Biosciences and Biotechnology Laboratory, 10300 Baltimore Avenue, B-307, Rm. 335, BARC-East, Beltsville, MD, 20705, USA
| | - Katarzyna B Miska
- USDA-ARS, NEA, Beltsville Agricultural Research Center, Animal Biosciences and Biotechnology Laboratory, 10300 Baltimore Avenue, B-307, Rm. 335, BARC-East, Beltsville, MD, 20705, USA
| | - Mark C Jenkins
- USDA-ARS, NEA, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD, USA
| | - Xianghe Yan
- USDA-ARS, NEA, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, MD, USA
| | - Monika Proszkowiec-Weglarz
- USDA-ARS, NEA, Beltsville Agricultural Research Center, Animal Biosciences and Biotechnology Laboratory, 10300 Baltimore Avenue, B-307, Rm. 335, BARC-East, Beltsville, MD, 20705, USA.
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Pires PGS, Oliveira GS, McManus C, Santos VM, Moraes PO. Impact of housing system on intestinal microbiota of laying hens - A systematic review. Res Vet Sci 2024; 170:105184. [PMID: 38382220 DOI: 10.1016/j.rvsc.2024.105184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 02/07/2024] [Accepted: 02/11/2024] [Indexed: 02/23/2024]
Abstract
Studies on the housing system's impact on laying hens' intestinal microbiota were retrieved from the Web of Science, PubMed, and Scopus (between 2017 and 2022). Inclusion criteria were studies that discussed measurable effects related to the topic written in English, Portuguese, and Spanish. Of 3281 articles in the identification stage, 12 studies were used in the systematic review. Asia developed most research relating to the subject. Most studies compared the intestinal microbiota of laying hens from conventional cages versus Cage-Free or Free-Range. However, no study has evaluated the intestinal microbiota of laying hens maintained in an organic system. Greengene and Silva were the most used reference in the studies. According to the results observed in the studies included in the systematic review, there is greater alpha diversity in the alternative system and a high dissimilarity between the conventional and alternative systems. Exposure to environmental factors such as soil, vegetation, natural lighting, access to pastures, and ingesting fibrous foods can lead to changes in the intestinal microbiota. A brief outline of published scientific evidence demonstrates that the housing system can change the gut microbiome of hens. This study summarises the relationship between the housing system and the intestinal microbiome of laying hens and provides a roadmap for future research regarding the gut microbiome of hens.
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Affiliation(s)
- P G S Pires
- Instituto Federal Catarinense, Campus Concórdia, SC, Brazil.
| | - G S Oliveira
- Faculty of Agronomy and Veterinary Medicine, University of Brasília, Brasília, Brazil
| | - C McManus
- Faculty of Agronomy and Veterinary Medicine, University of Brasília, Brasília, Brazil
| | - V M Santos
- Laboratory of Poultry Science, Federal Institute of Brasília - Campus Planaltina, Brasília, Brazil
| | - P O Moraes
- Department of Animal Sciences and Rural Development, Universidade Federal de Santa Catarina - Campus Florianópolis, SC, Brazil
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Zheng L, Han Z, Zhang J, Kang J, Li C, Pang Q, Liu S. Lactiplantibacillus plantarum and Saccharomyces cerevisiae-Fermented Coconut Water Alleviates Dextran Sodium Sulfate-Induced Enteritis in Wenchang Chicken: A Gut Microbiota and Metabolomic Approach. Animals (Basel) 2024; 14:575. [PMID: 38396543 PMCID: PMC10886277 DOI: 10.3390/ani14040575] [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: 12/12/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
In order to investigate the potential mechanisms of probiotic-fermented coconut water in treating enteritis, this study conducted a comprehensive analysis of the effects of probiotic intervention on the recovery from Dextran Sodium Sulfate-induced acute enteritis in Wenchang chicks. The analysis encompassed the assessment of growth performance, serum indicators, intestinal tissue structure, and metagenomic and metabolomic profiles of cecal contents in 60 Wenchang chicks subjected to intervention. This approach aimed to elucidate the impact of probiotic intervention on the recovery process from acute enteritis at both the genetic and metabolic levels in the avian model. The results revealed that intervention with Saccharomyces cerevisiae Y301 improved the growth rate of chicks. and intervention with Lactiplantibacillus plantarum MS2c regulated the glycerophospholipid metabolism pathway and reshaped the gut microbiota structure in modeling chicks with acute enteritis, reducing the abundance of potentially pathogenic bacteria from the Alistipes and increasing the abundance of potentially beneficial species from the Christensenellaceae. This intervention resulted in the production of specific gut metabolites, including Gentamicin C and polymyxin B2, recognized for their therapeutic effects on acute enteritis. The combined intervention of S. cerevisiae Y301 and L. plantarum MS2c not only enhanced growth performance but also mitigated intestinal wall damage and increased the abundance of gut metabolites such as gentamicin C and polymyxin B2, thereby mitigating symptoms of enteritis. Furthermore, this combined intervention reduced the levels of serum immune markers, including IL-10, IL-6, TNF-α, IFN-γ, and D-lactic acid, thus mitigating intestinal epithelial cell damage and promoting acute enteritis recovery. This study provides crucial insights into the mechanisms of action of probiotics and probiotic-fermented coconut water in acute enteritis recovery, offering new perspectives for sustainable farming practices for Wenchang chicken.
