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Hayashi M, Yonetamari J, Muto Y, Tanaka K. Complete genome sequence of Peptostreptococcus porci isolated from porcine endocarditis in Japan. Microbiol Resour Announc 2024:e0020124. [PMID: 38842319 DOI: 10.1128/mra.00201-24] [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: 02/29/2024] [Accepted: 05/09/2024] [Indexed: 06/07/2024] Open
Abstract
Peptostreptococcus porci is a recently described bacterium belonging to the Peptostreptococcaceae family, which was isolated in 2016 from pig intestine. Herein, we report the complete genome sequence of a clinical isolate of P. porci (GAI11004) obtained from porcine endocarditis in Japan. The genome contains a 2.4-Mb circular chromosome.
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Affiliation(s)
- Masahiro Hayashi
- Institute for Glyco-core Research iGCORE, Gifu University, Gifu City, Gifu, Japan
- Division of Anaerobe Research, Life Science Research Center, Gifu University, Gifu City, Gifu, Japan
- Gifu University Center for Conservation of Microbial Genetic Resource, Gifu City, Gifu, Japan
| | - Jun Yonetamari
- Division of Anaerobe Research, Life Science Research Center, Gifu University, Gifu City, Gifu, Japan
- Division of Clinical Laboratory, Gifu University Hospital, Gifu City, Gifu, Japan
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu City, Gifu, Japan
| | - Yoshinori Muto
- Division of Anaerobe Research, Life Science Research Center, Gifu University, Gifu City, Gifu, Japan
| | - Kaori Tanaka
- Institute for Glyco-core Research iGCORE, Gifu University, Gifu City, Gifu, Japan
- Division of Anaerobe Research, Life Science Research Center, Gifu University, Gifu City, Gifu, Japan
- Gifu University Center for Conservation of Microbial Genetic Resource, Gifu City, Gifu, Japan
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu City, Gifu, Japan
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Jia H, Chang Y, Song J. The pig as an optimal animal model for cardiovascular research. Lab Anim (NY) 2024; 53:136-147. [PMID: 38773343 DOI: 10.1038/s41684-024-01377-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 04/22/2024] [Indexed: 05/23/2024]
Abstract
Cardiovascular disease is a worldwide health problem and a leading cause of morbidity and mortality. Preclinical cardiovascular research using animals is needed to explore potential targets and therapeutic options. Compared with rodents, pigs have many advantages, with their anatomy, physiology, metabolism and immune system being more similar to humans. Here we present an overview of the available pig models for cardiovascular diseases, discuss their advantages over other models and propose the concept of standardized models to improve translation to the clinical setting and control research costs.
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Affiliation(s)
- Hao Jia
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Chang
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiangping Song
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Sanya Institute of China Agricultural University, Sanya, China.
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Hohmann M, Brunner V, Johannes W, Schum D, Carroll LM, Liu T, Sasaki D, Bosch J, Clavel T, Sieber SA, Zeller G, Tschurtschenthaler M, Janßen KP, Gulder TAM. Bacillamide D produced by Bacillus cereus from the mouse intestinal bacterial collection (miBC) is a potent cytotoxin in vitro. Commun Biol 2024; 7:655. [PMID: 38806706 PMCID: PMC11133360 DOI: 10.1038/s42003-024-06208-3] [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: 12/10/2023] [Accepted: 04/17/2024] [Indexed: 05/30/2024] Open
Abstract
The gut microbiota influences human health and the development of chronic diseases. However, our understanding of potentially protective or harmful microbe-host interactions at the molecular level is still in its infancy. To gain further insights into the hidden gut metabolome and its impact, we identified a cryptic non-ribosomal peptide BGC in the genome of Bacillus cereus DSM 28590 from the mouse intestine ( www.dsmz.de/miBC ), which was predicted to encode a thiazol(in)e substructure. Cloning and heterologous expression of this BGC revealed that it produces bacillamide D. In-depth functional evaluation showed potent cytotoxicity and inhibition of cell migration using the human cell lines HCT116 and HEK293, which was validated using primary mouse organoids. This work establishes the bacillamides as selective cytotoxins from a bacterial gut isolate that affect mammalian cells. Our targeted structure-function-predictive approach is demonstrated to be a streamlined method to discover deleterious gut microbial metabolites with potential effects on human health.
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Affiliation(s)
- Maximilian Hohmann
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069, Dresden, Germany
| | - Valentina Brunner
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany
- Division of Translational Cancer Research German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Widya Johannes
- Department of Surgery, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany
| | - Dominik Schum
- Department of Bioscience, Center for Functional Protein Assemblies, Technical University of Munich, 85748, Garching bei München, Germany
| | - Laura M Carroll
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 61997, Heidelberg, Germany
| | - Tianzhe Liu
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069, Dresden, Germany
| | - Daisuke Sasaki
- Department of Surgery, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany
- Research and Development Headquarters, Nitto Boseki Co., Ltd., 102-8489, Tokyo, Japan
| | - Johanna Bosch
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, 52074, Aachen, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, 52074, Aachen, Germany
| | - Stephan A Sieber
- Department of Bioscience, Center for Functional Protein Assemblies, Technical University of Munich, 85748, Garching bei München, Germany
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 61997, Heidelberg, Germany
| | - Markus Tschurtschenthaler
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany.
- Division of Translational Cancer Research German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.
| | - Klaus-Peter Janßen
- Department of Surgery, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany.
| | - Tobias A M Gulder
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069, Dresden, Germany.
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Natural Product Biotechnology, Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8.1, 66123, Saarbrücken, Germany.
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Malhotra M, Bello S, Gupta RS. Phylogenomic and molecular markers based studies on clarifying the evolutionary relationships among Peptoniphilus species. Identification of several Genus-Level clades of Peptoniphilus species and transfer of some Peptoniphilus species to the genus Aedoeadaptatus. Syst Appl Microbiol 2024; 47:126499. [PMID: 38428338 DOI: 10.1016/j.syapm.2024.126499] [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: 09/19/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/03/2024]
Abstract
To clarify the evolutionary relationships among Peptoniphilus species, whose members show association with increased risk for prostate cancer, detailed phylogenomic and comparative analyses were conducted on their genome sequences. In phylogenetic trees based on core genome proteins and 16S rRNA gene sequences, Peptoniphilus species formed eight distinct clades, with Aedoeadaptatus and Anaerosphaera species branching between them. The observed clades designated as Peptoniphilus sensu stricto (encompassing its type species), Harei, Lacrimalis, Duerdenii, Mikwangii, Stercorisuis, Catoniae and Aedoeadaptatus, show genus level divergence based on 16S rRNA similarity and average amino acid identity (AAI). The Genome Taxonomy Database also assigns most of these clades to distinct taxa. Several Peptoniphilus species (viz. P. coxii, P. ivorii, P. nemausensis and some non-validly published species) grouped reliably with the type species of Aedoeadaptatus (A. acetigenes) and are affiliated to this genus based on 16S rRNA similarity, AAI, and multiple uniquely shared molecular signatures. Hence, we are proposing the transfer of these species into the emended genus Aedoeadaptatus. Our analyses on protein sequences from Peptoniphilus genomes have also identified 54 novel molecular markers consisting of conserved signature indels (CSIs), which are specific for different Peptoniphilus species clades and provide reliable means for their demarcation in molecular terms. Lastly, we also show that based on the shared presence of these CSIs in the genomes of uncharacterized Peptoniphilus spp. (cultured and uncultured), their affiliations to the specific Peptoniphilus clades can be accurately predicted. These results should prove useful in understanding the potential involvement of Peptoniphilus-related species in diseases.
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Affiliation(s)
- Megha Malhotra
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Sarah Bello
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.
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Gonçalves JPR, Melo ADB, Yang Q, de Oliveira MJK, Marçal DA, Ortiz MT, Righetti Arnaut P, França I, Alves da Cunha Valini G, Silva CA, Korth N, Pavlovikj N, Campos PHRF, Brand HG, Htoo JK, Gomes-Neto JC, Benson AK, Hauschild L. Increased Dietary Trp, Thr, and Met Supplementation Improves Performance, Health, and Protein Metabolism of Weaned Piglets under Mixed Management and Poor Housing Conditions. Animals (Basel) 2024; 14:1143. [PMID: 38672291 PMCID: PMC11047353 DOI: 10.3390/ani14081143] [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: 02/22/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
A sanitary challenge was carried out to induce suboptimal herd health while investigating the effect of amino acids supplementation on piglet responses. Weaned piglets of high sanitary status (6.33 ± 0.91 kg of BW) were distributed in a 2 × 2 factorial arrangement into two similar facilities with contrasting sanitary conditions and two different diets. Our results suggest that increased Trp, Thr, and Met dietary supplementation could support the immune systems of piglets under a sanitary challenge. In this manner, AA+ supplementation improved the performance and metabolism of piglets under mixed management and poor sanitary conditions. No major temporal microbiome changes were associated with differences in performance regardless of sanitary conditions or diets. Since piglets often become mixed in multiple-site production systems and facility hygiene is also often neglected, this study suggests that increased Trp, Thr, and Met (AA+) dietary supplementation could contribute to mitigating the side effects of these harmful risk factors in modern pig farms.
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Affiliation(s)
- Joseane Penteado Rosa Gonçalves
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Campus Jaboticabal, São Paulo 14884-900, Brazil; (J.P.R.G.); (A.D.B.M.); (M.J.K.d.O.); (D.A.M.); (M.T.O.); (P.R.A.); (I.F.); (G.A.d.C.V.); (C.A.S.)
| | - Antonio Diego Brandão Melo
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Campus Jaboticabal, São Paulo 14884-900, Brazil; (J.P.R.G.); (A.D.B.M.); (M.J.K.d.O.); (D.A.M.); (M.T.O.); (P.R.A.); (I.F.); (G.A.d.C.V.); (C.A.S.)
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (Q.Y.); (N.K.); (J.C.G.-N.); (A.K.B.)
| | - Qinnan Yang
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (Q.Y.); (N.K.); (J.C.G.-N.); (A.K.B.)
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Marllon José Karpeggiane de Oliveira
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Campus Jaboticabal, São Paulo 14884-900, Brazil; (J.P.R.G.); (A.D.B.M.); (M.J.K.d.O.); (D.A.M.); (M.T.O.); (P.R.A.); (I.F.); (G.A.d.C.V.); (C.A.S.)
| | - Danilo Alves Marçal
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Campus Jaboticabal, São Paulo 14884-900, Brazil; (J.P.R.G.); (A.D.B.M.); (M.J.K.d.O.); (D.A.M.); (M.T.O.); (P.R.A.); (I.F.); (G.A.d.C.V.); (C.A.S.)
| | - Manoela Trevisan Ortiz
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Campus Jaboticabal, São Paulo 14884-900, Brazil; (J.P.R.G.); (A.D.B.M.); (M.J.K.d.O.); (D.A.M.); (M.T.O.); (P.R.A.); (I.F.); (G.A.d.C.V.); (C.A.S.)
| | - Pedro Righetti Arnaut
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Campus Jaboticabal, São Paulo 14884-900, Brazil; (J.P.R.G.); (A.D.B.M.); (M.J.K.d.O.); (D.A.M.); (M.T.O.); (P.R.A.); (I.F.); (G.A.d.C.V.); (C.A.S.)
| | - Ismael França
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Campus Jaboticabal, São Paulo 14884-900, Brazil; (J.P.R.G.); (A.D.B.M.); (M.J.K.d.O.); (D.A.M.); (M.T.O.); (P.R.A.); (I.F.); (G.A.d.C.V.); (C.A.S.)
| | - Graziela Alves da Cunha Valini
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Campus Jaboticabal, São Paulo 14884-900, Brazil; (J.P.R.G.); (A.D.B.M.); (M.J.K.d.O.); (D.A.M.); (M.T.O.); (P.R.A.); (I.F.); (G.A.d.C.V.); (C.A.S.)
| | - Cleslei Alisson Silva
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Campus Jaboticabal, São Paulo 14884-900, Brazil; (J.P.R.G.); (A.D.B.M.); (M.J.K.d.O.); (D.A.M.); (M.T.O.); (P.R.A.); (I.F.); (G.A.d.C.V.); (C.A.S.)
| | - Nate Korth
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (Q.Y.); (N.K.); (J.C.G.-N.); (A.K.B.)
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Natasha Pavlovikj
- Holland Computing Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | | | | | | | - João Carlos Gomes-Neto
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (Q.Y.); (N.K.); (J.C.G.-N.); (A.K.B.)
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Department of Animal Science, Center for Food Animal Health, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Andrew K. Benson
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (Q.Y.); (N.K.); (J.C.G.-N.); (A.K.B.)
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Luciano Hauschild
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Campus Jaboticabal, São Paulo 14884-900, Brazil; (J.P.R.G.); (A.D.B.M.); (M.J.K.d.O.); (D.A.M.); (M.T.O.); (P.R.A.); (I.F.); (G.A.d.C.V.); (C.A.S.)
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Hölzer M. POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy. BIOINFORMATICS (OXFORD, ENGLAND) 2024; 40:btae175. [PMID: 38561180 DOI: 10.1093/bioinformatics/btae175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/15/2024] [Accepted: 03/28/2024] [Indexed: 04/04/2024]
Abstract
SUMMARY Sequence technology advancements have led to an exponential increase in bacterial genomes, necessitating robust taxonomic classification methods. The Percentage Of Conserved Proteins (POCP), proposed initially by Qin et al. (2014), is a valuable metric for assessing prokaryote genus boundaries. Here, I introduce a computational pipeline for automated POCP calculation, aiming to enhance reproducibility and ease of use in taxonomic studies. AVAILABILITY AND IMPLEMENTATION The POCP-nf pipeline uses DIAMOND for faster protein alignments, achieving similar sensitivity to BLASTP. The pipeline is implemented in Nextflow with Conda and Docker support and is freely available on GitHub under https://github.com/hoelzer/pocp. The open-source code can be easily adapted for various prokaryotic genome and protein datasets. Detailed documentation and usage instructions are provided in the repository.
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Affiliation(s)
- Martin Hölzer
- Genome Competence Center (MF1), Robert Koch Institute, 13353 Berlin, Germany
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Cheng Y, Chen T, Zheng G, Yang J, Yu B, Ma C. Comprehensively assessing priority odorants emitted from swine slurry combining nontarget screening with olfactory threshold prediction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170428. [PMID: 38286275 DOI: 10.1016/j.scitotenv.2024.170428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/28/2023] [Accepted: 01/23/2024] [Indexed: 01/31/2024]
Abstract
The lack of one-to-one olfactory thresholds (OTs) poses an obstacle to the comprehensive assessment of priority odorants emitted from swine slurry using mass spectrometric nontarget screening. This study screened out highly performing quantitative structure-activity relationship (QSAR) models of OT prediction to complement nontarget screening in olfactory perception evaluation. A total of 27 compounds emitted at different slurry removal frequencies were identified and quantified using gas chromatography-mass spectrometry (GC-MS), including thiirane, dimethyl trisulfide (DMTS), and dimethyl tetrasulfide (DMQS) without OT records. Ridge regression (RR, R2 = 0.77, RMSE = 0.93, MAE = 0.73) and random forest regression (RFR, R2 = 0.76, RMSE = 0.97, MAE = 0.69) rather than the commonly used principal component regression (PCR) and partial least squares regression (PLSR) were used to assign OTs and assess the contributions of emerging volatile sulfur compounds (VSCs) to the sum of odor activity value (SOAV). Priority odorants were p-cresol (25.0-58.9 %) > valeric acid (8.3-31.7 %) > isovaleric acid (6.7-19.0 %) > dimethyl disulfide (4.7-15.7 %) > methanethiol (0-13.6 %) > isobutyric acid (0-8.6 %), whereas the contributions of three emerging VSCs were below 10 %. Vital olfactory active structures were identified by QSAR models as having high molecular polarity, high hydrophilicity, high charge quantity, flexible structure, high reactivity, and a high number of sulfur atoms. This protocol can be further extended to evaluate odor pollution levels for distinct odor sources and guide the development of pertinent deodorization technologies.
