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Kitson L, Becker AAMJ, Hartmann K, Bergmann M, Sepulveda-Garcia P, Canales N, Muller A. Characterizing the blood microbiota in healthy and febrile domestic cats via 16s rRNA sequencing. Sci Rep 2024; 14:10584. [PMID: 38719878 PMCID: PMC11079020 DOI: 10.1038/s41598-024-61023-4] [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: 12/25/2023] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
This study aimed to evaluate the blood bacterial microbiota in healthy and febrile cats. High-quality sequencing reads from the 16S rRNA gene variable region V3-V4 were obtained from genomic blood DNA belonging to 145 healthy cats, and 140 febrile cats. Comparisons between the blood microbiota of healthy and febrile cats revealed dominant presence of Actinobacteria, followed by Firmicutes and Proteobacteria, and a lower relative abundance of Bacteroidetes. Upon lower taxonomic levels, the bacterial composition was significantly different between healthy and febrile cats. The families Faecalibacterium and Kineothrix (Firmicutes), and Phyllobacterium (Proteobacteria) experienced increased abundance in febrile samples. Whereas Thioprofundum (Proteobacteria) demonstrated a significant decrease in abundance in febrile. The bacterial composition and beta diversity within febrile cats was different according to the affected body system (Oral/GI, systemic, skin, and respiratory) at both family and genus levels. Sex and age were not significant factors affecting the blood microbiota of febrile cats nor healthy ones. Age was different between young adult and mature adult healthy cats. Alpha diversity was unaffected by any factors. Overall, the findings suggest that age, health status and nature of disease are significant factors affecting blood microbiota diversity and composition in cats, but sex is not.
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Affiliation(s)
- Liam Kitson
- Graduate Program, Ross University School of Veterinary Medicine, West Farm, West Indies, Saint Kitts and Nevis
| | - Anne A M J Becker
- One Health Center for Zoonoses and Tropical Veterinary Medicine, Biomedical Sciences Department, Ross University School of Veterinary Medicine, West Farm, West Indies, Saint Kitts and Nevis
| | - Katrin Hartmann
- LMU Small Animal Clinic, Centre for Clinical Veterinary Medicine, LMU Munich, Munich, Germany
| | - Michèle Bergmann
- LMU Small Animal Clinic, Centre for Clinical Veterinary Medicine, LMU Munich, Munich, Germany
| | - Paulina Sepulveda-Garcia
- Instituto de Medicina Preventiva Veterinaria, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
- Escuela de Graduados, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Nivia Canales
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Ananda Muller
- One Health Center for Zoonoses and Tropical Veterinary Medicine, Biomedical Sciences Department, Ross University School of Veterinary Medicine, West Farm, West Indies, Saint Kitts and Nevis.
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Alharbi K, Ekesi N, Hasan A, Asnayanti A, Liu J, Murugesan R, Ramirez S, Rochell S, Kidd MT, Alrubaye A. Deoxynivalenol and fumonisin predispose broilers to bacterial chondronecrosis with osteomyelitis lameness. Poult Sci 2024; 103:103598. [PMID: 38489885 PMCID: PMC10951539 DOI: 10.1016/j.psj.2024.103598] [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: 11/15/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Bacterial chondronecrosis with osteomyelitis (BCO) lameness is the most critical animal health and welfare issue facing the broiler industry worldwide. It is estimated that 1 to 2% of bird condemnation at marketing age is caused by BCO lameness, resulting in tens of millions of dollars in annual losses. Fast-growing broilers are prone to mechanical stress that triggers bacterial translocation across epithelial barriers into the bloodstream, followed by bacterial colonization in the growth plate of long bones, and eventually, bone necrosis and lameness. Mycotoxins (MTX) are secondary metabolites produced naturally by microfungi, of which deoxynivalenol (DON), fumonisin (FUM), and zearalenone are the most prevalent in corn and soybean-meal-based diets. The presence of these mycotoxins in feed has been proven to reduce the barrier strength of the intestinal tracts and trigger immunosuppressive effects. In this study, we investigated the effects of the DON and FUM-contaminated feeds on the incidence of BCO lameness in broilers reared in both wire- and litter-floors. 720 one-day-old broiler chicks were assigned to the 2 × 2 factorial design: 2 MTX diets containing DON and FUM on wire flooring (MTX-W) and litter flooring (MTX-L), and 2 diets without MTX contamination on control wire flooring (CW) and control litter flooring (CL). Throughout the trial, the cumulative incidence of lameness per treatment was assessed by necropsying the lame birds. Birds in the MTX-W group had a higher incidence of lameness compared to those in CW (73.3% vs. 62.0%) (P < 0.05), and birds in the MTX-L group had a higher incidence of lameness compared to birds in CL (54.0% vs. 34.0%) (P < 0.05). MTX elicited net increases in BCO to a greater degree on litter (+20%) than on wire flooring (+12%). The increased incidence of BCO lameness in the MTX-W coincided with increased intestinal permeability supporting a correlation between intestinal barrier integrity and BCO lameness. To conclude, DON and FUM are predisposing factors for increasing BCO. However, no significant interaction exists between the diet and floor types in inducing lameness in broilers.