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Affiliation(s)
- Leijie Zheng
- School of Food Science and Engineering, Hainan University, Haikou 570228, China; (L.Z.)
| | - Zhe Han
- School of Food Science and Engineering, Hainan University, Haikou 570228, China; (L.Z.)
| | - Jiachao Zhang
- School of Food Science and Engineering, Hainan University, Haikou 570228, China; (L.Z.)
| | - Jiamu Kang
- School of Food Science and Engineering, Hainan University, Haikou 570228, China; (L.Z.)
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou 570228, China
| | - Congfa Li
- School of Food Science and Engineering, Hainan University, Haikou 570228, China; (L.Z.)
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou 570228, China
- Key Laboratory of Tropical Agricultural Products Processing Technology of Haikou City, Haikou 570228, China
| | - Qing Pang
- School of Food Science and Engineering, Hainan University, Haikou 570228, China; (L.Z.)
| | - Sixin Liu
- School of Food Science and Engineering, Hainan University, Haikou 570228, China; (L.Z.)
- Key Laboratory of Tropical Agricultural Products Processing Technology of Haikou City, Haikou 570228, China
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Zou X, Nakura Y, Kawaguchi H, Nishiumi F, Wu HN, Yanagihara I. Comparison of databases useful for the analysis of vaginal microbiota in Japanese women using next-generation sequencing data (QIIME 2 software). J Appl Microbiol 2023; 134:lxad283. [PMID: 38012110 DOI: 10.1093/jambio/lxad283] [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: 05/31/2023] [Revised: 11/17/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
AIMS Approximately 10% of children are born prematurely, and bacterial vaginosis during pregnancy is associated with preterm delivery. Highly accurate species-level vaginal microflora analysis helps control bacteria-induced preterm birth. Therefore, we aimed to conduct a bioinformatic analysis of gene sequences using 16S databases and compare their efficacy in comprehensively identifying potentially pathogenic vaginal microbiota in Japanese women. METHODS AND RESULTS The 16 s rRNA databases, Silva, Greengenes, and the basic local alignment search tool (BLAST) were compared to determine whether the classification quality could be improved using the V3-V4 region next-generation sequencing (NGS) sequences. It was found that NGS data were aligned using the BLAST database with the QIIME 2 platform, whose classification quality was higher than that of Silva, and the combined Silva and Greengenes databases based on the mutual complementarity of the two databases. CONCLUSIONS The reference database selected during the bioinformatic processing influenced the recognized sequence percentage, taxonomic rankings, and accuracy. This study showed that the BLAST database was the best choice for NGS data analysis of Japanese women's vaginal microbiota.