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Affiliation(s)
- Yuan Cheng
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tongbin Chen
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guodi Zheng
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Junxing Yang
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bao Yu
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuang Ma
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, Zhengzhou University of Light Industry, Zhengzhou 450000, China
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8
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Wang Y, Hils M, Fischer A, Wölbing F, Biedermann T, Schnieke A, Fischer K. Gene-edited pigs: a translational model for human food allergy against alpha-Gal and anaphylaxis. Front Immunol 2024; 15:1358178. [PMID: 38469303 PMCID: PMC10925645 DOI: 10.3389/fimmu.2024.1358178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/06/2024] [Indexed: 03/13/2024] Open
Abstract
The prevalence of food allergy is rising and is estimated to approach 10%. Red meat allergy is the first known food allergy elicited by immunoglobulin E (IgE) antibodies recognizing a carbohydrate. Due to the loss of function of the alpha-1,3-galactosyltransferase (GGTA1) gene in humans, the disaccharide galactose-α-1,3-galactose (α-Gal) cannot be synthesized and therefore became immunogenic. IgE sensitization is elicited through the skin by repetitive tick bites transmitting α-Gal. The underlying mechanisms regarding innate and adaptive immune cell activation, including the B-cell isotype switch to IgE, are poorly understood, requiring further research and physiologically relevant animal models. Here, we describe a new animal model of red meat allergy using percutaneous α-Gal sensitization of gene-edited GGTA1-deficient pigs. Total and α-Gal-specific IgG, IgG1, IgG2, IgG4, and IgE levels were tracked. Further key factors associated with allergic skin inflammation, type 2 immunity, and allergy development were measured in PBMCs and skin samples. Significant increases in α-Gal-specific IgG1 and IgE levels indicated successful sensitization to the allergen α-Gal. Intracutaneous sensitizations with α-Gal recruited lymphocytes to the skin, including elevated numbers of T helper 2 (Th2) cells. Finally, α-Gal-sensitized pigs not only recognized α-Gal as non-self-antigen following α-Gal exposure through the skin but also developed anaphylaxis upon antigen challenge. Based on the similarities between the porcine and human skin, this new large animal model for α-Gal allergy should help to unveil the consecutive steps of cutaneous sensitization and aid the development of prophylactic and treatment interventions.
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Affiliation(s)
- Ying Wang
- Chair of Livestock Biotechnology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Miriam Hils
- Department of Dermatology and Allergy Biederstein, School of Medicine, Technical University of Munich, Munich, Germany
| | - Andrea Fischer
- Chair of Livestock Biotechnology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Florian Wölbing
- Department of Dermatology and Allergy Biederstein, School of Medicine, Technical University of Munich, Munich, Germany
| | - Tilo Biedermann
- Department of Dermatology and Allergy Biederstein, School of Medicine, Technical University of Munich, Munich, Germany
| | - Angelika Schnieke
- Chair of Livestock Biotechnology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Konrad Fischer
- Chair of Livestock Biotechnology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
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9
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Argentini C, Lugli GA, Tarracchini C, Fontana F, Mancabelli L, Viappiani A, Anzalone R, Angelini L, Alessandri G, Bianchi MG, Taurino G, Bussolati O, Milani C, van Sinderen D, Turroni F, Ventura M. Ecology- and genome-based identification of the Bifidobacterium adolescentis prototype of the healthy human gut microbiota. Appl Environ Microbiol 2024; 90:e0201423. [PMID: 38294252 PMCID: PMC10880601 DOI: 10.1128/aem.02014-23] [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: 11/07/2023] [Accepted: 11/20/2023] [Indexed: 02/01/2024] Open
Abstract
Bifidobacteria are among the first microbial colonizers of the human gut, being frequently associated with human health-promoting activities. In the current study, an in silico methodology based on an ecological and phylogenomic-driven approach allowed the selection of a Bifidobacterium adolescentis prototype strain, i.e., B. adolescentis PRL2023, which best represents the overall genetic content and functional features of the B. adolescentis taxon. Such features were confirmed by in vitro experiments aimed at evaluating the ability of this strain to survive in the gastrointestinal tract of the host and its ability to interact with human intestinal cells and other microbial gut commensals. In this context, co-cultivation of B. adolescentis PRL2023 and several gut commensals revealed various microbe-microbe interactions and indicated co-metabolism of particular plant-derived glycans, such as xylan.IMPORTANCEThe use of appropriate bacterial strains in experimental research becomes imperative in order to investigate bacterial behavior while mimicking the natural environment. In the current study, through in silico and in vitro methodologies, we were able to identify the most representative strain of the Bifidobacterium adolescentis species. The ability of this strain, B. adolescentis PRL2023, to cope with the environmental challenges imposed by the gastrointestinal tract, together with its ability to switch its carbohydrate metabolism to compete with other gut microorganisms, makes it an ideal choice as a B. adolescentis prototype and a member of the healthy microbiota of adults. This strain possesses a genetic blueprint appropriate for its exploitation as a candidate for next-generation probiotics.
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Affiliation(s)
- Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- GenProbio srl, Parma, Italy
| | - Leonardo Mancabelli
- Microbiome Research Hub, University of Parma, Parma, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | | | | | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Massimiliano G. Bianchi
- Microbiome Research Hub, University of Parma, Parma, Italy
- Department of Medicine and Surgery, Laboratory of General Pathology, University of Parma, Parma, Italy
| | - Giuseppe Taurino
- Microbiome Research Hub, University of Parma, Parma, Italy
- Department of Medicine and Surgery, Laboratory of General Pathology, University of Parma, Parma, Italy
| | - Ovidio Bussolati
- Microbiome Research Hub, University of Parma, Parma, Italy
- Department of Medicine and Surgery, Laboratory of General Pathology, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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10
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Abou Chacra L, Bonnet M, Heredia M, Haddad G, Armstrong N, Alibar S, Bretelle F, Fenollar F. Peptoniphilus genitalis sp. nov. and Mobiluncus massiliensis sp. nov.: Novel Bacteria Isolated from the Vaginal Microbiome. Curr Microbiol 2024; 81:97. [PMID: 38372813 PMCID: PMC10876752 DOI: 10.1007/s00284-023-03584-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/07/2023] [Indexed: 02/20/2024]
Abstract
The strains Marseille-Q7072T (= CSUR Q7072T = CECT 30604 T) and Marseille-Q7826T (= CSUR Q7826T = CECT 30727 T) were isolated from vaginal samples. As MALDI-TOF mass spectrometry failed to identify them, their genomes were directly sequenced to determine their taxogenomic identities. Both strains are anaerobic without any oxidase and catalase activity. C16:0 is the most abundant fatty acid for both strains. Strain Marseille-Q7072T is non-spore-forming, non-motile, Gram-stain-positive, and coccus-shaped, while strain Marseille-Q7826T is non-spore-forming, motile, Gram-stain-variable, and curved rod-shaped. The genomic comparison of the Marseille-Q7072T and Marseille-Q7826T strains showed that all digital DNA-DNA hybridisation (dDDH) and mean orthologous nucleotide identity (OrthoANI) values were below published species thresholds (70% and 95-96%, respectively) with other closely related species with standing in nomenclature. Thus, we conclude that both strains are new bacterial species. Strain Marseille-Q7072T is a new member of the Bacillota phylum, for which the name Peptoniphilus genitalis sp. nov. is proposed, while the Marseille-Q7826T strain is a new member of the Actinomycetota phylum, for which the name Mobiluncus massiliensis sp. nov. is proposed.
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Affiliation(s)
- Linda Abou Chacra
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Marion Bonnet
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Mégane Heredia
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Gabriel Haddad
- IHU-Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | | | | | - Florence Bretelle
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- Department of Gynaecology and Obstetrics, Gynépole, La Conception, AP-HM, Marseille, France
| | - Florence Fenollar
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France.
- IHU-Méditerranée Infection, Marseille, France.
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11
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Barducci RS, Santos AAD, Pacheco LG, Putarov TC, Koch JFA, Callegari MA, Dias CP, de Carvalho RH, da Silva CA. Enhancing Weaned Piglet Health and Performance: The Role of Autolyzed Yeast ( Saccharomyces cerevisiae) and β-Glucans as a Blood Plasma Alternative in Diets. Animals (Basel) 2024; 14:631. [PMID: 38396599 PMCID: PMC10886371 DOI: 10.3390/ani14040631] [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: 12/14/2023] [Revised: 01/23/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
The objective of this study was to evaluate the inclusion of the autolyzed yeast (AY) Saccharomyces cerevisiae with or without an immunomodulator (1,3/1,6 β-glucans) as a total/partial substitute for blood plasma (BP) in the diet of post-weaning piglets; zootechnical performance, intestinal health and microbiota, immune responses and energy metabolism were assessed. A total of 240 castrated male and female piglets, with a mean age of 22 days and mean initial weight of 5.24 ± 0.82 kg, were randomly divided into blocks of four treatments with 12 replicates. The dietary inclusions were blood plasma (BP), autolyzed yeast (AY), autolyzed yeast + immunomodulator (AYI) and 50% BP and 50% AY (BPAY). In pre-initial phase II (29-35 days), piglets fed AY showed better feed conversion (FCR = 1.358) than the piglets in the BP (1.484), AYI (1.379) and BPAY (1.442) groups, i.e., 8.49% (0.126), 1.52% (0.021) and 4.50% (0.084), respectively (p = 0.0293). In the total period (21-42 days), better FCR was observed in the AYI (1.458) group, i.e., 4.64% (0.071), 1.15% (0.017) and 4.58% (0.070), than in the BP (1.529), AY (1.475) and BPAY (1.528) groups, respectively (p = 0.0150). In piglets fed AY (n = 3) and BPAY (n = 2), there was a reduction in the number of medications, i.e., 82.35% (-14n) and 88.23% (-15n), respectively (p = 0.0001), compared with that in the BP group (n = 17). In the AY group (73.83 mg/dL), AYI group (69.92 mg/dL), and BPAY group (69.58 mg/dL), piglets exhibited increases in triglyceride levels of 79.32%, 69.83%, and 69.00%, respectively, in comparison to those in the BP group, which had triglyceride levels of 41.17 mg/dL (p = 0.0400). The beta-hydroxybutyrate concentration in the AY group (79.96 ng/μL) was lower by 31.95%, 22.64%, and 5.89% compared to the BP group (117.50 ng/μL), AYI group (103.36 ng/μL), and BPAY group (84.67 ng/μL), respectively (p = 0.0072). In the AYI group, there was modulation of the microbiota, with an increase in the relative abundance of bacteria of the genera Lactobacillus, Collinsella and Bulleidia. AY, associated or not associated with an immunomodulator, is a potential substitute for BP in diets for piglets in the nursery phase, with positive effects on immune, metabolic, and intestinal microbial performance.
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Affiliation(s)
- Robson Sfaciotti Barducci
- Biorigin, Lençóis Paulista 18680-900, SP, Brazil; (R.S.B.); (A.A.D.S.); (L.G.P.); (T.C.P.); (J.F.A.K.)
| | | | - Leticia Graziele Pacheco
- Biorigin, Lençóis Paulista 18680-900, SP, Brazil; (R.S.B.); (A.A.D.S.); (L.G.P.); (T.C.P.); (J.F.A.K.)
| | - Thaila Cristina Putarov
- Biorigin, Lençóis Paulista 18680-900, SP, Brazil; (R.S.B.); (A.A.D.S.); (L.G.P.); (T.C.P.); (J.F.A.K.)
| | - João Fernando Albers Koch
- Biorigin, Lençóis Paulista 18680-900, SP, Brazil; (R.S.B.); (A.A.D.S.); (L.G.P.); (T.C.P.); (J.F.A.K.)
| | | | | | - Rafael Humberto de Carvalho
- Akei Animal Research, Fartura 18870-970, SP, Brazil; (M.A.C.); (C.P.D.); (R.H.d.C.)
- Animal Science Program, Center of Agrarian Sciences, State University of Londrina, Londrina 86057-970, PR, Brazil
| | - Caio Abércio da Silva
- Animal Science Program, Center of Agrarian Sciences, State University of Londrina, Londrina 86057-970, PR, Brazil
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12
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Argentini C, Lugli GA, Tarracchini C, Fontana F, Mancabelli L, Viappiani A, Anzalone R, Angelini L, Alessandri G, Longhi G, Bianchi MG, Taurino G, Bussolati O, Milani C, van Sinderen D, Turroni F, Ventura M. Genomic and ecological approaches to identify the Bifidobacterium breve prototype of the healthy human gut microbiota. Front Microbiol 2024; 15:1349391. [PMID: 38426063 PMCID: PMC10902438 DOI: 10.3389/fmicb.2024.1349391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
Members of the genus Bifidobacterium are among the first microorganisms colonizing the human gut. Among these species, strains of Bifidobacterium breve are known to be commonly transmitted from mother to her newborn, while this species has also been linked with activities supporting human wellbeing. In the current study, an in silico approach, guided by ecology- and phylogenome-based analyses, was employed to identify a representative strain of B. breve to be exploited as a novel health-promoting candidate. The selected strain, i.e., B. breve PRL2012, was found to well represent the genetic content and functional genomic features of the B. breve taxon. We evaluated the ability of PRL2012 to survive in the gastrointestinal tract and to interact with other human gut commensal microbes. When co-cultivated with various human gut commensals, B. breve PRL2012 revealed an enhancement of its metabolic activity coupled with the activation of cellular defense mechanisms to apparently improve its survivability in a simulated ecosystem resembling the human microbiome.
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Affiliation(s)
- Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- GenProbio srl, Parma, Italy
| | - Leonardo Mancabelli
- Microbiome Research Hub, University of Parma, Parma, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | | | | | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Massimiliano G. Bianchi
- Microbiome Research Hub, University of Parma, Parma, Italy
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Giuseppe Taurino
- Microbiome Research Hub, University of Parma, Parma, Italy
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Ovidio Bussolati
- Microbiome Research Hub, University of Parma, Parma, Italy
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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13
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Jennings SAV, Clavel T. Synthetic Communities of Gut Microbes for Basic Research and Translational Approaches in Animal Health and Nutrition. Annu Rev Anim Biosci 2024; 12:283-300. [PMID: 37963399 DOI: 10.1146/annurev-animal-021022-025552] [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: 11/16/2023]
Abstract
Microbes and animals have a symbiotic relationship that greatly influences nutrient uptake and animal health. This relationship can be studied using selections of microbes termed synthetic communities, or SynComs. SynComs are used in many different animal hosts, including agricultural animals, to investigate microbial interactions with nutrients and how these affect animal health. The most common host focuses for SynComs are currently mouse and human, from basic mechanistic research through to translational disease models and live biotherapeutic products (LBPs) as treatments. We discuss SynComs used in basic research models and findings that relate to human and animal health and nutrition. Translational use cases of SynComs are discussed, followed by LBPs, especially within the context of agriculture. SynComs still face challenges, such as standardization for reproducibility and contamination risks. However, the future of SynComs is hopeful, especially in the areas of genome-guided SynCom design and custom SynCom-based treatments.