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Affiliation(s)
- Khawla Alharbi
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas, USA; Department of Poultry Science, University of Arkansas, Fayetteville, Arkansas, USA
| | - Nnamdi Ekesi
- Department of Natural Sciences, Northeastern State University, Tahlequah, OK, USA
| | - Amer Hasan
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas, USA; Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA; Department of Veterinary Public Health, College of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
| | - Andi Asnayanti
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas, USA; Department of Poultry Science, University of Arkansas, Fayetteville, Arkansas, USA
| | - Jundi Liu
- Department of Poultry Science, University of Georgia, Athens, GA 30602, USA
| | - Raj Murugesan
- Department of Poultry Science, Auburn University, Auburn, Alabama, USA
| | | | - Samuel Rochell
- Department of Poultry Science, Auburn University, Auburn, Alabama, USA
| | - Michael T Kidd
- Department of Poultry Science, University of Arkansas, Fayetteville, Arkansas, USA
| | - Adnan Alrubaye
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas, USA; Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA; Department of Poultry Science, University of Arkansas, Fayetteville, Arkansas, USA.
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Adriaensen V, Van Immerseel F, Ducatelle R, Kettunen H, Vuorenmaa J, Goossens E. Enterobacteriaceae and Enterococcaceae are the dominant bacterial families translocating to femur heads in broiler chicks. Avian Pathol 2024; 53:115-123. [PMID: 38096268 DOI: 10.1080/03079457.2023.2288872] [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] [Accepted: 11/21/2023] [Indexed: 12/20/2023]
Abstract
RESEARCH HIGHLIGHTS Large number of bacteria isolated from femoral heads of clinically healthy broilers.The prevailing taxa in femoral heads were Escherichia/Shigella and Enterococcus spp.Continuous presence of bacteria in blood and liver of clinically healthy broilers.Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae prevail in blood and liver.
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Affiliation(s)
| | | | - Richard Ducatelle
- Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | | | | | - Evy Goossens
- Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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Choppa VSR, Kim WK. A Review on Pathophysiology, and Molecular Mechanisms of Bacterial Chondronecrosis and Osteomyelitis in Commercial Broilers. Biomolecules 2023; 13:1032. [PMID: 37509068 PMCID: PMC10377700 DOI: 10.3390/biom13071032] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Modern day broilers have a great genetic potential to gain heavy bodyweights with a huge metabolic demand prior to their fully mature ages. Moreover, this made the broilers prone to opportunistic pathogens which may enter the locomotory organs under stress causing bacterial chondronecrosis and osteomyelitis (BCO). Such pathogenic colonization is further accelerated by microfractures and clefts that are formed in the bones due to rapid growth rate of the broilers along with ischemia of blood vessels. Furthermore, there are several pathways which alter bone homeostasis like acute phase response, and intrinsic and extrinsic cell death pathways. In contrast, all the affected birds may not exhibit clinical lameness even with the presence of lameness associated factors causing infection. Although Staphylococcus, E. coli, and Enterococcus are considered as common bacterial pathogens involved in BCO, but there exist several other non-culturable bacteria. Any deviation from maintaining a homeostatic environment in the gut might lead to bacterial translocation through blood followed by proliferation of pathogenic bacteria in respective organs including bones. It is important to alleviate dysbiosis of the blood which is analogous to dysbiosis in the gut. This can be achieved by supplementing pro, pre, and synbiotics which helps in providing a eubiotic environment abating the bacterial translocation that was studied to the incidence of BCO. This review focused on potential and novel biomarkers, pathophysiological mechanism, the economic significance of BCO, immune mechanisms, and miscellaneous factors causing BCO. In addition, the role of gut microbiomes along with their diversity and cell culture models from compact bones of chicken in better understanding of BCO were explored.