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Affiliation(s)
- Xianya Zou
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan
- Department of Pediatric and Neonatal-Perinatal Research, Graduate School of Medicine, Osaka University, 1-1 Yamadaoka, Suita City, Osaka 565-0871, Japan
| | - Yukiko Nakura
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan
| | - Haruna Kawaguchi
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan
- Department of Obstetrics, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan
| | - Fumiko Nishiumi
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan
| | - Heng Ning Wu
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan
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Dai X, Han YX, Shen QY, Tang H, Cheng LZ, Yang FP, Wei WH, Yang SM. Effect of Food Restriction on Food Grinding in Brandt's Voles. Animals (Basel) 2023; 13:3424. [PMID: 37958179 PMCID: PMC10647212 DOI: 10.3390/ani13213424] [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: 09/02/2023] [Revised: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023] Open
Abstract
Food grinding is supposed to be influenced by multiple factors. However, how those factors affecting this behavior remain unclear. In this study, we investigated the effect of food restriction on food grinding in Brandt's voles (Lasiopodomys brandtii), as well as the potential role of the gut microbiota in this process, through a comparison of the variations between voles with different food supplies. Food restriction reduced the relative amount of ground food to a greater extent than it lowered the relative food consumption, and altered the abundance of Staphylococcus, Aerococcus, Jeotgalicoccus, and Un--s-Clostridiaceae bacterium GM1. Fecal acetate content for the 7.5 g-food supply group was lower than that for the 15 g-food supply group. Our study indicated that food restriction could effectively inhibit food grinding. Further, Un--s-Clostridiaceae bacterium GM1 abundance, Aerococcus abundance, and acetate content were strongly related to food grinding. Variations in gut microbial abundance and short-chain fatty acid content induced by food restriction likely promote the inhibition of food grinding. These results could potentially provide guidance for reducing food waste during laboratory rodent maintenance.
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Affiliation(s)
- Xin Dai
- College of Bioscience and Biotechnology, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China; (X.D.); (Y.-X.H.); (Q.-Y.S.); (H.T.); (L.-Z.C.); (F.-P.Y.); (W.-H.W.)
| | - Yu-Xuan Han
- College of Bioscience and Biotechnology, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China; (X.D.); (Y.-X.H.); (Q.-Y.S.); (H.T.); (L.-Z.C.); (F.-P.Y.); (W.-H.W.)
| | - Qiu-Yi Shen
- College of Bioscience and Biotechnology, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China; (X.D.); (Y.-X.H.); (Q.-Y.S.); (H.T.); (L.-Z.C.); (F.-P.Y.); (W.-H.W.)
| | - Hao Tang
- College of Bioscience and Biotechnology, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China; (X.D.); (Y.-X.H.); (Q.-Y.S.); (H.T.); (L.-Z.C.); (F.-P.Y.); (W.-H.W.)
| | - Li-Zhi Cheng
- College of Bioscience and Biotechnology, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China; (X.D.); (Y.-X.H.); (Q.-Y.S.); (H.T.); (L.-Z.C.); (F.-P.Y.); (W.-H.W.)
| | - Feng-Ping Yang
- College of Bioscience and Biotechnology, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China; (X.D.); (Y.-X.H.); (Q.-Y.S.); (H.T.); (L.-Z.C.); (F.-P.Y.); (W.-H.W.)
| | - Wan-Hong Wei
- College of Bioscience and Biotechnology, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China; (X.D.); (Y.-X.H.); (Q.-Y.S.); (H.T.); (L.-Z.C.); (F.-P.Y.); (W.-H.W.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Sheng-Mei Yang
- College of Bioscience and Biotechnology, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China; (X.D.); (Y.-X.H.); (Q.-Y.S.); (H.T.); (L.-Z.C.); (F.-P.Y.); (W.-H.W.)
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Lorenzo-Rebenaque L, Casto-Rebollo C, Diretto G, Frusciante S, Rodríguez JC, Ventero MP, Molina-Pardines C, Vega S, Marin C, Marco-Jiménez F. Modulation of Caecal Microbiota and Metabolome Profile in Salmonella-Infected Broilers by Phage Therapy. Int J Mol Sci 2023; 24:15201. [PMID: 37894882 PMCID: PMC10607084 DOI: 10.3390/ijms242015201] [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: 09/20/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Bacteriophage therapy is considered one of the most promising tools to control zoonotic bacteria, such as Salmonella, in broiler production. Phages exhibit high specificity for their targeted bacterial hosts, causing minimal disruption to the niche microbiota. However, data on the gut environment's response to phage therapy in poultry are limited. This study investigated the influence of Salmonella phage on host physiology through caecal microbiota and metabolome modulation using high-throughput 16S rRNA gene sequencing and an untargeted metabolomics approach. We employed 24 caecum content samples and 24 blood serum samples from 4-, 5- and 6-week-old broilers from a previous study where Salmonella phages were administered via feed in Salmonella-infected broilers, which were individually weighed weekly. Phage therapy did not affect the alpha or beta diversity of the microbiota. Specifically, we observed changes in the relative abundance of 14 out of the 110 genera using the PLS-DA and Bayes approaches. On the other hand, we noted changes in the caecal metabolites (63 up-accumulated and 37 down-accumulated out of the 1113 caecal metabolites). Nevertheless, the minimal changes in blood serum suggest a non-significant physiological response. The application of Salmonella phages under production conditions modulates the caecal microbiome and metabolome profiles in broilers without impacting the host physiology in terms of growth performance.