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Affiliation(s)
- Susan A V Jennings
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany;
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany;
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14
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Liao SF, Ji F, Fan P, Denryter K. Swine Gastrointestinal Microbiota and the Effects of Dietary Amino Acids on Its Composition and Metabolism. Int J Mol Sci 2024; 25:1237. [PMID: 38279233 PMCID: PMC10816286 DOI: 10.3390/ijms25021237] [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: 11/05/2023] [Revised: 01/05/2024] [Accepted: 01/12/2024] [Indexed: 01/28/2024] Open
Abstract
Many researchers consider gut microbiota (trillions of microorganisms) an endogenous organ of its animal host, which confers a vast genetic diversity in providing the host with essential biological functions. Particularly, the gut microbiota regulates not only gut tissue structure but also gut health and gut functionality. This paper first summarized those common bacterial species (dominated by the Firmicutes, Bacteroidota, and Proteobacteria phyla) in swine gut and then briefly discussed their roles in swine nutrition and health, which include roles in nutrient metabolism, pathogen exclusion, and immunity modulation. Secondly, the current knowledge on how dietary nutrients and feed additives affect the gut bacterial composition and nutrient metabolism in pigs was discussed. Finally, how dietary amino acids affect the relative abundances and metabolism of bacteria in the swine gut was reviewed. Tryptophan supplementation promotes the growth of beneficial bacteria and suppresses pathogens, while arginine metabolism affects nitrogen recycling, impacting gut immune response and health. Glutamate and glutamine supplementations elevate the levels of beneficial bacteria and mitigate pathogenic ones. It was concluded that nutritional strategies to manipulate gut microbial ecosystems are useful measures to optimize gut health and gut functions. For example, providing pigs with nutrients that promote the growth of Lactobacillus and Bifidobacterium can lead to better gut health and growth performance, especially when dietary protein is limited. Further research to establish the mechanistic cause-and-effect relationships between amino acids and the dynamics of gut microbiota will allow swine producers to reap the greatest return on their feed investment.
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Affiliation(s)
- Shengfa F. Liao
- Department of Animal and Dairy Sciences, Mississippi State University, Starkville, MS 39762, USA; (P.F.)
| | - Feng Ji
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China;
| | - Peixin Fan
- Department of Animal and Dairy Sciences, Mississippi State University, Starkville, MS 39762, USA; (P.F.)
| | - Kristin Denryter
- Department of Animal and Dairy Sciences, Mississippi State University, Starkville, MS 39762, USA; (P.F.)
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15
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Kirby TO, Sapp PA, Townsend JR, Govaert M, Duysburgh C, Marzorati M, Marshall TM, Esposito R. AG1 ® Induces a Favorable Impact on Gut Microbial Structure and Functionality in the Simulator of Human Intestinal Microbial Ecosystem ® Model. Curr Issues Mol Biol 2024; 46:557-569. [PMID: 38248338 PMCID: PMC10814853 DOI: 10.3390/cimb46010036] [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: 12/08/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
Modulation of the human gut microbiome has become an area of interest in the nutraceutical space. We explored the effect of the novel foundational nutrition supplement AG1® on the composition of human microbiota in an in vitro experimental design. Employing the Simulator of Human Intestinal Microbial Ecosystem (SHIME®) model, AG1® underwent digestion, absorption, and subsequent colonic microenvironment simulation under physiologically relevant conditions in healthy human fecal inocula. Following 48 h of colonic simulation, the gut microbiota were described using shallow shotgun, whole genome sequencing. Metagenomic data were used to describe changes in community structure (alpha diversity, beta diversity, and changes in specific taxa) and community function (functional heterogeneity and changes in specific bacterial metabolic pathways). Results showed no significant change in alpha diversity, but a significant effect of treatment and donor and an interaction between the treatment and donor effect on structural heterogeneity likely stemming from the differential enrichment of eight bacterial taxa. Similar findings were observed for community functional heterogeneity likely stemming from the enrichment of 20 metabolic pathways characterized in the gene ontology term database. It is logical to conclude that an acute dose of AG1 has significant effects on gut microbial composition that may translate into favorable effects in humans.
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Affiliation(s)
- Trevor O. Kirby
- Research, Nutrition, and Innovation, Athletic Greens International, Carson City, NV 89701, USA; (P.A.S.); (J.R.T.); (T.M.M.); (R.E.)
| | - Philip A. Sapp
- Research, Nutrition, and Innovation, Athletic Greens International, Carson City, NV 89701, USA; (P.A.S.); (J.R.T.); (T.M.M.); (R.E.)
| | - Jeremy R. Townsend
- Research, Nutrition, and Innovation, Athletic Greens International, Carson City, NV 89701, USA; (P.A.S.); (J.R.T.); (T.M.M.); (R.E.)
- Health & Human Performance, Concordia University Chicago, River Forest, IL 60305, USA
| | - Marlies Govaert
- ProDigest BVBA, B-9052 Ghent, Belgium; (M.G.); (C.D.); (M.M.)
| | - Cindy Duysburgh
- ProDigest BVBA, B-9052 Ghent, Belgium; (M.G.); (C.D.); (M.M.)
| | - Massimo Marzorati
- ProDigest BVBA, B-9052 Ghent, Belgium; (M.G.); (C.D.); (M.M.)
- Center of Microbial Ecology and Technology (CMET), Ghent University, B-9000 Ghent, Belgium
| | - Tess M. Marshall
- Research, Nutrition, and Innovation, Athletic Greens International, Carson City, NV 89701, USA; (P.A.S.); (J.R.T.); (T.M.M.); (R.E.)
| | - Ralph Esposito
- Research, Nutrition, and Innovation, Athletic Greens International, Carson City, NV 89701, USA; (P.A.S.); (J.R.T.); (T.M.M.); (R.E.)
- Department of Nutrition, Food Studies, and Public Health, New York University-Steinhardt, New York, NY 10003, USA
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16
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Liu HY, Zhu C, Zhu M, Yuan L, Li S, Gu F, Hu P, Chen S, Cai D. Alternatives to antibiotics in pig production: looking through the lens of immunophysiology. STRESS BIOLOGY 2024; 4:1. [PMID: 38163818 PMCID: PMC10758383 DOI: 10.1007/s44154-023-00134-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 11/02/2023] [Indexed: 01/03/2024]
Abstract
In the livestock production system, the evolution of porcine gut microecology is consistent with the idea of "The Hygiene Hypothesis" in humans. I.e., improved hygiene conditions, reduced exposure to environmental microorganisms in early life, and frequent use of antimicrobial drugs drive immune dysregulation. Meanwhile, the overuse of antibiotics as feed additives for infectious disease prevention and animal growth induces antimicrobial resistance genes in pathogens and spreads related environmental pollutants. It justifies our attempt to review alternatives to antibiotics that can support optimal growth and improve the immunophysiological state of pigs. In the current review, we first described porcine mucosal immunity, followed by discussions of gut microbiota dynamics during the critical weaning period and the impacts brought by antibiotics usage. Evidence of in-feed additives with immuno-modulatory properties highlighting probiotics, prebiotics, and phytobiotics and their cellular and molecular networking are summarized and reviewed. It may provide insights into the immune regulatory mechanisms of antibiotic alternatives and open new avenues for health management in pig production.
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Affiliation(s)
- Hao-Yu Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agricultural & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Chuyang Zhu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, PR China
| | - Miaonan Zhu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, PR China
| | - Long Yuan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, PR China
| | - Shicheng Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, PR China
| | - Fang Gu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, PR China
| | - Ping Hu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, PR China
| | - Shihao Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agricultural & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Demin Cai
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, PR China.
- Joint International Research Laboratory of Agricultural & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China.
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17
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Wang X, Xie W, Cai L, Han C, Kuang H, Shao Y, Zhang S, Zhang Q, Li J, Cui W, Jiang Y, Tang L. Microencapsulated Limosilactobacillus reuteri Encoding Lactoferricin-Lactoferrampin Targeted Intestine against Salmonella typhimurium Infection. Nutrients 2023; 15:5141. [PMID: 38140400 PMCID: PMC10745908 DOI: 10.3390/nu15245141] [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: 11/14/2023] [Revised: 12/07/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (S. typhimurium) is an important foodborne pathogen that infects both humans and animals and develops acute gastroenteritis. As porcine intestines are relatively similar to the human ones due to their relatively similar sizes and structural similarity, S. typhimurium causes analogous symptoms in both. Novel strategies for controlling S. typhimurium infection are also desired, such as mucosal-targeted delivery of probiotics and antimicrobial peptides. The bovine lactoferricin-lactoferrampin-encoding Limosilactobacillus reuteri (LR-LFCA) strain improves intestinal barrier function by strengthening the intestinal barrier. Weaned piglets were selected for oral administration of microencapsulated LR-LFCA (microcapsules entrap LR-LFCA into gastro-resistant polymers) and then infected with S. typhimurium for 3 days. We found that orally administering microencapsulated LR-LFCA to weaned piglets attenuated S. typhimurium-induced production of inflammatory factors in the intestinal mucosa by inhibiting the nuclear factor-kappa B (NF-κB) and P38 mitogen-activated protein kinases (MAPK) signaling pathway. Moreover, microencapsulated LR-LFCA administration significantly suppressed the oxidative stress that may correlate with gut microbiota (reduced Salmonella population and increased α-diversity and Lactobacillus abundance) and intestinal function (membrane transport and metabolism). Our work demonstrated that microencapsulated LR-LFCA effectively targeted intestine delivery of Lactobacillus and antimicrobial peptides and modulated gut microbiota and mucosal immunity. This study reveals a novel targeting mucosal strategy against S. typhimurium infection.
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Affiliation(s)
- Xueying Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China; (X.W.); (W.X.); (L.C.); (C.H.); (H.K.); (Y.S.); (S.Z.); (Q.Z.); (J.L.); (W.C.)
| | - Weichun Xie
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China; (X.W.); (W.X.); (L.C.); (C.H.); (H.K.); (Y.S.); (S.Z.); (Q.Z.); (J.L.); (W.C.)
| | - Limeng Cai
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China; (X.W.); (W.X.); (L.C.); (C.H.); (H.K.); (Y.S.); (S.Z.); (Q.Z.); (J.L.); (W.C.)
| | - Chuang Han
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China; (X.W.); (W.X.); (L.C.); (C.H.); (H.K.); (Y.S.); (S.Z.); (Q.Z.); (J.L.); (W.C.)
| | - Hongdi Kuang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China; (X.W.); (W.X.); (L.C.); (C.H.); (H.K.); (Y.S.); (S.Z.); (Q.Z.); (J.L.); (W.C.)
| | - Yilan Shao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China; (X.W.); (W.X.); (L.C.); (C.H.); (H.K.); (Y.S.); (S.Z.); (Q.Z.); (J.L.); (W.C.)
| | - Senhao Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China; (X.W.); (W.X.); (L.C.); (C.H.); (H.K.); (Y.S.); (S.Z.); (Q.Z.); (J.L.); (W.C.)
| | - Qi Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China; (X.W.); (W.X.); (L.C.); (C.H.); (H.K.); (Y.S.); (S.Z.); (Q.Z.); (J.L.); (W.C.)
| | - Jiaxuan Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China; (X.W.); (W.X.); (L.C.); (C.H.); (H.K.); (Y.S.); (S.Z.); (Q.Z.); (J.L.); (W.C.)
| | - Wen Cui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China; (X.W.); (W.X.); (L.C.); (C.H.); (H.K.); (Y.S.); (S.Z.); (Q.Z.); (J.L.); (W.C.)
| | - Yanping Jiang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China; (X.W.); (W.X.); (L.C.); (C.H.); (H.K.); (Y.S.); (S.Z.); (Q.Z.); (J.L.); (W.C.)
| | - Lijie Tang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China; (X.W.); (W.X.); (L.C.); (C.H.); (H.K.); (Y.S.); (S.Z.); (Q.Z.); (J.L.); (W.C.)
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Northeast Agricultural University, Harbin 150030, China
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18
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Low A, Koh XQ, Ding Y, Seedorf H. Complete genome sequence of Paramuribaculum intestinale DSM 100749 T, isolated from feces of C57BL/6 laboratory mice. Microbiol Resour Announc 2023; 12:e0079723. [PMID: 37906020 PMCID: PMC10652918 DOI: 10.1128/mra.00797-23] [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: 08/28/2023] [Accepted: 09/24/2023] [Indexed: 11/02/2023] Open
Abstract
Here, the complete genome of Paramuribaculum intestinale type strain DSM 100749T(=JCM 33114T) is presented. P. intestinale is a recently described species of Muribaculaceae and was isolated from the gut of C57BL/6 laboratory mice. The genome can serve as an important resource for comparative genomics approaches.
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Affiliation(s)
- Adrian Low
- Temasek Life Sciences Laboratory, Research Link, Singapore, Singapore
| | - Xiu Qi Koh
- Temasek Life Sciences Laboratory, Research Link, Singapore, Singapore
| | - Yichen Ding
- Temasek Life Sciences Laboratory, Research Link, Singapore, Singapore
| | - Henning Seedorf
- Temasek Life Sciences Laboratory, Research Link, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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19
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Tan H, Zhou A, Jia L, Duan Y, Liu Z, Zhao W, He Z, Liu W, Yue X. Tailored short-chain fatty acids conversion from waste activated sludge fermentation via persulfate oxidation and C3-C5 io-SRB metabolizers. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 346:118967. [PMID: 37714089 DOI: 10.1016/j.jenvman.2023.118967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/23/2023] [Accepted: 09/09/2023] [Indexed: 09/17/2023]
Abstract
Boosting acetate production from waste activated sludge (WAS) fermentation is often hindered by the inefficient solubilization in the hydrolysis step and the high hydrogen pressure ( [Formula: see text] ) during the acidogenesis of C3-C5 short-chain fatty acid (SCFAs), i.e., propionate (HPr), butyrate (HBu) and valerate (HVa). Therefore, this study employed persulfate (PS) oxidation and C3-C5 incomplete-oxidative sulfate reducing bacteria (io-SRB) metabolizers to tailor SCFAs conversion from WAS fermentation. The decomposition efficiency, performance of SCFAs production was investigated. Results showed that the PS significantly promoted WAS decomposition, with a dissolution rate of 39.4%, which is 26.0% higher than the un-treated test. Furthermore, SCFAs yields were increased to 462.7 ± 42 mg COD/g VSS in PS-HBu-SRB, which was 7.4 and 2.2 times higher than that of un-treated and sole PS tests, respectively. In particular, the sum of acetate and HPr reached the peak value of 85%, indicating that HBu-SRB mediation promoted the biotransformation of HBu and macromolecular organics by reducing the [Formula: see text] restriction. Meanwhile, sulfate radical (SO4∙-)-based oxidation (SR-AOPs) was effective in the decomposition of WAS, the oxidative product, i.e., sulfate served the necessary electron acceptor for the metabolism of io-SRB. Further analysis of Mantel test revealed the cluster of the functional genus and their interaction with environmental variables. Additionally, molecular ecological network analysis explored the potential synergistic and competitive relationships between critical genera. Additionally, the potential synergistic and competitive relationships between critical genera was explored by molecular ecological network analysis. This study provides new insights into the integration of SR-AOPs with microbial mediation in accelerating SCFAs production from WAS fermentation.