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Affiliation(s)
| | - Woo Kyun Kim
- Department of Poultry Science, University of Georgia, Athens, GA 30602, USA
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5
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Herder EA, Skeen HR, Lutz HL, Hird SM. Body Size Poorly Predicts Host-Associated Microbial Diversity in Wild Birds. Microbiol Spectr 2023; 11:e0374922. [PMID: 37039681 PMCID: PMC10269867 DOI: 10.1128/spectrum.03749-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/12/2023] [Indexed: 04/12/2023] Open
Abstract
The composition and diversity of avian microbiota are shaped by many factors, including host ecologies and environmental variables. In this study, we examine microbial diversity across 214 bird species sampled in Malawi at five major body sites: blood, buccal cavity, gizzard, intestinal tract, and cloaca. Microbial community dissimilarity differed significantly across body sites. Ecological theory predicts that as area increases, so does diversity. We tested the hypothesis that avian microbiota diversity is correlated with body size, used as a proxy for area, using comparative phylogenetic methods. Using Pagel's lambda, we found that few microbial diversity metrics had significant phylogenetic signals. Phylogenetic generalized least squares identified a significant but weak negative correlation between host size and microbial diversity of the blood and a similarly significant but weakly positive correlation between the cloacal microbiota and host size among birds within the order Passeriformes. Phylosymbiosis, or a congruent branching pattern between host phylogeny and their associated microbiota similarity, was tested and found to be weak or not significant in four of the body sites with sufficient sample size (blood, buccal, cloaca, and intestines). Taken together, these results suggest that the avian microbiome is highly variable, with microbiota diversity demonstrating few clear associations with bird size. Finally, the blood microbiota have a unique relationship with host size. IMPORTANCE All animals coexist and interact with microorganisms, including bacteria, archaea, microscopic eukaryotes, and viruses. These microorganisms can have an enormous influence on the biology and health of macro-organisms. However, the general rules that govern these host-associated microbial communities are poorly described, especially in wild animals. In this paper, we investigate the microbial communities of over 200 species of birds from Malawi and characterize five body site bacterial microbiota in depth. Because the evolutionary relationships of the host underlie the relationship between any host-associated microbiota relationships, we use phylogenetic comparative methods to account for this relationship. We find that the size of a host (the bird) and the diversity and composition of the microbiota are largely uncorrelated. We also find that the general pattern of similarity between host phylogeny and microbiota similarity is weak. Together, we see that bird microbiota are not strongly tied to host size or evolutionary history.