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Affiliation(s)
- Laura Lorenzo-Rebenaque
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (L.L.-R.); (S.V.); (C.M.)
| | - Cristina Casto-Rebollo
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain;
| | - Gianfranco Diretto
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Biotechnology Laboratory, Centro Ricerche Casaccia, Via Anguillarese, 301, Santa Maria di Galeria, 00123 Rome, Italy; (G.D.); (S.F.)
| | - Sarah Frusciante
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Biotechnology Laboratory, Centro Ricerche Casaccia, Via Anguillarese, 301, Santa Maria di Galeria, 00123 Rome, Italy; (G.D.); (S.F.)
| | - Juan Carlos Rodríguez
- Microbiology Department, Dr. Balmis University General Hospital, Microbiology Division, Miguel Hernández University, ISABIAL, 03010 Alicante, Spain;
| | - María-Paz Ventero
- Microbiology Department, Dr. Balmis University General Hospital, ISABIAL, 03010 Alicante, Spain; (M.-P.V.); (C.M.-P.)
| | - Carmen Molina-Pardines
- Microbiology Department, Dr. Balmis University General Hospital, ISABIAL, 03010 Alicante, Spain; (M.-P.V.); (C.M.-P.)
| | - Santiago Vega
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (L.L.-R.); (S.V.); (C.M.)
| | - Clara Marin
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (L.L.-R.); (S.V.); (C.M.)
| | - Francisco Marco-Jiménez
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain;
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Nayman EI, Schwartz BA, Polanco FC, Firek AK, Gumabong AC, Hofstee NJ, Narasimhan G, Cickovski T, Mathee K. Microbiome depiction through user-adapted bioinformatic pipelines and parameters. J Med Microbiol 2023; 72. [PMID: 37823280 DOI: 10.1099/jmm.0.001756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Introduction. The role of the microbiome in health and disease continues to be increasingly recognized. However, there is significant variability in the bioinformatic protocols for analysing genomic data. This, in part, has impeded the potential incorporation of microbiomics into the clinical setting and has challenged interstudy reproducibility. In microbial compositional analysis, there is a growing recognition for the need to move away from a one-size-fits-all approach to data processing.Gap Statement. Few evidence-based recommendations exist for setting parameters of programs that infer microbiota community profiles despite these parameters significantly impacting the accuracy of taxonomic inference.Aim. To compare three commonly used programs (DADA2, QIIME2, and mothur) and optimize them into four user-adapted pipelines for processing paired-end amplicon reads. We aim to increase the accuracy of compositional inference and help standardize microbiomic protocol.Methods. Two key parameters were isolated across four pipelines: filtering sequence reads based on a whole-number error threshold (maxEE) and truncating read ends based on a quality score threshold (QTrim). Closeness of sample inference was then evaluated using a mock community of known composition.Results. We observed that raw genomic data lost were proportionate to how stringently parameters were set. Exactly how much data were lost varied by pipeline. Accuracy of sample inference correlated with increased sequence read retention. Falsely detected taxa and unaccounted for microbial constituents were unique to pipeline and parameter. Implementation of optimized parameter values led to better approximation of the known mock community.Conclusions. Microbial compositions generated based on the 16S rRNA marker gene should be interpreted with caution. To improve microbial community profiling, bioinformatic protocols must be user-adapted. Analysis should be performed with consideration for the select target amplicon, pipelines and parameters used, and taxa of interest.