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Affiliation(s)
- Huijie Tan
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China; Shanxi Shanan Lide Environmental Science & Technology Co., LTD, Taiyuan, 030032, China.
| | - Aijuan Zhou
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China; Shanxi-Zheda Institute of Advanced Materials and Chemical Engineering, Taiyuan, 030000, China.
| | - Lijun Jia
- Shanxi Shanan Lide Environmental Science & Technology Co., LTD, Taiyuan, 030032, China.
| | - Yanqing Duan
- Department of Environmental and Safety Engineering, Taiyuan Institute of Technology, Taiyuan, 030008, China.
| | - Zhihong Liu
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China.
| | - Wenjing Zhao
- Shanxi Shanan Lide Environmental Science & Technology Co., LTD, Taiyuan, 030032, China.
| | - Zhangwei He
- Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China.
| | - Wenzong Liu
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 51805, China.
| | - Xiuping Yue
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China; Shanxi-Zheda Institute of Advanced Materials and Chemical Engineering, Taiyuan, 030000, China; Shanxi Engineer Research Institute of Sludge Disposition and Resources, Taiyuan University of Technology, Taiyuan, 030024, China.
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20
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TSUJIKAWA Y, NISHIYAMA K, NAMAI F, IMAMURA Y, SAKUMA T, SAHA S, SUZUKI M, SAKURAI M, IWATA R, MATSUO K, TAKAMORI H, SUDA Y, ZHOU B, FUKUDA I, VILLENA J, SAKANE I, OSAWA R, KITAZAWA H. Establishment of porcine fecal-derived ex vivo microbial communities to evaluate the impact of livestock feed on gut microbiome. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2023; 43:100-109. [PMID: 38577893 PMCID: PMC10981943 DOI: 10.12938/bmfh.2023-085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 10/24/2023] [Indexed: 04/06/2024]
Abstract
Sustainable livestock production requires reducing competition for food and feed resources and increasing the utilization of food by-products in livestock feed. This study describes the establishment of an anaerobic batch culture model to simulate pig microbiota and evaluate the effects of a food by-product, wakame seaweed stalks, on ex vivo microbial communities. We selected one of the nine media to support the growth of a bacterial community most similar in composition and diversity to that observed in pig donor feces. Supplementation with wakame altered the microbial profile and short-chain fatty acid composition in the ex vivo model, and a similar trajectory was observed in the in vivo pig experimental validation. Notably, the presence of wakame increased the abundance of Lactobacillus species, which may have been due to cross-feeding with Bacteroides. These results suggest the potential of wakame as a livestock feed capable of modulating the pig microbiome. Collectively, this study highlights the ability to estimate the microbiome changes that occur when pigs are fed a specific feed using an ex vivo culture model.
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Affiliation(s)
- Yuji TSUJIKAWA
- Food and Feed Immunology Group, Laboratory of Animal Food
Function, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramakiaoba,
Aoba-ku, Sendai-shi, Miyagi 980-8572, Japan
- Central Research Institute, Ito En Ltd., 21 Mekami,
Sagara-cho, Haibara-gun, Shizuoka 421-0516, Japan
- Department of Agrobioscience, Graduate School of Agricultural
Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe-shi, Hyogo 657-8501, Japan
| | - Keita NISHIYAMA
- Food and Feed Immunology Group, Laboratory of Animal Food
Function, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramakiaoba,
Aoba-ku, Sendai-shi, Miyagi 980-8572, Japan
- Livestock Immunology Unit, International Education and
Research Center for Food and Agricultural Immunology (CFAI), Graduate School of
Agricultural Science, Tohoku University, 41 Kawauchi, Aoba-ku, Sendai-shi, Miyagi
980-8576, Japan
| | - Fu NAMAI
- Food and Feed Immunology Group, Laboratory of Animal Food
Function, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramakiaoba,
Aoba-ku, Sendai-shi, Miyagi 980-8572, Japan
- Livestock Immunology Unit, International Education and
Research Center for Food and Agricultural Immunology (CFAI), Graduate School of
Agricultural Science, Tohoku University, 41 Kawauchi, Aoba-ku, Sendai-shi, Miyagi
980-8576, Japan
| | - Yoshiya IMAMURA
- Food and Feed Immunology Group, Laboratory of Animal Food
Function, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramakiaoba,
Aoba-ku, Sendai-shi, Miyagi 980-8572, Japan
| | - Taiga SAKUMA
- Food and Feed Immunology Group, Laboratory of Animal Food
Function, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramakiaoba,
Aoba-ku, Sendai-shi, Miyagi 980-8572, Japan
| | - Sudeb SAHA
- Food and Feed Immunology Group, Laboratory of Animal Food
Function, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramakiaoba,
Aoba-ku, Sendai-shi, Miyagi 980-8572, Japan
- Livestock Immunology Unit, International Education and
Research Center for Food and Agricultural Immunology (CFAI), Graduate School of
Agricultural Science, Tohoku University, 41 Kawauchi, Aoba-ku, Sendai-shi, Miyagi
980-8576, Japan
- Department of Dairy Science, Faculty of Veterinary, Animal
and Biomedical Sciences, Sylhet Agricultural University, Sylhet-3100, Bangladesh
- JSPS Fellow
| | - Masahiko SUZUKI
- Food and Feed Immunology Group, Laboratory of Animal Food
Function, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramakiaoba,
Aoba-ku, Sendai-shi, Miyagi 980-8572, Japan
- Central Research Institute, Ito En Ltd., 21 Mekami,
Sagara-cho, Haibara-gun, Shizuoka 421-0516, Japan
| | - Mitsuki SAKURAI
- Food and Feed Immunology Group, Laboratory of Animal Food
Function, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramakiaoba,
Aoba-ku, Sendai-shi, Miyagi 980-8572, Japan
| | - Ryo IWATA
- Department of Agrobioscience, Graduate School of Agricultural
Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe-shi, Hyogo 657-8501, Japan
| | - Kengo MATSUO
- Miyagi Prefecture Animal Industry Experiment Station, Osaki,
Miyagi 989-6445, Japan
| | - Hironori TAKAMORI
- Miyagi Prefecture Animal Industry Experiment Station, Osaki,
Miyagi 989-6445, Japan
| | - Yoshihito SUDA
- Department of Food, Agriculture and Environmental Science,
Miyagi University, 468-1 Aramakiaoba, Aoba-ku, Sendai-shi, Miyagi 980-8572, Japan
| | - Binghui ZHOU
- Food and Feed Immunology Group, Laboratory of Animal Food
Function, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramakiaoba,
Aoba-ku, Sendai-shi, Miyagi 980-8572, Japan
- Livestock Immunology Unit, International Education and
Research Center for Food and Agricultural Immunology (CFAI), Graduate School of
Agricultural Science, Tohoku University, 41 Kawauchi, Aoba-ku, Sendai-shi, Miyagi
980-8576, Japan
| | - Itsuko FUKUDA
- Department of Agrobioscience, Graduate School of Agricultural
Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe-shi, Hyogo 657-8501, Japan
| | - Julio VILLENA
- Food and Feed Immunology Group, Laboratory of Animal Food
Function, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramakiaoba,
Aoba-ku, Sendai-shi, Miyagi 980-8572, Japan
- Livestock Immunology Unit, International Education and
Research Center for Food and Agricultural Immunology (CFAI), Graduate School of
Agricultural Science, Tohoku University, 41 Kawauchi, Aoba-ku, Sendai-shi, Miyagi
980-8576, Japan
- Laboratory of Immunobiotechnology, Reference Centre for
Lactobacilli (CERELA-CONICET), Tucuman 4000, Argentina
| | - Iwao SAKANE
- Central Research Institute, Ito En Ltd., 21 Mekami,
Sagara-cho, Haibara-gun, Shizuoka 421-0516, Japan
| | - Ro OSAWA
- Food and Feed Immunology Group, Laboratory of Animal Food
Function, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramakiaoba,
Aoba-ku, Sendai-shi, Miyagi 980-8572, Japan
- Department of Agrobioscience, Graduate School of Agricultural
Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe-shi, Hyogo 657-8501, Japan
| | - Haruki KITAZAWA
- Food and Feed Immunology Group, Laboratory of Animal Food
Function, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramakiaoba,
Aoba-ku, Sendai-shi, Miyagi 980-8572, Japan
- Livestock Immunology Unit, International Education and
Research Center for Food and Agricultural Immunology (CFAI), Graduate School of
Agricultural Science, Tohoku University, 41 Kawauchi, Aoba-ku, Sendai-shi, Miyagi
980-8576, Japan
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Yun JU, Jung HS, Jung MJ, Song HS, Kim YB, Kim Y, Kim JG, Roh SW, Lee SH, Lee JS, Whon TW. Cutibacterium equinum sp. nov., isolated from horse faeces. Int J Syst Evol Microbiol 2023; 73. [PMID: 37910171 DOI: 10.1099/ijsem.0.006099] [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: 11/03/2023] Open
Abstract
Strain CBA3108T is a Gram-positive, non-spore-forming, obligately anaerobic bacterium isolated from horse faecal samples obtained in Jeju Island, Republic of Korea. The cells of CBA3108T are non-motile short rods that have been assessed as catalase-positive and oxidase-negative. Growth of the strain occurs under the following conditions: 25-45 °C (optimum, 35 °C); pH 6-9 (optimum, pH 6); and in the presence of 0-6 % (w/v) NaCl (optimum, 2%). Major fatty acids in the strain include C15 : 0 iso and C15 : 0 iso DMA, while major polar lipids include phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. Based on phylogenetic analysis using 16S rRNA gene sequences, strain CBA3108T forms a phyletic lineage distinct from other closely related species within the genus Cutibacterium. It was found to be most closely related to Cutibacterium avidum ATCC 25577T (98.27 % 16S rRNA gene sequence similarity) and other strains within the genus (≤98.0 %). The genomic DNA G+C content of strain CBA3108T was 63.2 mol%. The in silico DNA-DNA hybridization values of strain CBA3108T with C. avidum ATCC 25577T, C. porci WCA-380-WT-3AT and C. acnes subsp. acnes DSM 1897T were 33.6, 21.7 and 22.7 %, respectively. Its phenotypic, chemotaxonomic and molecular properties support the hypothesis that strain CBA3108T represents a novel species in the genus Cutibacterium, for which we propose the name Cutibacterium equinum sp. nov. The type strain is CBA3108T (=KACC 22889T=JCM 35966T).
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Affiliation(s)
- Jeong Ui Yun
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
- Department of Life Science, Chosun University, Gwangju 61452, Republic of Korea
| | - Hye Su Jung
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
- Biobank, Institut Pasteur Korea, Seongnam, 13488, Republic of Korea
| | - Mi-Ja Jung
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Hye Seon Song
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Yeon Bee Kim
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Yujin Kim
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Joon-Gyu Kim
- Department of Equine Science, Cheju Halla University, Jeju, 63092, Republic of Korea
| | - Seong Woon Roh
- Microbiome Research Team, LISCure Biosciences Inc., Seongnam 13486, Republic of Korea
| | - Se Hee Lee
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Jun Sik Lee
- Department of Life Science, Chosun University, Gwangju 61452, Republic of Korea
| | - Tae Woong Whon
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
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22
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Li Q, Wang H, Xu R, Su Y, Zhu W. Dynamic analysis of metabolomics reveals the potential associations between colonic peptides and serum appetite-related hormones. Food Res Int 2023; 173:113376. [PMID: 37803714 DOI: 10.1016/j.foodres.2023.113376] [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: 01/02/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 10/08/2023]
Abstract
Gut signals, including hormones and metabolites are crucial zeitgebers that regulate the circadian rhythm of host metabolism, but the potential links have been explored more in rodents. Herein, we performed an hour-scale metabolomics analysis of serum and colonic digesta to characterize the circadian rhythmic metabolic patterns using a pig model under ad libitum feeding conditions. Importantly, our findings identified potential associations between colonic and body metabolism, revealing the potential relationships between colonic peptides and host appetite regulation. Concretely, amino acids accounted for the highest proportion in rhythmic serum metabolites, whereas lipids accounted for the highest proportion in rhythmic colonic metabolites. The diurnal difference analysis revealed that the levels of most amino acids and peptides were higher in the light phase, while the levels of most lipids were higher in the dark phase. And more correlations were be checked between serum amino acids, lipids, peptides and colonic metabolites in the light and more correlations were be checked between serum carbohydrates, cofactors and vitamins, energy, nucleotides, xenobiotics and colonic metabolites in the dark. Interestingly, peptides oscillated to a similar extent in serum and colonic digesta. Of note, colonic peptides composed of valine, proline and leucine were checked in positive associations to glucagon-like peptide-1 (GLP-1) in serum. And these peptides were positive with the genera Butyricicoccus, Streptococcus, Clostridioides, Bariatricus and Coriobacteriia_norank, and negative with Prevotella, and showed the potential relationships with colonic microbial biosynthesis of amino acids. Collectively, we mapped the rhythmic profiling on pig serum and colonic metabolites and revealed the relationships between host and gut metabolism. However, the underlying regulatory mechanisms remains to be further investigated.
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Affiliation(s)
- Qiuke Li
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongyu Wang
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Rongying Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Yong Su
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China.
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
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23
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Wen Y, Yang L, Wang Z, Liu X, Gao M, Zhang Y, Wang J, He P. Blocked conversion of Lactobacillus johnsonii derived acetate to butyrate mediates copper-induced epithelial barrier damage in a pig model. MICROBIOME 2023; 11:218. [PMID: 37777765 PMCID: PMC10542248 DOI: 10.1186/s40168-023-01655-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 08/23/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND High-copper diets have been widely used to promote growth performance of pigs, but excess copper supplementation can also produce negative effects on ecosystem stability and organism health. High-copper supplementation can damage the intestinal barrier and disturb the gut microbiome community. However, the specific relationship between high-copper-induced intestinal damage and gut microbiota or its metabolites is unclear. OBJECTIVE Using fecal microbiota transplantation and metagenomic sequencing, responses of colonic microbiota to a high-copper diet was profiled. In addition, via comparison of specific bacteria and its metabolites rescue, we investigated a network of bacteria-metabolite interactions involving conversion of specific metabolites as a key mechanism linked to copper-induced damage of the colon. RESULTS High copper induced colonic damage, Lactobacillus extinction, and reduction of SCFA (acetate and butyrate) concentrations in pigs. LefSe analysis and q-PCR results confirmed the extinction of L. johnsonii. In addition, transplanting copper-rich fecal microbiota to ABX mice reproduced the gut characteristics of the pig donors. Then, L. johnsonii rescue could restore decreased SCFAs (mainly acetate and butyrate) and colonic barrier damage including thinner mucus layer, reduced colon length, and tight junction protein dysfunction. Given that acetate and butyrate concentrations exhibited a positive correlation with L. johnsonii abundance, we investigated how L. johnsonii exerted its effects by supplementing acetate and butyrate. L. johnsonii and butyrate administration but not acetate could correct the damaged colonic barrier. Acetate administration had no effects on butyrate concentration, indicating blocked conversion from acetate to butyrate. Furthermore, L. johnsonii rescue enriched a series of genera with butyrate-producing ability, mainly Lachnospiraceae NK4A136 group. CONCLUSIONS For the first time, we reveal the microbiota-mediated mechanism of high-copper-induced colonic damage in piglets. A high-copper diet can induce extinction of L. johnsonii which leads to colonic barrier damage and loss of SCFA production. Re-establishment of L. johnsonii normalizes the SCFA-producing pathway and restores colonic barrier function. Mechanistically, Lachnospiraceae NK4A136 group mediated conversion of acetate produced by L. johnsonii to butyrate is indispensable in the protection of colonic barrier function. Collectively, these findings provide a feasible mitigation strategy for gut damage caused by high-copper diets. Video Abstract.