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Affiliation(s)
- Elizabeth A. Herder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Heather R. Skeen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Holly L. Lutz
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
- Department of Pediatrics, UC San Diego School of Medicine, La Jolla, California, USA
| | - Sarah M. Hird
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
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Ramser A, Hawken R, Greene E, Okimoto R, Flack B, Christopher CJ, Campagna SR, Dridi S. Bone Metabolite Profile Differs between Normal and Femur Head Necrosis (FHN/BCO)-Affected Broilers: Implications for Dysregulated Metabolic Cascades in FHN Pathophysiology. Metabolites 2023; 13:metabo13050662. [PMID: 37233703 DOI: 10.3390/metabo13050662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/28/2023] [Accepted: 04/30/2023] [Indexed: 05/27/2023] Open
Abstract
Femur head necrosis (FHN), also known as bacterial chondronecrosis with osteomyelitis (BCO), has remained an animal welfare and production concern for modern broilers regardless of efforts to select against it in primary breeder flocks. Characterized by the bacterial infection of weak bone, FHN has been found in birds without clinical lameness and remains only detectable via necropsy. This presents an opportunity to utilize untargeted metabolomics to elucidate potential non-invasive biomarkers and key causative pathways involved in FHN pathology. The current study used ultra-performance liquid chromatography coupled with high-resolution mass spectrometry (UPLC-HRMS) and identified a total of 152 metabolites. Mean intensity differences at p < 0.05 were found in 44 metabolites, with 3 significantly down-regulated and 41 up-regulated in FHN-affected bone. Multivariate analysis and a partial least squares discriminant analysis (PLS-DA) scores plot showed the distinct clustering of metabolite profiles from FHN-affected vs. normal bone. Biologically related molecular networks were predicted using an ingenuity pathway analysis (IPA) knowledge base. Using a fold-change cut off of -1.5 and 1.5, top canonical pathways, networks, diseases, molecular functions, and upstream regulators were generated using the 44 differentially abundant metabolites. The results showed the metabolites NAD+, NADP+, and NADH to be downregulated, while 5-Aminoimidazole-4-carboxamide ribonucleotide (AICAR) and histamine were significantly increased in FHN. Ascorbate recycling and purine nucleotides degradation were the top canonical pathways, indicating the potential dysregulation of redox homeostasis and osteogenesis. Lipid metabolism and cellular growth and proliferation were some of the top molecular functions predicted based on the metabolite profile in FHN-affected bone. Network analysis showed significant overlap across metabolites and predicted upstream and downstream complexes, including AMP-activated protein kinase (AMPK), insulin, collagen type IV, mitochondrial complex, c-Jun N-terminal kinase (Jnk), extracellular signal-regulated kinase (ERK), and 3β-hydroxysteroid dehydrogenase (3β HSD). The qPCR analysis of relevant factors showed a significant decrease in AMPKα2 mRNA expression in FHN-affected bone, supporting the predicted downregulation found in the IPA network analysis. Taken as a whole, these results demonstrate a shift in energy production, bone homeostasis, and bone cell differentiation that is distinct in FHN-affected bone, with implications for how metabolites drive the pathology of FHN.
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Affiliation(s)
- Alison Ramser
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
| | | | - Elizabeth Greene
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ron Okimoto
- Cobb-Vantress, Siloam Springs, AR 72761, USA
| | | | | | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA
- Biological and Small Molecule Mass Spectrometry Core, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
| | - Sami Dridi
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
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7
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Fronton F, Ferchiou S, Caza F, Villemur R, Robert D, St-Pierre Y. Insights into the circulating microbiome of Atlantic and Greenland halibut populations: the role of species-specific and environmental factors. Sci Rep 2023; 13:5971. [PMID: 37045892 PMCID: PMC10097863 DOI: 10.1038/s41598-023-32690-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
Establishing long-term microbiome-based monitoring programs is critical for managing and conserving wild fish populations in response to climate change. In most cases, these studies have been conducted on gut and, to a lesser extent, skin (mucus) microbiomes. Here, we exploited the concept of liquid biopsy to study the circulating bacterial microbiome of two Northern halibut species of economic and ecological importance. Amplification and sequencing of the 16S rRNA gene were achieved using a single drop of blood fixed on FTA cards to identify the core blood microbiome of Atlantic and Greenland halibut populations inhabiting the Gulf of St. Lawrence, Canada. We provide evidence that the circulating microbiome DNA (cmDNA) is driven by genetic and environmental factors. More specifically, we found that the circulating microbiome signatures are species-specific and vary according to sex, size, temperature, condition factor, and geographical localization. Overall, our study provides a novel approach for detecting dysbiosis signatures and the risk of disease in wild fish populations for fisheries management, most notably in the context of climate change.