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Affiliation(s)
- Eric I Nayman
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Brooke A Schwartz
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Fantaysia C Polanco
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Alexandra K Firek
- Translational Glycobiology Institute, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Alayna C Gumabong
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Nolan J Hofstee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Giri Narasimhan
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Trevor Cickovski
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Kalai Mathee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
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Pietruska A, Bortoluzzi C, Hauck R. A meta-analysis of the effect of Eimeria spp. and/or Clostridium perfringens infection on the microbiota of broiler chickens. Poult Sci 2023; 102:102652. [PMID: 37019075 PMCID: PMC10106964 DOI: 10.1016/j.psj.2023.102652] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023] Open
Abstract
Coccidiosis in chickens is caused by Eimeria spp. The infection provides a growth advantage to Clostridium perfringens (CP), frequently leading to necrotic enteritis. One approach to alleviate the negative impacts of the diseases is to improve the bacterial composition in chickens, and many experiments investigating chicken enteric health in recent years include the characterization of the bacterial microbiota. This meta-analysis synthesized the data of studies investigating the intestinal microbiota after infection with coccidia and/or CP to provide a basis for future research. Inclusion criteria were that experiments contained a group infected with one or both pathogens and an uninfected control group, the use of 16SrRNA Illumina sequencing and the availability of raw data. A total of 17 studies could be included. Meta-analyses of 3 different data sets were performed: 1 on data of 9 experiments on chickens infected with coccidia only; the second on data of 4 studies on chickens infected with CP only; the third on raw data of 8 experiments with chickens infected with coccidia and CP. The meta-analysis of relative abundance and alpha diversity of the data sets was performed in R using the SIAMCAT and metafor packages. The number of families of interest identified by the analyses of experiments with infection with coccidia only, CP only and the combined infection were 23, 2, and 29, respectively. There was an overlap of 13 families identified by analyses of experiments with infection with coccidia only and of experiments with the combined infections. Machine learning was not able to find a model to predict changes of the microbiota in either 1 of the 3 analyses. Meta-analyses of functional profiles showed a more uniform reaction to the infections with the relative abundance of many pathways significantly altered. Alpha diversity was not affected by infection with either pathogen or the combination. In conclusion, the heterogeneity of these microbiota studies makes recognizing common trends difficult, although it seems that coccidia infection affects the microbiota more than an infection with CP. Future studies should focus on the bacterial functions that are changed due to these infections using metagenome techniques.
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Campos PM, Miska KB, Jenkins MC, Yan X, Proszkowiec-Weglarz M. Effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the duodenum and jejunum in broiler chickens. Front Microbiol 2023; 14:1147579. [PMID: 37020716 PMCID: PMC10067739 DOI: 10.3389/fmicb.2023.1147579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/27/2023] [Indexed: 04/07/2023] Open
Abstract
The intestinal disease coccidiosis, caused by Eimeria parasites, impacts nutrient absorption in broiler chickens, leading to weight gain depression and major losses in the poultry industry. To develop alternatives to antibiotics for treating infected chickens, the gut microbiota has been researched because of its association with health factors such as nutrient exchange, immune system modulation, digestive system physiology, and pathogen exclusion. The aim of this study was to determine the effect of Eimeria acervulina infection on the luminal and mucosal microbiota of both the duodenum (DuoL and DuoM) and jejunum (JejL and JejM) at multiple time points (days 3, 5, 7, 10, and 14) post-infection. 16S rRNA amplicon sequencing was utilized to characterize the microbiota and analyze differences in alpha and beta diversity between infected (IF) and control (C) birds at each time point. Alpha diversity differed between IF and C birds in DuoM and JejM microbiota. Combined with beta diversity results, DuoM microbiota appeared to be affected by infection in the longer-term, while JejM microbiota were affected in the shorter-term. Relative abundances of bacterial taxa known for short-chain fatty acid (SCFA) production, such as Lachnospiraceae, Subdoligranulum, and Peptostreptococcaceae, tended to be lower in IF birds for all four microbiota. Moreover, predicted functional abundances showed MetaCyc pathways related to SCFA production, especially butyrate, may be influenced by these differences in bacterial relative abundance. Our findings expand understanding of how Eimeria infection affects luminal and mucosal microbiota in the duodenum and jejunum, and further research on metagenomic function may provide insights on the degree of influence duodenal and jejunal bacteria have on chicken health.