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Affiliation(s)
- Yang Wen
- State Key Laboratory of Animal Nutrition, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Luqing Yang
- State Key Laboratory of Animal Nutrition, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Zhenyu Wang
- State Key Laboratory of Animal Nutrition, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Xiaoyi Liu
- State Key Laboratory of Animal Nutrition, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Meng Gao
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yunhui Zhang
- College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Junjun Wang
- State Key Laboratory of Animal Nutrition, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Pingli He
- State Key Laboratory of Animal Nutrition, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
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24
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Liang X, Zhai Z, Ren F, Jie Y, Kim SK, Niu KM, Wu X. Metagenomic characterization of the cecal microbiota community and functions in finishing pigs fed fermented Boehmeria nivea. Front Vet Sci 2023; 10:1253778. [PMID: 37841475 PMCID: PMC10569026 DOI: 10.3389/fvets.2023.1253778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/05/2023] [Indexed: 10/17/2023] Open
Abstract
Ramie (Boehmeria nivea, BN) is used as livestock forage through suitable silage fermentation owing to its nutritional value. To date, relatively few studies have investigated the effects of dietary fermented BN (FBN) on gut health in finishing pigs. The aim of the present study was to investigate the effects of dietary supplementation with 20% FBN on intestinal morphology, gene expression, and the functional response of the gut microbiota in finishing pigs. We found that FBN did not significantly affect serum antioxidant enzyme activities, ileal morphology, or the expression of genes encoding antioxidant enzymes, inflammatory cytokines, or tight junction proteins in the liver of the pigs. However, the gene expression levels of aryl hydrocarbon receptor (AHR) and interleukin 6 (IL6) were significantly downregulated in the ileum. A metagenomic analysis demonstrated that, compared with that seen in the control group, the cecal microbiota of pigs in the FBN treatment group was more closely clustered and contained a greater number of unique microbes. Bacteria were the predominant kingdom in the cecal microbiota, while Firmicutes, Bacteroidetes, and Proteobacteria were the dominant phyla, and Streptococcus, Lactobacillus, and Prevotella were the dominant genera. Dietary FBN significantly increased the abundance of the probiotic bacterium Roseburia inulinivorans (p < 0.05). Functional analysis of the cecal microbiota showed that ABC transporter levels and glycolysis/gluconeogenesis-associated functions were diminished in FBN-fed pigs. Meanwhile, CAZyme analysis revealed that dietary FBN significantly downregulated the contents of carbohydrate-active enzymes, such as GT2, GH1, GH25, and GH13_31. In addition, cytochrome P450 analysis revealed that the abundance of CYP51 and CYP512 decreased with FBN treatment. An assessment of antibiotic resistance based on the Comprehensive Antibiotic Resistance Database (CARD) annotation indicated that the cecal microbes from pigs in the FBN treatment group had increased resistance to lincosamide, streptogramin, and chloramphenicol and reduced resistance to amikacin, isepamicin, neomycin, lividomycin, gentamicin, paromomycin, ribostamycin, and butirosin. Finally, virulence factor-related analysis showed that putative hemolysin-associated functions were decreased, whereas fibronectin-binding protein, flagella, and alginate-associated functions were increased. Taken together, our data showed that FBN supplementation exerted only minor effects on intestinal morphology and microbial community composition, suggesting that it is potentially safe for use as a supplement in the diets of finishing pigs. However, more studies are needed to validate its functionality.
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Affiliation(s)
- Xiaoxiao Liang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Zhenya Zhai
- Jiangxi Functional Feed Additive Engineering Laboratory, Institute of Biological Resource, Jiangxi Academy of Sciences, Nanchang, China
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, China
| | - Fengyun Ren
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Yucheng Jie
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Soo-Ki Kim
- Department of Animal Science and Technology, Konkuk University, Seoul, Republic of Korea
| | - Kai-Min Niu
- Jiangxi Functional Feed Additive Engineering Laboratory, Institute of Biological Resource, Jiangxi Academy of Sciences, Nanchang, China
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, China
| | - Xin Wu
- Jiangxi Functional Feed Additive Engineering Laboratory, Institute of Biological Resource, Jiangxi Academy of Sciences, Nanchang, China
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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Diao M, Dyksma S, Koeksoy E, Ngugi DK, Anantharaman K, Loy A, Pester M. Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction. FEMS Microbiol Rev 2023; 47:fuad058. [PMID: 37796897 PMCID: PMC10591310 DOI: 10.1093/femsre/fuad058] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/07/2023] Open
Abstract
Sulfate/sulfite-reducing microorganisms (SRM) are ubiquitous in nature, driving the global sulfur cycle. A hallmark of SRM is the dissimilatory sulfite reductase encoded by the genes dsrAB. Based on analysis of 950 mainly metagenome-derived dsrAB-carrying genomes, we redefine the global diversity of microorganisms with the potential for dissimilatory sulfate/sulfite reduction and uncover genetic repertoires that challenge earlier generalizations regarding their mode of energy metabolism. We show: (i) 19 out of 23 bacterial and 2 out of 4 archaeal phyla harbor uncharacterized SRM, (ii) four phyla including the Desulfobacterota harbor microorganisms with the genetic potential to switch between sulfate/sulfite reduction and sulfur oxidation, and (iii) the combination as well as presence/absence of different dsrAB-types, dsrL-types and dsrD provides guidance on the inferred direction of dissimilatory sulfur metabolism. We further provide an updated dsrAB database including > 60% taxonomically resolved, uncultured family-level lineages and recommendations on existing dsrAB-targeted primers for environmental surveys. Our work summarizes insights into the inferred ecophysiology of newly discovered SRM, puts SRM diversity into context of the major recent changes in bacterial and archaeal taxonomy, and provides an up-to-date framework to study SRM in a global context.
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Affiliation(s)
- Muhe Diao
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - Stefan Dyksma
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - Elif Koeksoy
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - David Kamanda Ngugi
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna A-1030, Austria
| | - Michael Pester
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
- Technical University of Braunschweig, Institute of Microbiology, Braunschweig D-38106, Germany
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Ridlon JM, Daniel SL, Gaskins HR. The Hylemon-Björkhem pathway of bile acid 7-dehydroxylation: history, biochemistry, and microbiology. J Lipid Res 2023; 64:100392. [PMID: 37211250 PMCID: PMC10382948 DOI: 10.1016/j.jlr.2023.100392] [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: 04/14/2023] [Revised: 05/07/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023] Open
Abstract
Bile acids are detergents derived from cholesterol that function to solubilize dietary lipids, remove cholesterol from the body, and act as nutrient signaling molecules in numerous tissues with functions in the liver and gut being the best understood. Studies in the early 20th century established the structures of bile acids, and by mid-century, the application of gnotobiology to bile acids allowed differentiation of host-derived "primary" bile acids from "secondary" bile acids generated by host-associated microbiota. In 1960, radiolabeling studies in rodent models led to determination of the stereochemistry of the bile acid 7-dehydration reaction. A two-step mechanism was proposed, which we have termed the Samuelsson-Bergström model, to explain the formation of deoxycholic acid. Subsequent studies with humans, rodents, and cell extracts of Clostridium scindens VPI 12708 led to the realization that bile acid 7-dehydroxylation is a result of a multi-step, bifurcating pathway that we have named the Hylemon-Björkhem pathway. Due to the importance of hydrophobic secondary bile acids and the increasing measurement of microbial bai genes encoding the enzymes that produce them in stool metagenome studies, it is important to understand their origin.
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Affiliation(s)
- Jason M Ridlon
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA; Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA; Center for Advanced Study, University of Illinois Urbana-Champaign, Urbana, IL, USA; Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA.
| | - Steven L Daniel
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL, USA
| | - H Rex Gaskins
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA; Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA; Department of Biomedical and Translational Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA; Department of Pathobiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
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Poothong S, Tanasupawat S, Chanpongsang S, Phongsopitanun W, Nuengjamnong C. Selenomonas caprae sp. nov., an obligately anaerobic and volatile fatty acid producing bacterium from ruminal fluid of domestic goat ( Capra hircus L.). Int J Syst Evol Microbiol 2023; 73. [PMID: 37339073 DOI: 10.1099/ijsem.0.005936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023] Open
Abstract
A novel Gram-stain-negative, motile, obligately anaerobic bacterium strain mPRGC8T was isolated from the ruminal fluid of a domestic goat (Capra hircus L.) in Nakhon Pathom province, Thailand. The strain grew at 20-45 °C (optimum, 37 °C), pH 6.0-9.0 (optimum, pH 7.5) and 3 % (w/v) NaCl. It produced acetate, propionate, valerate, caproate and heptanoate from glucose. The 16S rRNA gene sequence analysis indicated that strain mPRGC8T belonged to the genus Selenomonas and was closely related to Selenomonas ruminantium subsp. ruminantium DSM 2150T (98.0 %) and Selenomonas ruminantium subsp. lactilytica JCM 6582T (97.9 %). The in silico DNA G+C content was 53.0 mol %. Strain mPRGC8T showed average nucleotide identity, digital DNA-DNA hybridization and average animo acid identity values with Selenomonas montiformis JCM 34373T, S. ruminantium subsp. lactilytica JCM 6582T and S. ruminantium subsp. ruminantium DSM 2150T ranging from 84.9 to 86.0 %, 21.3 to 21.8 % and 73.8 to 76.1 %, respectively. The predominant cellular fatty acids were C16 : 1 ω9c and C18 : 1 ω9c. Phosphatidylethanolamine, three unidentified aminophospholipids, two unidentified ninhydrin positive glycolipids, an unidentified phospholipid and an unidentified lipid were detected as polar lipids. The genomic and phenotypic characteristics of strain mPRGC8T strongly support its classification as representative of new species of the genus Selenomonas for which the name Selenomonas caprae sp. nov. is proposed. The type strain is mPRGC8T (=JCM 33725T=KCTC 25178T).
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Affiliation(s)
- Saranporn Poothong
- Department of Animal Husbandry, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Somchai Chanpongsang
- Department of Animal Husbandry, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wongsakorn Phongsopitanun
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chackrit Nuengjamnong
- Department of Animal Husbandry, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence for Food and Water Risk Analysis (FAWRA), Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
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Zhu J, Dong G, Shih CJ, Wu YC, Lai SJ, You YT, Qiu W, Wu CH, Liao CH, Gong Y, Chen SC. Complete Genome Sequence of Tissierella sp. Strain Yu-01, Isolated from the Feces of the Black Soldier Fly. Microbiol Resour Announc 2023:e0027723. [PMID: 37154723 DOI: 10.1128/mra.00277-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
We report the complete genome sequence of Tissierella sp. strain Yu-01 (=BCRC 81391), isolated from the feces of black soldier fly (Hermetia illucens) larvae. This fly has increasingly been gaining attention because of its usefulness for recycling organic waste. The genome of strain Yu-01 was selected for further species delineation.
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Affiliation(s)
- Junyu Zhu
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian, People's Republic of China
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, People's Republic of China
| | - Guowen Dong
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian, People's Republic of China
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, People's Republic of China
| | - Chao-Jen Shih
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, Republic of China
| | - Yen-Chi Wu
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, Republic of China
| | - Shu-Jung Lai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung City, Taiwan, Republic of China
- Research Center for Cancer Biology, China Medical University, Taichung City, Taiwan, Republic of China
| | - Yi-Ting You
- Department of Life Sciences, National Chung Hsing University, Taichung City, Taiwan, Republic of China
| | - Wanling Qiu
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, People's Republic of China
| | - Chih-Hung Wu
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian, People's Republic of China
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, People's Republic of China
| | - Ching-Hua Liao
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, People's Republic of China
| | - Yan Gong
- People's Government of Zhongcun Township, Sanyuan District, Sanming City, Fujian, People's Republic of China
| | - Sheng-Chung Chen
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian, People's Republic of China
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, People's Republic of China
- Department of Life Sciences, National Chung Hsing University, Taichung City, Taiwan, Republic of China
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Horvathova K, Modrackova N, Splichal I, Splichalova A, Amin A, Ingribelli E, Killer J, Doskocil I, Pechar R, Kodesova T, Vlkova E. Defined Pig Microbiota with a Potential Protective Effect against Infection with Salmonella Typhimurium. Microorganisms 2023; 11:microorganisms11041007. [PMID: 37110429 PMCID: PMC10146858 DOI: 10.3390/microorganisms11041007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
A balanced microbiota is a main prerequisite for the host's health. The aim of the present work was to develop defined pig microbiota (DPM) with the potential ability to protect piglets against infection with Salmonella Typhimurium, which causes enterocolitis. A total of 284 bacterial strains were isolated from the colon and fecal samples of wild and domestic pigs or piglets using selective and nonselective cultivation media. Isolates belonging to 47 species from 11 different genera were identified by MALDI-TOF mass spectrometry (MALDI-TOF MS). The bacterial strains for the DPM were selected for anti-Salmonella activity, ability to aggregate, adherence to epithelial cells, and to be bile and acid tolerant. The selected combination of 9 strains was identified by sequencing of the 16S rRNA gene as Bacillus sp., Bifidobacterium animalis subsp. lactis, B. porcinum, Clostridium sporogenes, Lactobacillus amylovorus, L. paracasei subsp. tolerans, Limosilactobacillus reuteri subsp. suis, and Limosilactobacillus reuteri (two strains) did not show mutual inhibition, and the mixture was stable under freezing for at least 6 months. Moreover, strains were classified as safe without pathogenic phenotype and resistance to antibiotics. Future experiments with Salmonella-infected piglets are needed to test the protective effect of the developed DPM.