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Affiliation(s)
- Fanny Fronton
- INRS-Centre Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Sophia Ferchiou
- INRS-Centre Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - France Caza
- INRS-Centre Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Richard Villemur
- INRS-Centre Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Dominique Robert
- Institut des Sciences de la Mer, Université du Québec à Rimouski, 310, allée des Ursulines, C.P. 3300, Rimouski, QC, G5L 3A1, Canada
| | - Yves St-Pierre
- INRS-Centre Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada.
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8
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Scarsella E, Meineri G, Sandri M, Ganz HH, Stefanon B. Characterization of the Blood Microbiome and Comparison with the Fecal Microbiome in Healthy Dogs and Dogs with Gastrointestinal Disease. Vet Sci 2023; 10:vetsci10040277. [PMID: 37104432 PMCID: PMC10144428 DOI: 10.3390/vetsci10040277] [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: 02/20/2023] [Revised: 03/25/2023] [Accepted: 04/04/2023] [Indexed: 04/28/2023] Open
Abstract
Recent studies have found bacterial DNA in the blood of healthy individuals. To date, most studies on the blood microbiome have focused on human health, but this topic is an expanding research area in animal health as well. This study aims to characterize the blood microbiome of both healthy dogs and those with chronic gastro-enteropathies. For this study, blood and fecal samples were collected from 18 healthy and 19 sick subjects, DNA was extracted through commercial kits, and the V3-V4 regions of the 16S rRNA gene were sequenced on the Illumina platform. The sequences were analyzed for taxonomic annotation and statistical analysis. Alpha and beta diversities of fecal microbiome were significantly different between the two groups of dogs. Principal coordinates analysis revealed that healthy and sick subjects were significantly clustered for both blood and fecal microbiome samples. Moreover, bacterial translocation from the gut to the bloodstream has been suggested because of found shared taxa. Further studies are needed to determine the origin of the blood microbiome and the bacteria viability. The characterization of a blood core microbiome in healthy dogs has potential for use as a diagnostic tool to monitor for the development of gastro-intestinal disease.
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Affiliation(s)
- Elisa Scarsella
- AnimalBiome, 400 29th Street, Suite 101, Oakland, CA 94609, USA
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Giorgia Meineri
- Department of Veterinary Science, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Misa Sandri
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Holly H Ganz
- AnimalBiome, 400 29th Street, Suite 101, Oakland, CA 94609, USA
| | - Bruno Stefanon
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
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Diester Chlorogenoborate Complex: A New Naturally Occurring Boron-Containing Compound. INORGANICS 2023. [DOI: 10.3390/inorganics11030112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
The natural compounds of boron have many applications, primarily as a dietary supplement. The research is based on the discovery that the diester chlorogenoborate complex can be detected and quantified from green coffee beans. The study reports that such a diester molecule can also be synthesized in a stable form via the direct reaction of boric acid and chlorogenic acid in a mixture of acetonitrile–water (1:1, v/v) and left to evaporate over a period of 48 h at room temperature, resulting in a spirocyclic form (diester complex). The diester complex, with its molecular structure and digestibility attributes, has potential application as a prebiotic in gut health and oral health, and as a micronutrient essential for microbiota in humans and animals.