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Affiliation(s)
- Philip M. Campos
- USDA-ARS Research Participation Program, Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, United States
- USDA-ARS, NEA Bioinformatics, Statistics Group, Beltsville, MD, United States
- Animal Biosciences and Biotechnology Laboratory, USDA-ARS, NEA, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Katarzyna B. Miska
- Animal Biosciences and Biotechnology Laboratory, USDA-ARS, NEA, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Mark C. Jenkins
- Animal Parasitic Diseases Laboratory, USDA-ARS, NEA, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Xianghe Yan
- Environmental Microbial and Food Safety Laboratory, USDA-ARS, NEA, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Monika Proszkowiec-Weglarz
- Animal Biosciences and Biotechnology Laboratory, USDA-ARS, NEA, Beltsville Agricultural Research Center, Beltsville, MD, United States
- *Correspondence: Monika Proszkowiec-Weglarz,
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Lorenzo-Rebenaque L, Casto-Rebollo C, Diretto G, Frusciante S, Rodríguez JC, Ventero MP, Molina-Pardines C, Vega S, Marin C, Marco-Jiménez F. Examining the effects of Salmonella phage on the caecal microbiota and metabolome features in Salmonella-free broilers. Front Genet 2022; 13:1060713. [PMID: 36437955 PMCID: PMC9691336 DOI: 10.3389/fgene.2022.1060713] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 10/29/2023] Open
Abstract
Bacteriophages selectively infect and kill their target bacterial host, being a promising approach to controlling zoonotic bacteria in poultry production. To ensure confidence in its use, fundamental questions of safety and toxicity monitoring of phage therapy should be raised. Due to its high specificity, a minimal impact on the gut ecology is expected; however, more in-depth research into key parameters that influence the success of phage interventions has been needed to reach a consensus on the impact of bacteriophage therapy in the gut. In this context, this study aimed to investigate the interaction of phages with animals; more specifically, we compared the caecum microbiome and metabolome after a Salmonella phage challenge in Salmonella-free broilers, evaluating the role of the phage administration route. To this end, we employed 45 caecum content samples from a previous study where Salmonella phages were administered via drinking water or feed for 24 h from 4, 5 to 6-weeks-old broilers. High-throughput 16S rRNA gene sequencing showed a high level of similarity (beta diversity) but revealed a significant change in alpha diversity between broilers with Salmonella-phage administered in the drinking water and control. Our results showed that the phages affected only a few genera of the microbiota's structure, regardless of the administration route. Among these, we found a significant increase in Streptococcus and Sellimonas in the drinking water and Lactobacillus, Anaeroplasma and Clostridia_vadinBB60_group in the feed. Nevertheless, the LC-HRMS-based metabolomics analyses revealed that despite few genera were significantly affected, a substantial number of metabolites, especially in the phage administered in the drinking water were significantly altered (64 and 14 in the drinking water and feed groups, respectively). Overall, our study shows that preventive therapy with bacteriophages minimally alters the caecal microbiota but significantly impacts their metabolites, regardless of the route of administration.
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Affiliation(s)
- Laura Lorenzo-Rebenaque
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Valencia, Spain
| | - Cristina Casto-Rebollo
- Institute of Science and Animal Technology, Universitat Politècnica de València, Valencia, Spain
| | - Gianfranco Diretto
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Biotechnology Laboratory, Centro Ricerche Casaccia, Santa Maria di Galeria, Rome, Italy
| | - Sarah Frusciante
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Biotechnology Laboratory, Centro Ricerche Casaccia, Santa Maria di Galeria, Rome, Italy
| | - Juan Carlos Rodríguez
- Microbiology Department, Balmis General University Hospital, Microbiology Division, Miguel Hernández University, ISABIAL, Alicante, Spain
| | - María-Paz Ventero
- Microbiology Department, Balmis General University Hospital, ISABIAL, Alicante, Spain
| | | | - Santiago Vega
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Valencia, Spain
| | - Clara Marin
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Valencia, Spain
| | - Francisco Marco-Jiménez
- Institute of Science and Animal Technology, Universitat Politècnica de València, Valencia, Spain
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