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Affiliation(s)
- Kristyna Horvathova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
| | - Nikol Modrackova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
| | - Igor Splichal
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic
| | - Alla Splichalova
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic
| | - Ahmad Amin
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
| | - Eugenio Ingribelli
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
| | - Jiri Killer
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Ivo Doskocil
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
| | - Radko Pechar
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
| | - Tereza Kodesova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
| | - Eva Vlkova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
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Karnachuk OV, Beletsky AV, Rakitin AL, Ikkert OP, Avakyan MR, Zyusman VS, Napilov A, Mardanov AV, Ravin NV. Antibiotic-Resistant Desulfovibrio Produces H2S from Supplements for Animal Farming. Microorganisms 2023; 11:microorganisms11040838. [PMID: 37110261 PMCID: PMC10146906 DOI: 10.3390/microorganisms11040838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Sulphate-reducing bacteria, primarily Desulfovibrio, are responsible for the active generation of H2S in swine production waste. The model species for sulphate reduction studies, Desulfovibrio vulgaris strain L2, was previously isolated from swine manure characterized by high rates of dissimilatory sulphate reduction. The source of electron acceptors in low-sulphate swine waste for the high rate of H2S formation remains uncertain. Here, we demonstrate the ability of the L2 strain to use common animal farming supplements including L-lysine-sulphate, gypsum and gypsum plasterboards as electron acceptors for H2S production. Genome sequencing of strain L2 revealed the presence of two megaplasmids and predicted resistance to various antimicrobials and mercury, which was confirmed in physiological experiments. Most of antibiotic resistance genes (ARG) are carried by two class 1 integrons located on the chromosome and on the plasmid pDsulf-L2-2. These ARGs, predicted to confer resistance to beta-lactams, aminoglycosides, lincosamides, sulphonamides, chloramphenicol and tetracycline, were probably laterally acquired from various Gammaproteobacteria and Firmicutes. Resistance to mercury is likely enabled by two mer operons also located on the chromosome and on pDsulf-L2-2 and acquired via horizontal gene transfer. The second megaplasmid, pDsulf-L2-1, encoded nitrogenase, catalase and type III secretion system suggesting close contact of the strain with intestinal cells in the swine gut. The location of ARGs on mobile elements allows us to consider D. vulgaris strain L2 as a possible vector transferring antimicrobials resistance determinants between the gut microbiote and microbial communities in environmental biotopes.
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Gaffney J, Embree J, Gilmore S, Embree M. Chordicoccus furentiruminis, gen. nov., sp. nov., a novel succinic acid producing bacterium isolated from a steer on a high grain diet. Int J Syst Evol Microbiol 2023; 73. [PMID: 36861667 DOI: 10.1099/ijsem.0.005751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
This study presents MP1D12T (=NRRL B-67553T=NCTC 14480T), an isolate from the ruminal content of an Angus steer fed a high grain diet. Phenotypic and genotypic traits of the isolate were explored. MP1D12T was found to be a strictly anaerobic, catalase-negative, oxidase-negative, coccoid bacterium that frequently grows in chains. Analysis of metabolic products as a result of carbohydrate fermentation showed succinic acid as the major organic acid produced with lactic acid and acetic acid as minor products. Phylogenetic analysis of MP1D12T based on 16S rRNA nucleotide sequence and amino acid sequences from the whole genome presents a divergent lineage from other members in the family Lachnospiraceae. 16S rRNA sequence comparison, whole genome average nucleotide identity digital DNA-DNA hybridization and average amino acid identity results suggest that MP1D12T represents a novel species in a novel genus within the family Lachnospiraceae. We propose the creation of the genus Chordicoccus in which MP1D12T represents the type strain for the novel species Chordicoccus furentiruminis.
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Affiliation(s)
- James Gaffney
- Native Microbials, 10255 Science Center Drive Suite C2, San Diego, CA 92121, USA
| | - Jordan Embree
- Native Microbials, 10255 Science Center Drive Suite C2, San Diego, CA 92121, USA
| | - Sean Gilmore
- Native Microbials, 10255 Science Center Drive Suite C2, San Diego, CA 92121, USA
| | - Mallory Embree
- Native Microbials, 10255 Science Center Drive Suite C2, San Diego, CA 92121, USA
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Fang D, Xu T, Sun J, Shi J, Li F, Yin Y, Wang Z, Liu Y. Nicotinamide Mononucleotide Ameliorates Sleep Deprivation-Induced Gut Microbiota Dysbiosis and Restores Colonization Resistance against Intestinal Infections. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207170. [PMID: 36698264 PMCID: PMC10037695 DOI: 10.1002/advs.202207170] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Indexed: 06/12/2023]
Abstract
Gut microbiota-mediated colonization resistance (CR) is crucial in protecting the host from intestinal infections. Sleep deprivation (SD) is an important contributor in the disturbances of intestinal homeostasis. However, whether and how SD affects host CR remains largely unknown. Here, it is shown that SD impairs intestinal CR in mice, whereas nicotinamide mononucleotide (NMN) supplementation restores it. Microbial diversity and metabolomic analyses suggest that gut microbiota and metabolite profiles in SD-treated mice are highly shaped, whereas NMN reprograms these differences. Specifically, the altered gut microbiota in SD mice further incurs the disorder of secondary bile acids pool accompanied by a decrease in deoxycholic acid (DCA). Conversely, NMN supplementation retakes the potential benefits of DCA, which is associated with specific gut microbiota involved in primary bile acids metabolic flux. In animal models of infection, DCA is effective in preventing and treating bacterial infections when used alone or in combination with antibiotics. Mechanistically, DCA alone disrupts membrane permeability and aggravates oxidative damage, thereby reducing intestinal pathogen burden. Meanwhile, exogenous DCA promotes antibiotic accumulation and destroys oxidant-antioxidant system, thus potentiating antibiotic efficacy. Overall, this work highlights the important roles of gut microbiota and bile acid metabolism in the maintenance of intestinal CR.
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Affiliation(s)
- Dan Fang
- College of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
| | - Tianqi Xu
- College of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
| | - Jingyi Sun
- College of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
| | - Jingru Shi
- College of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
| | - Fulei Li
- College of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
| | - Yanqing Yin
- College of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
| | - Zhiqiang Wang
- College of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
- Jiangsu Co‐innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesJoint International Research Laboratory of Agriculture and Agri‐Product Safety the Ministry of Education of ChinaYangzhou UniversityYangzhou225009P. R. China
- Institute of Comparative MedicineYangzhou UniversityYangzhou225009P. R. China
| | - Yuan Liu
- College of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
- Jiangsu Co‐innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesJoint International Research Laboratory of Agriculture and Agri‐Product Safety the Ministry of Education of ChinaYangzhou UniversityYangzhou225009P. R. China
- Institute of Comparative MedicineYangzhou UniversityYangzhou225009P. R. China
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33
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An Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Domestic Animals Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0028122. [PMID: 36533907 PMCID: PMC9945509 DOI: 10.1128/jcm.00281-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Novel bacterial taxonomy and nomenclature revisions can have significant impacts on clinical practice, disease epidemiology, and veterinary microbiology laboratory operations. Expansion of research on the microbiota of humans, animals, and insects has significant potential impacts on the taxonomy of organisms of clinical interest. Implications of taxonomic changes may be especially important when considering zoonotic diseases. Here, we address novel taxonomy and nomenclature revisions of veterinary significance. Noteworthy discussion centers around descriptions of novel mastitis pathogens in Streptococcaceae, Staphylococcaceae, and Actinomycetaceae; bovine reproductive tract pathogens in Corynebacteriaceae; novel members of Mannheimia spp., Leptospira spp., and Mycobacterium spp.; the transfer of Ochrobactrum spp. to Brucella spp.; and revisions to the genus Mycoplasma.
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Karnachuk OV, Panova IA, Panov VL, Ikkert OP, Kadnikov VV, Rusanov II, Avakyan MR, Glukhova LB, Lukina AP, Rakitin AV, Begmatov S, Beletsky AV, Pimenov NV, Ravin NV. Active Sulfate-Reducing Bacterial Community in the Camel Gut. Microorganisms 2023; 11:microorganisms11020401. [PMID: 36838366 PMCID: PMC9963290 DOI: 10.3390/microorganisms11020401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/18/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
The diversity and activity of sulfate-reducing bacteria (SRB) in the camel gut remains largely unexplored. An abundant SRB community has been previously revealed in the feces of Bactrian camels (Camelus bactrianus). This study aims to combine the 16S rRNA gene profiling, sulfate reduction rate (SRR) measurement with a radioactive tracer, and targeted cultivation to shed light on SRB activity in the camel gut. Fresh feces of 55 domestic Bactrian camels grazing freely on semi-arid mountain pastures in the Kosh-Agach district of the Russian Altai area were analyzed. Feces were sampled in early winter at an ambient temperature of -15 °C, which prevented possible contamination. SRR values measured with a radioactive tracer in feces were relatively high and ranged from 0.018 to 0.168 nmol S cm-3 day-1. The 16S rRNA gene profiles revealed the presence of Gram-negative Desulfovibrionaceae and spore-forming Desulfotomaculaceae. Targeted isolation allowed us to obtain four pure culture isolates belonging to Desulfovibrio and Desulforamulus. An active SRB community may affect the iron and copper availability in the camel intestine due to metal ions precipitation in the form of sparingly soluble sulfides. The copper-iron sulfide, chalcopyrite (CuFeS2), was detected by X-ray diffraction in 36 out of 55 analyzed camel feces. In semi-arid areas, gypsum, like other evaporite sulfates, can be used as a solid-phase electron acceptor for sulfate reduction in the camel gastrointestinal tract.
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Affiliation(s)
- Olga V. Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
- Correspondence:
| | - Inna A. Panova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Vasilii L. Panov
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Olga P. Ikkert
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, 119071 Moscow, Russia
| | - Igor I. Rusanov
- Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Marat R. Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Lubov B. Glukhova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Anastasia P. Lukina
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Anatolii V. Rakitin
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Shahjahon Begmatov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, 119071 Moscow, Russia
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, 119071 Moscow, Russia
| | - Nikolai V. Pimenov
- Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, 119071 Moscow, Russia
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Shedleur-Bourguignon F, Duchemin T, P. Thériault W, Longpré J, Thibodeau A, Hocine MN, Fravalo P. Distinct Microbiotas Are Associated with Different Production Lines in the Cutting Room of a Swine Slaughterhouse. Microorganisms 2023; 11:microorganisms11010133. [PMID: 36677425 PMCID: PMC9862343 DOI: 10.3390/microorganisms11010133] [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: 12/12/2022] [Revised: 12/31/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
The microorganisms found on fresh, raw meat cuts at a slaughterhouse can influence the meat's safety and spoilage patterns along further stages of processing. However, little is known about the general microbial ecology of the production environment of slaughterhouses. We used 16s rRNA sequencing and diversity analysis to characterize the microbiota heterogeneity on conveyor belt surfaces in the cutting room of a swine slaughterhouse from different production lines (each associated with a particular piece/cut of meat). Variation of the microbiota over a period of time (six visits) was also evaluated. Significant differences of alpha and beta diversity were found between the different visits and between the different production lines. Bacterial genera indicative of each visit and production line were also identified. We then created random forest models that, based on the microbiota of each sample, allowed us to predict with 94% accuracy to which visit a sample belonged and to predict with 88% accuracy from which production line it was taken. Our results suggest a possible influence of meat cut on processing surface microbiotas, which could lead to better prevention, surveillance, and control of microbial contamination of meat during processing.
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Affiliation(s)
- Fanie Shedleur-Bourguignon
- NSERC Industrial Research Chair in Meat Safety (CRSV), Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Tom Duchemin
- MESuRS Laboratory (Modelling, Epidemiology and Surveillance of Health Risks), Conservatoire National des Arts et Métiers (Cnam), 75003 Paris, France
| | - William P. Thériault
- NSERC Industrial Research Chair in Meat Safety (CRSV), Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Jessie Longpré
- F. Ménard, Division d’Olymel s.e.c., Ange-Gardien, QC J0E 1E0, Canada
| | - Alexandre Thibodeau
- NSERC Industrial Research Chair in Meat Safety (CRSV), Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
- CRIPA Swine and Poultry Infectious Diseases Research Center, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Mounia N. Hocine
- MESuRS Laboratory (Modelling, Epidemiology and Surveillance of Health Risks), Conservatoire National des Arts et Métiers (Cnam), 75003 Paris, France
| | - Philippe Fravalo
- Le Conservatoire National des Arts et Métiers (Cnam), 75003 Paris, France
- Correspondence:
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Nam N, Luong M, Yudina N, Ponamoreva ON, Alferov SV, Chi T, Dung N, Duyen P, Nghia V. Distribution of nitrogen-transforming bacteria in an artificial reservoir populated with aquatic higher plants. PROCEEDINGS OF UNIVERSITIES. APPLIED CHEMISTRY AND BIOTECHNOLOGY 2023. [DOI: 10.21285/2227-2925-2022-12-4-589-598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This article examines the distribution of nitrogen-transforming bacteria in an artificial reservoir (pond) populated with aquatic higher plants of common reed (Phragmites australis) and cattail (Typha) for treating swine wastewater. In the pond occupied by Phragmites australis, 7 strains of ammonium oxidising and 14 denitrifying bacteria were identified, while, in the pond occupied by Typha, 6 strains of ammonium oxidising and 19 denitrifying bacteria were distinguished. A comparative analysis of bacterial count at various sampling points revealed their decrease along the artificial pond. Most of the bacteria strains oxidising ammonium were identified in the samples collected from the surface layer of the pond, while denitrifying bacteria dominated the bottom layer. The isolated microorganisms identified by 16S rRNA sequencing belonged to the genus Pantoea, Enterobacter and Bacillus. An artificial pond having aquatic higher plants is characterised by a diverse microbiota, whose composition strongly depends on the wastewater source rather than on the cultivated plant species. The ammonia transformation and denitrification capacity of isolated bacterial strains was determined. The highest conversion efficiency of ammonia (up to 56%) was observed for Enterobacter cloacae bacteria isolated from the surface layer of the pond. Denitrifying bacteria sampled from the bottom layer allowed for the reduction in nitrate content from 20 to 10 mg/L in 72 h. The obtained results confirm the role of bacteria in the treatment of wastewater against nitrogen-containing pollutants, with the average efficiency of removal of inorganic nitrogen compounds being 50%.
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Affiliation(s)
- N.V.T. Nam
- Southern Branch of Joint Vietnam-Russia Tropical Science and Technology Research Center
| | - M.T. Luong
- Southern Branch of Joint Vietnam-Russia Tropical Science and Technology Research Center
| | | | | | | | - T.N.L. Chi
- Southern Branch of Joint Vietnam-Russia Tropical Science and Technology Research Center
| | - N.T. Dung
- Southern Branch of Joint Vietnam-Russia Tropical Science and Technology Research Center
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Huang L, Chen C. Employing pigs to decipher the host genetic effect on gut microbiome: advantages, challenges, and perspectives. Gut Microbes 2023; 15:2205410. [PMID: 37122143 PMCID: PMC10153013 DOI: 10.1080/19490976.2023.2205410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
The gut microbiota is a complex and diverse ecosystem comprised of trillions of microbes and plays an essential role in host's immunity, metabolism, and even behaviors. Environmental and host factors drive the huge variations in the gut microbiome among individuals. Here, we summarize accumulated evidences about host genetic effect on the gut microbial compositions with emphases on the correlation between host genetic kinship and the similarity of microbial compositions, heritability estimates of microbial taxa, and identification of genomic variants associated with the gut microbiome in pigs as well as in humans. A proportion of bacterial taxa have been reported to be heritable, and numerous variants associated with the diversity of the gut microbiota or specific taxa have been identified in both humans and pigs. LCT and ABO gene have been replicated in multiple studies, and its mechanism have been elucidated clearly. We also discuss the main advantages and challenges using pigs as experimental animals in exploring host genetic effect on the gut microbial composition and provided our insights on the perspectives in this area.
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Affiliation(s)
- Lusheng Huang
- National Key Laboratory of Pig Genetic Improvement, Jiangxi Agricultural University, Nanchang, China
| | - Congying Chen
- National Key Laboratory of Pig Genetic Improvement, Jiangxi Agricultural University, Nanchang, China
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Lin L, Lai Z, Yang H, Zhang J, Qi W, Xie F, Mao S. Genome-centric investigation of bile acid metabolizing microbiota of dairy cows and associated diet-induced functional implications. THE ISME JOURNAL 2023; 17:172-184. [PMID: 36261508 PMCID: PMC9750977 DOI: 10.1038/s41396-022-01333-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
Although the importance of bile acid (BA)-related microbial strains and enzymes is increasingly recognized for monogastric animals, a lack of knowledge about BA metabolism in dairy cows limits functional applications aimed at the targeted modulation of microbe-host interactions for animal production and health. In the present study, 108 content samples from six intestinal regions of dairy cows were used for shotgun metagenomic sequencing. Overall, 372 high-quality metagenome-assembled genomes (MAGs) were involved in BA deconjugation, oxidation, and dehydroxylation pathways. Furthermore, the BA-metabolizing microbiome predominately occurred in the large intestine, resulting in the accumulation of secondary unconjugated BAs. Comparative genomic analysis revealed that the bile salt hydrolase (BSH)-carrying microbial populations managed with the selective environment of the dairy cow intestine by adopting numerous host mucin glycan-degrading abilities. A sequence similarity network analysis classified 439 BSH homologs into 12 clusters and identified different clusters with diverse evolution, taxonomy, signal peptides, and ecological niches. Our omics data further revealed that the strains of Firmicutes bacterium CAG-110 processed the increased abundance of BSHs from Cluster 1, coinciding with the changes in the colon cholic acid concentration after grain introduction, and were intricately related to intestinal inflammation. This study is the first to use a genome-centric approach and whole intestine-targeted metabolomics to reveal microbial BA metabolism and its diet-induced functional implications in dairy cows. These findings provide insight into the manipulation of intestinal microorganisms for improving host health.
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Affiliation(s)
- Limei Lin
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zheng Lai
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Huisheng Yang
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jiyou Zhang
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Weibiao Qi
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Fei Xie
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China. .,Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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Gut Microbiome Studies in Livestock: Achievements, Challenges, and Perspectives. Animals (Basel) 2022; 12:ani12233375. [PMID: 36496896 PMCID: PMC9736591 DOI: 10.3390/ani12233375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/16/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
The variety and makeup of the gut microbiome are frequently regarded as the primary determinants of health and production performances in domestic animals. High-throughput DNA/RNA sequencing techniques (NGS) have recently gained popularity and permitted previously unheard-of advancements in the study of gut microbiota, particularly for determining the taxonomic composition of such complex communities. Here, we summarize the existing body of knowledge on livestock gut microbiome, discuss the state-of-the-art in sequencing techniques, and offer predictions for next research. We found that the enormous volumes of available data are biased toward a small number of globally distributed and carefully chosen varieties, while local breeds (or populations) are frequently overlooked despite their demonstrated resistance to harsh environmental circumstances. Furthermore, the bulk of this research has mostly focused on bacteria, whereas other microbial components such as protists, fungi, and viruses have received far less attention. The majority of these data were gathered utilizing traditional metabarcoding techniques that taxonomically identify the gut microbiota by analyzing small portions of their genome (less than 1000 base pairs). However, to extend the coverage of microbial genomes for a more precise and thorough characterization of microbial communities, a variety of increasingly practical and economical shotgun techniques are currently available.
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Zhu C, Yao J, Zhu M, Zhu C, Yuan L, Li Z, Cai D, Chen S, Hu P, Liu HY. A meta-analysis of Lactobacillus-based probiotics for growth performance and intestinal morphology in piglets. Front Vet Sci 2022; 9:1045965. [PMID: 36425121 PMCID: PMC9679148 DOI: 10.3389/fvets.2022.1045965] [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: 09/16/2022] [Accepted: 10/25/2022] [Indexed: 11/15/2023] Open
Abstract
Antibiotics are widely used as growth promoters (AGPs) in livestock production to improve animal performance and health. However, pig producers today face the prohibition of in-feed antimicrobials and have to find safe and effective alternatives. Lactobacillus species are active microorganisms that convey multiple beneficial effects to the host and are one of the most promising AGPs replacements. Here, we aim to comprehensively assess the effects of Lactobacillus spp. supplementation on growth performance and intestinal morphology (villus height [VH], crypt depth [CD], and the V/C ratio) of piglets. Among the 196 identified studies, 20 met the criteria and were included in the meta-analysis. The effects of Lactobacillus-based probiotics supplementation on growth performance and intestinal morphology were analyzed using a random-effects model. And the publication bias was evaluated by funnel plots. Our results revealed that Lactobacillus spp. supplementation significantly improved the growth performance, including average daily feed intake (ADFI), average daily gain (ADG), and the gain-to-feed ratio (G/F) in piglets (P < 0.05). Meanwhile, Lactobacillus spp. remarkably increased VH and the V/C ratio (P < 0.05) in the small intestine, including the duodenum, jejunum, and ileum, which might contribute to an improved digestive capacity of these animals. In conclusion, our findings provide concrete evidence of the growth-promoting effects of Lactobacillus spp. supplementation in piglets and a better understanding of the potential of Lactobacillus-based probiotics as AGPs alternatives in pig production.
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Affiliation(s)
- Cuipeng Zhu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jiacheng Yao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Miaonan Zhu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Chuyang Zhu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Long Yuan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhaojian Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Demin Cai
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Shihao Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, China
| | - Ping Hu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Hao-Yu Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, China
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Yi SW, Lee HG, So KM, Kim E, Jung YH, Kim M, Jeong JY, Kim KH, Oem JK, Hur TY, Oh SI. Effect of feeding raw potato starch on the composition dynamics of the piglet intestinal microbiome. Anim Biosci 2022; 35:1698-1710. [PMID: 36108705 PMCID: PMC9659463 DOI: 10.5713/ab.22.0045] [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: 01/28/2022] [Accepted: 07/04/2022] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVE Raw potato starch (RPS) is resistant to digestion, escapes absorption, and is metabolized by intestinal microflora in the large intestine and acts as their energy source. In this study, we compared the effect of different concentrations of RPS on the intestinal bacterial community of weaned piglets. METHODS Male weaned piglets (25-days-old, 7.03±0.49 kg) were either fed a corn/soybean-based control diet (CON, n = 6) or two treatment diets supplemented with 5% RPS (RPS5, n = 4) or 10% RPS (RPS10, n = 4) for 20 days and their fecal samples were collected. The day 0 and 20 samples were analyzed using a 16S rRNA gene sequencing technology, followed by total genomic DNA extraction, library construction, and high-throughput sequencing. After statistical analysis, five phyla and 45 genera accounting for over 0.5% of the reads in any of the three groups were further analyzed. Furthermore, short-chain fatty acids (SCFAs) in the day 20 fecal samples were analyzed using gas chromatography. RESULTS Significant changes were not observed in the bacterial composition at the phylum level even after 20 d post feeding (dpf); however, the abundance of Intestinimonas and Barnesiella decreased in both RPS treatment groups compared to the CON group. Consumption of 5% RPS increased the abundance of Roseburia (p<0.05) and decreased the abundance of Clostridium (p<0.01) and Mediterraneibacter (p< 0.05). In contrast, consumption of 10% RPS increased the abundance of Olsenella (p<0.05) and decreased the abundance of Campylobacter (p<0.05), Kineothrix (p<0.05), Paraprevotella (p<0.05), and Vallitalea (p<0.05). Additionally, acetate (p<0.01), butyrate (p<0.05), valerate (p = 0.01), and total SCFAs (p = 0.01) were upregulated in the RPS5 treatment group. CONCLUSION Feeding 5% RPS altered bacterial community composition and promoted gut health in weaned piglets. Thus, resistant starch as a feed additive may prevent diarrhea in piglets during weaning.
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Affiliation(s)
- Seung-Won Yi
- Division of Animal Diseases & Health, National Institute of Animal Science, Rural Development Administration, Wanju 55365,
Korea
| | - Han Gyu Lee
- Division of Animal Diseases & Health, National Institute of Animal Science, Rural Development Administration, Wanju 55365,
Korea,Laboratory of Veterinary Infectious Disease, College of Veterinary Medicine, Jeonbuk National University, Iksan 54596,
Korea
| | - Kyoung-Min So
- Division of Animal Diseases & Health, National Institute of Animal Science, Rural Development Administration, Wanju 55365,
Korea
| | - Eunju Kim
- Division of Animal Diseases & Health, National Institute of Animal Science, Rural Development Administration, Wanju 55365,
Korea
| | - Young-Hun Jung
- Division of Animal Diseases & Health, National Institute of Animal Science, Rural Development Administration, Wanju 55365,
Korea
| | - Minji Kim
- Animal Nutrition and Physiology Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365,
Korea
| | - Jin Young Jeong
- Animal Nutrition and Physiology Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365,
Korea
| | - Ki Hyun Kim
- Animal Welfare Research Team, National Institute of Animal Science, Rural Development Administration, Wanju 55365,
Korea
| | - Jae-Ku Oem
- Laboratory of Veterinary Infectious Disease, College of Veterinary Medicine, Jeonbuk National University, Iksan 54596,
Korea
| | - Tai-Young Hur
- Division of Animal Diseases & Health, National Institute of Animal Science, Rural Development Administration, Wanju 55365,
Korea
| | - Sang-Ik Oh
- Division of Animal Diseases & Health, National Institute of Animal Science, Rural Development Administration, Wanju 55365,
Korea,Corresponding Author: Sang-Ik Oh, Tel: +82-63-238-7228, Fax: +82-63-238-7235, E-mail:
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Lee AY, Chen CH, Liou JS, Lin YC, Hamada M, Wang YT, Peng LL, Chang SC, Chen CC, Lin CF, Huang L, Huang CH. Micrococcus porci sp. nov., Isolated from Feces of Black Pig ( Sus scrofa). Life (Basel) 2022; 12:life12111749. [PMID: 36362904 PMCID: PMC9697426 DOI: 10.3390/life12111749] [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: 10/08/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
An aerobic bacterium, designated as strain KD337-16T, was isolated from the fecal samples of a black pig. It exhibited spherical, non-motile and non−spore-forming, Gram-positive cells. KD337-16T was identified as a member of the genus Micrococcus through 16S rRNA gene sequencing, and its closest relatives were found to be Micrococcus endophyticus YIM 56238T (99.5% similarity), Micrococcus luteus NCTC 2665T (99.1%), Micrococcus yunnanensis YIM 65004T (99.1%), Micrococcus aloeverae AE-6T (99.1%), Micrococcus antarcticus T2T (98.9%), and Micrococcus flavus LW4T (98.7%). Phylogenomic trees were constructed, and strain KD337-16T was found to form its own cluster as an independent lineage of M. flavus LW4T. Between KD337-16T and its close relatives, the average nucleotide identity, average amino acid identity, and digital DNA−DNA hybridization were below the respective species delineation thresholds at 82.1−86.6%, 78.1−86.1%, and 24.4−34.9%. The major cellular fatty acids and polar lipids were anteiso-C15:0 and iso-C15:0, and DPG and PG, respectively. The predominant menaquinone was MK-8(H2). Taken together, the results indicate that strain KD337-16T is a novel species of the genus Micrococcus, for which the name Micrococcus porci sp. nov. is proposed. The type strain is KD337-16T (=BCRC 81318T = NBRC 115578T).
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Affiliation(s)
- Ai-Yun Lee
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan
| | - Chia-Hsuan Chen
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan
| | - Jong-Shian Liou
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan
| | - Yu-Chun Lin
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Yu-Ting Wang
- Division of Research and Analysis, Food and Drug Administration, Ministry of Health and Welfare, Taipei 11561, Taiwan
| | - Lin-Liang Peng
- Kaohsiung Animal Propagation Station, COA-LRI, Pingtung 91247, Taiwan
| | - Shen-Chang Chang
- Kaohsiung Animal Propagation Station, COA-LRI, Pingtung 91247, Taiwan
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Chuen-Fu Lin
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan
| | - Lina Huang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan
- Correspondence: ; Tel.: +886-3-522-3191; Fax: +886-3-522-4171
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Zhang G, Lv X, Cheng Y, Lai XH, Yang J, Jin D, Lu S, Pu J, Liu L, Xu J. New members of the family Eggerthellaceae isolated from Marmota himalayana: Xiamenia xianingshaonis gen. nov., sp. nov., from intestinal contents, and Berryella wangjianweii sp. nov., from trachea. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four strictly anaerobic, Gram-stain-positive, urease-, oxidase- and catalase-negative, rod-shaped strains (zg-886T/zg-887 and zg-1050T/zg-1084) were isolated from Marmota himalayana. Comparison analysis of 16S rRNA genes showed that the two strain pairs belong to the family
Eggerthellaceae
: zg-1050T and zg-1084 were most closely related to
Berryella intestinalis
68-1-3T (97.2 %), while zg-886T/zg-887 had the highest similarity to
Slackia piriformis
YIT 12062T (91.6 %), followed by
Paraeggerthella hongkongensis
DSM 16106T (91.4 %) and
Gordonibacter urolithinfaciens
DSM 27213T (91.4 %). Phylogenetic analyses based on 16S rRNA genes and genomes showed that the two strain pairs represent two different lineages within the family
Eggerthellaceae
. The genomic G+C contents of strains zg-886T and zg-1050T were 63.0 and 66.3 mol%, respectively. The values of digital DNA–DNA hybridization, average nucleotide identity, average amino acid identity and the percentage of conserved proteins between the two new type strains and members of the family
Eggerthellaceae
were lower than the respective thresholds for delineation of a species or genus. In contrast to the absence of any known quinones in strain zg-1050T, strain zg-886T contained MK-6 (42.5 %), MMK-6 (25.0 %) and DMMK-6 (32.5 %). The four strains grew optimally at pH 7.0, 37 ºC and 0.5 % NaCl (w/v). According to these polyphasic analyses, two new members within the family
Eggerthellaceae
are proposed, Xiamenia xianingshaonis gen. nov., sp. nov. (zg-886T=JCM 34097T=GDMCC 1.1710T) and Berryella wangjianweii sp. nov. (zg-1050T=GDMCC 1.2426T=JCM 34748T).
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Affiliation(s)
- Gui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
| | - Xianglian Lv
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
| | - Yanpeng Cheng
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518073, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu 476000, PR China
| | - Jing Yang
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dong Jin
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shan Lu
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jianguo Xu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- Institute of Public Health, Nankai University, Tianjin 300071, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
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IJdema F, De Smet J, Crauwels S, Lievens B, Van Campenhout L. Meta-analysis of larvae of the black soldier fly (Hermetia illucens) microbiota based on 16S rRNA gene amplicon sequencing. FEMS Microbiol Ecol 2022; 98:fiac094. [PMID: 35977400 PMCID: PMC9453823 DOI: 10.1093/femsec/fiac094] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/16/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
Black soldier fly larvae (BSFL) belong to the most widely reared insects as an alternative protein source at industrial scale. Bacteria in the larval gut can provide benefits for the animal, though some bacteria can also be pathogenic for the insect. Accurate characterization of the BSFL microbiota is important for the production of BSFL in terms of yield and microbiological safety. In this study, 16S ribosomal RNA gene sequence data sets from 11 studies were re-analysed to gain better insights in the BSFL gut microbiota, potential factors that influence their composition, and differences between the gut and the whole larvae microbiota. A core gut microbiota was found consisting of members of Enterococcus, Klebsiella, Morganella, Providencia, and Scrofimicrobium. Further, the factors 'Study', 'Age' and 'Feed' (i.e. rearing substrate of the larvae) significantly affected the microbiota gut composition. When compared to whole larvae, a significantly lower diversity was found for gut samples, suggesting that the larvae harboured additional microbes on their cuticle or in the insect body. Universal choices in insect sample type, primer selection and bio-informatics analysis pipeline can strengthen future meta-analyses and improve our understanding of the BSFL gut microbiota towards the optimization of insect rearing conditions and substrates.
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Affiliation(s)
- Freek IJdema
- CLMT Research Group for Insect Production and Processing, Department of Microbial and Molecular Systems (MS), KU Leuven, B-3001, Campus Geel, Geel, B-2440, Belgium
- KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, B-3001, Belgium
| | - Jeroen De Smet
- CLMT Research Group for Insect Production and Processing, Department of Microbial and Molecular Systems (MS), KU Leuven, B-3001, Campus Geel, Geel, B-2440, Belgium
- KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, B-3001, Belgium
| | - Sam Crauwels
- CMPG Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M²S), KU Leuven, Leuven, B-3001, Belgium
| | - Bart Lievens
- CMPG Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M²S), KU Leuven, Leuven, B-3001, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, B-3001, Belgium
| | - Leen Van Campenhout
- CLMT Research Group for Insect Production and Processing, Department of Microbial and Molecular Systems (MS), KU Leuven, B-3001, Campus Geel, Geel, B-2440, Belgium
- KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, B-3001, Belgium
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45
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Weber M, Fuchs TM. Metabolism in the Niche: a Large-Scale Genome-Based Survey Reveals Inositol Utilization To Be Widespread among Soil, Commensal, and Pathogenic Bacteria. Microbiol Spectr 2022; 10:e0201322. [PMID: 35924911 PMCID: PMC9430895 DOI: 10.1128/spectrum.02013-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/22/2022] [Indexed: 11/20/2022] Open
Abstract
Phytate is the main phosphorus storage molecule of plants and is therefore present in large amounts in the environment and in the diet of humans and animals. Its dephosphorylated form, the polyol myo-inositol (MI), can be used by bacteria as a sole carbon and energy source. The biochemistry and regulation of MI degradation were deciphered in Bacillus subtilis and Salmonella enterica, but a systematic survey of this catabolic pathway has been missing until now. For a comprehensive overview of the distribution of MI utilization, we analyzed 193,757 bacterial genomes, representing a total of 24,812 species, for the presence, organization, and taxonomic prevalence of inositol catabolic gene clusters (IolCatGCs). The genetic capacity for MI degradation was detected in 7,384 (29.8%) of all species for which genome sequences were available. IolCatGC-positive species were particularly found among Actinobacteria and Proteobacteria and to a much lesser extent in Bacteroidetes. IolCatGCs are very diverse in terms of gene number and functions, whereas the order of core genes is highly conserved on the phylum level. We predict that 111 animal pathogens, more than 200 commensals, and 430 plant pathogens or rhizosphere bacteria utilize MI, underscoring that IolCatGCs provide a growth benefit within distinct ecological niches. IMPORTANCE This study reveals that the capacity to utilize inositol is unexpectedly widespread among soil, commensal, and pathogenic bacteria. We assume that this yet-neglected metabolism plays a pivotal role in the microbial turnover of phytate and inositols. The bioinformatic tool established here enables predicting to which extent and genetic variance a bacterial determinant is present in all genomes sequenced so far.
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Affiliation(s)
- Michael Weber
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
| | - Thilo M. Fuchs
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
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46
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Basic M, Dardevet D, Abuja PM, Bolsega S, Bornes S, Caesar R, Calabrese FM, Collino M, De Angelis M, Gérard P, Gueimonde M, Leulier F, Untersmayr E, Van Rymenant E, De Vos P, Savary-Auzeloux I. Approaches to discern if microbiome associations reflect causation in metabolic and immune disorders. Gut Microbes 2022; 14:2107386. [PMID: 35939623 PMCID: PMC9361767 DOI: 10.1080/19490976.2022.2107386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Our understanding of microorganisms residing within our gut and their roles in the host metabolism and immunity advanced greatly over the past 20 years. Currently, microbiome studies are shifting from association and correlation studies to studies demonstrating causality of identified microbiome signatures and identification of molecular mechanisms underlying these interactions. This transformation is crucial for the efficient translation into clinical application and development of targeted strategies to beneficially modulate the intestinal microbiota. As mechanistic studies are still quite challenging to perform in humans, the causal role of microbiota is frequently evaluated in animal models that need to be appropriately selected. Here, we provide a comprehensive overview on approaches that can be applied in addressing causality of host-microbe interactions in five major animal model organisms (Caenorhabditis elegans, Drosophila melanogaster, zebrafish, rodents, and pigs). We particularly focused on discussing methods available for studying the causality ranging from the usage of gut microbiota transfer, diverse models of metabolic and immune perturbations involving nutritional and chemical factors, gene modifications and surgically induced models, metabolite profiling up to culture-based approached. Furthermore, we addressed the impact of the gut morphology, physiology as well as diet on the microbiota composition in various models and resulting species specificities. Finally, we conclude this review with the discussion on models that can be applied to study the causal role of the gut microbiota in the context of metabolic syndrome and host immunity. We hope this review will facilitate important considerations for appropriate animal model selection.
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Affiliation(s)
- Marijana Basic
- Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Dominique Dardevet
- Human Nutrition Unit, UMR1019, University Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Peter Michael Abuja
- Diagnostic & Research Centre of Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Silvia Bolsega
- Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Stéphanie Bornes
- University Clermont Auvergne, Inrae, VetAgro Sup, Umrf, Aurillac, France
| | - Robert Caesar
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Massimo Collino
- Rita Levi-Montalcini Department of Neuroscience, University of Turin, Turin, Italy
| | - Maria De Angelis
- Department of Soil, Plant and Science, “Aldo Moro” University Bari, Bari, Italy
| | - Philippe Gérard
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, France
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, IPLA-CSIC;Villaviciosa, Spain
| | - François Leulier
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, UMR5242 CNRS, Université Claude Bernard-Lyon1, Lyon, France
| | - Eva Untersmayr
- Institute of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Austria
| | - Evelien Van Rymenant
- Flanders Research Institute for Agriculture, Fisheries and Food (Ilvo), Merelbeke, Belgium
| | - Paul De Vos
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University Medical Center Groningen; Groningen, Netherlands
| | - Isabelle Savary-Auzeloux
- Human Nutrition Unit, UMR1019, University Clermont Auvergne, INRAE, Clermont-Ferrand, France,CONTACT Isabelle Savary-Auzeloux Human Nutrition Unit, UMR1019, University Clermont Auvergne, INRAE, Clermont-Ferrand, France
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47
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Mbaye B, Lo CI, Dione N, Benabdelkader S, Tidjani Alou M, Brahimi S, Armstrong N, Alibar S, Raoult D, Moal V, Million M, Fournier PE, Fenollar F. Peptoniphilus coli sp. nov. and Peptoniphilus urinae sp. nov., isolated from humans. Arch Microbiol 2022; 204:506. [PMID: 35857142 PMCID: PMC9300514 DOI: 10.1007/s00203-022-03044-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 11/23/2022]
Abstract
Strains Marseille-P3761 and Marseille-P3195 are representatives of two bacterial species isolated from human specimens. Strain Marseille-P3761 was isolated from the stool of a healthy volunteer, while strain Marseille-P3915 was cultivated from the urine of a kidney transplant recipient. Both strains are anaerobic Gram-positive coccoid bacteria. Both are catalase-negative and oxidase-negative and grow optimally at 37 °C in anaerobic conditions. They also metabolize carbohydrates, such as galactose, glucose, fructose, and glycerol. The major fatty acids were hexadecanoic acid for both strains. The highest digital DNA–DNA hybridization (dDDH) values of Marseille-P3761 and Marseille-P3195 strains when compared to their closest phylogenetic relatives were 52.3% and 56.4%, respectively. Strains Marseille-P3761 and Marseille-P3195 shared an OrthoANI value of 83.5% which was the highest value found with Peptoniphilus species studied here. The morphological, biochemical, phenotypic and genomic characteristics strongly support that these strains are new members of the Peptoniphilus genus. Thus, we suggest that Peptoniphilus coli sp. nov., and Peptoniphilus urinae sp. nov., are new species for which strains Marseille-P3761 (CSUR P3761 = CCUG 71,569) and Marseille-P3195 (CSUR P3195 = DSM 103,468) are their type strains, respectively of two new Peptoniphilus species, for which we propose the names Peptoniphilus coli sp. nov. and Peptoniphilus urinae sp. nov., respectively.
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Affiliation(s)
- Babacar Mbaye
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Cheikh Ibrahima Lo
- IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Niokhor Dione
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Sarah Benabdelkader
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Maryam Tidjani Alou
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Samy Brahimi
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Nicholas Armstrong
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Stéphane Alibar
- IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Valérie Moal
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,AP-HM, Hôpital Conception, Centre de Néphrologie Et Transplantation Rénale, Centre Hospitalo-Universitaire Conception, Marseille, France
| | - Matthieu Million
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Florence Fenollar
- IHU-Méditerranée Infection, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France. .,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.
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48
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Li Y, Wang Y, Liu J. Genomic Insights Into the Interspecific Diversity and Evolution of Mobiluncus, a Pathogen Associated With Bacterial Vaginosis. Front Microbiol 2022; 13:939406. [PMID: 35865929 PMCID: PMC9294530 DOI: 10.3389/fmicb.2022.939406] [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: 05/09/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial vaginosis (BV) is a common vaginal infection and has been associated with increased risk for a wide array of health issues. BV is linked with a variety of heterogeneous pathogenic anaerobic bacteria, among which Mobiluncus is strongly associated with BV diagnosis. However, their genetic features, pathogenicity, interspecific diversity, and evolutionary characters have not been illustrated at genomic level. The current study performed phylogenomic and comparative genomic analyses of Mobiluncus. Phylogenomic analyses revealed remarkable phylogenetic distinctions among different species. Compared with M. curtisii, M. mulieris had a larger genome and pangenome size with more insertion sequences but less CRISPR-Cas systems. In addition, these two species were diverse in profile of virulence factors, but harbored similar antibiotic resistance genes. Statistically different functional genome profiles between strains from the two species were determined, as well as correlations of some functional genes/pathways with putative pathogenicity. We also showed that high levels of horizontal gene transfer might be an important strategy for species diversification and pathogenicity. Collectively, this study provides the first genome sequence level description of Mobiluncus, and may shed light on its virulence/pathogenicity, functional diversification, and evolutionary dynamics. Our study could facilitate the further investigations of this important pathogen, and might improve the future treatment of BV.
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49
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Vasquez R, Oh JK, Song JH, Kang DK. Gut microbiome-produced metabolites in pigs: a review on their
biological functions and the influence of probiotics. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2022; 64:671-695. [PMID: 35969697 PMCID: PMC9353353 DOI: 10.5187/jast.2022.e58] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/23/2022] [Accepted: 07/04/2022] [Indexed: 11/20/2022]
Abstract
The gastrointestinal tract is a complex ecosystem that contains a large number of
microorganisms with different metabolic capacities. Modulation of the gut
microbiome can improve the growth and promote health in pigs. Crosstalk between
the host, diet, and the gut microbiome can influence the health of the host,
potentially through the production of several metabolites with various
functions. Short-chain and branched-chain fatty acids, secondary bile acids,
polyamines, indoles, and phenolic compounds are metabolites produced by the gut
microbiome. The gut microbiome can also produce neurotransmitters (such as
γ-aminobutyric acid, catecholamines, and serotonin), their precursors,
and vitamins. Several studies in pigs have demonstrated the importance of the
gut microbiome and its metabolites in improving growth performance and feed
efficiency, alleviating stress, and providing protection from pathogens. The use
of probiotics is one of the strategies employed to target the gut microbiome of
pigs. Promising results have been published on the use of probiotics in
optimizing pig production. This review focuses on the role of gut
microbiome-derived metabolites in the performance of pigs and the effects of
probiotics on altering the levels of these metabolites.
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Affiliation(s)
- Robie Vasquez
- Department of Animal Resources Science,
Dankook University, Cheonan 31116, Korea
| | - Ju Kyoung Oh
- Department of Animal Resources Science,
Dankook University, Cheonan 31116, Korea
| | - Ji Hoon Song
- Department of Animal Resources Science,
Dankook University, Cheonan 31116, Korea
| | - Dae-Kyung Kang
- Department of Animal Resources Science,
Dankook University, Cheonan 31116, Korea
- Corresponding author: Dae-Kyung Kang,
Department of Animal Resources Science, Dankook University, Cheonan 31116,
Korea. Tel: +82-41-550-3655, E-mail:
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50
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Baholet D, Skalickova S, Batik A, Malyugina S, Skladanka J, Horky P. Importance of Zinc Nanoparticles for the Intestinal Microbiome of Weaned Piglets. Front Vet Sci 2022; 9:852085. [PMID: 35720843 PMCID: PMC9201420 DOI: 10.3389/fvets.2022.852085] [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: 01/10/2022] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
The scientific community is closely monitoring the replacement of antibiotics with doses of ZnO in weaned piglets. Since 2022, the use of zinc in medical doses has been banned in the European Union. Therefore, pig farmers are looking for other solutions. Some studies have suggested that zinc nanoparticles might replace ZnO for the prevention of diarrhea in weaning piglets. Like ZnO, zinc nanoparticles are effective against pathogenic microorganisms, e.g., Enterobacteriaceae family in vitro and in vivo. However, the effect on probiotic Lactobacillaceae appears to differ for ZnO and zinc nanoparticles. While ZnO increases their numbers, zinc nanoparticles act in the opposite way. These phenomena have been also confirmed by in vitro studies that reported a strong antimicrobial effect of zinc nanoparticles against Lactobacillales order. Contradictory evidence makes this topic still controversial, however. In addition, zinc nanoparticles vary in their morphology and properties based on the method of their synthesis. This makes it difficult to understand the effect of zinc nanoparticles on the intestinal microbiome. This review is aimed at clarifying many circumstances that may affect the action of nanoparticles on the weaning piglets' microbiome, including a comprehensive overview of the zinc nanoparticles in vitro effects on bacterial species occurring in the digestive tract of weaned piglets.
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Affiliation(s)
- Daria Baholet
- Department of Animal Nutrition and Forage Production, Mendel University in Brno, Brno, Czechia
| | - Sylvie Skalickova
- Department of Animal Nutrition and Forage Production, Mendel University in Brno, Brno, Czechia
| | - Andrej Batik
- Department of Animal Morphology, Physiology and Genetics, Mendel University in Brno, Brno, Czechia
| | - Svetlana Malyugina
- Department of Animal Nutrition and Forage Production, Mendel University in Brno, Brno, Czechia
| | - Jiri Skladanka
- Department of Animal Nutrition and Forage Production, Mendel University in Brno, Brno, Czechia
| | - Pavel Horky
- Department of Animal Nutrition and Forage Production, Mendel University in Brno, Brno, Czechia
- *Correspondence: Pavel Horky
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