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10
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Liver Microbiome in Healthy Rats: The Hidden Inhabitants of Hepatocytes. Cell Microbiol 2023. [DOI: 10.1155/2023/7369034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The tumor and tissue microbiota of human beings have recently been investigated. Gut permeability is known as a possible resource for the positive detection of tissue bacteria. Herein, we report that microbiota were detected in high abundance in the hepatocytes of healthy rats and that they were shared with the gut microbiota to an extent. We assessed male Sprague Dawley (SD) rats for the 16S ribosomal ribonucleic acid (rRNA) gene. After the rats were sacrificed by blood drainage from the portal vein, we extracted total deoxyribonucleic acid (DNA) from their ileal and colonic contents and liver tissues. The V3–V4 region of the 16S rRNA gene was amplified by polymerase chain reaction (PCR) and sequenced using an Illumina HiSeq 2500 platform. Sequences were assigned taxonomically by the SILVA database. We also detected bacterial lipopolysaccharide (LPS) and lipoteichoic acid (LTA) in situ using immunofluorescence (IF) and western blotting and the 16S rRNA gene using fluorescent in situ hybridization (FISH). In the livers of six rats, we detected
effective tags of the 16S rRNA gene and clustered them into 1003 kinds of operational taxonomic units (OTUs;
, 729–893). Rats showed conservation of bacterial richness, abundance, and evenness. LPS and the 16S rRNA gene were detected in the nuclei of hepatocytes. The main function composition of the genomes of annotated bacteria was correlated with metabolism (
). Gram negativity was about 1.6 times higher than gram positivity. The liver microbiome was shared with both the small and large intestines but showed significantly higher richness and evenness than the gut microbiome, and the β-diversity results showed that the liver microbiome exhibited significantly higher similarity than the small and large intestines (
). Our results suggest that the bacteria in the liver microbiome are hidden intracellular inhabitants in healthy rat livers.
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Tsafarova B, Hodzhev Y, Yordanov G, Tolchkov V, Kalfin R, Panaiotov S. Morphology of blood microbiota in healthy individuals assessed by light and electron microscopy. Front Cell Infect Microbiol 2023; 12:1091341. [PMID: 36741978 PMCID: PMC9889553 DOI: 10.3389/fcimb.2022.1091341] [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: 11/06/2022] [Accepted: 12/30/2022] [Indexed: 01/20/2023] Open
Abstract
Introduction The blood microbiome is still an enigma. The existence of blood microbiota in clinically healthy individuals was proven during the last 50 years. Indirect evidence from radiometric analysis suggested the existence of living microbial forms in erythrocytes. Recently targeted nucleic acid sequencing demonstrated rich microbial biodiversity in the blood of clinically healthy individuals. The morphology and proliferation cycle of blood microbiota in peripheral blood mononuclear cells (PBMC) isolated from freshly drawn and cultured whole blood are obscure. Methods To study the life cycle of blood microbiota we focused on light, and electron microscopy analysis. Peripheral blood mononuclear cells isolated from freshly drawn blood and stress-cultured lysed whole blood at 43°C in presence of vitamin K from healthy individuals were studied. Results Here, we demonstrated that free circulating microbiota in the PMBC fraction possess a well-defined cell wall and proliferate by budding or through a mechanism similar to the extrusion of progeny bodies. By contrast, stress-cultured lysed whole blood microbiota proliferated as cell-wall deficient microbiota by forming electron-dense or electron-transparent bodies. The electron-dense bodies proliferated by fission or produce in chains Gram-negatively stained progeny cells or enlarged and burst to release progeny cells of 180 - 200 nm size. On the other hand, electron-transparent bodies enlarged and emitted progeny cells through the membrane. A novel proliferation mechanism of blood microbiota called by us "a cell within a cell" was observed. It combines proliferation of progeny cells within a progeny cell which is growing within the "mother" cell. Discussion The rich biodiversity of eukaryotic and prokaryotic microbiota identified in blood by next-generation sequencing technologies and our microscopy results suggest different proliferation mechanisms in whole and cultured blood. Our documented evidence and conclusions provide a more comprehensive view of the existence of normal blood microbiota in healthy individuals.
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Affiliation(s)
- Borislava Tsafarova
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Yordan Hodzhev
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Georgi Yordanov
- Faculty of Chemistry and Pharmacy, Sofia University, Sofia, Bulgaria
| | - Vladimir Tolchkov
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Reni Kalfin
- Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
- Department of Health Care, South-West University “Neofit Rilski”, Blagoevgrad, Bulgaria
| | - Stefan Panaiotov
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
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12
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Li C, Li S, Dang G, Jia R, Chen S, Deng X, Liu G, Beckers Y, Cai H. Screening and characterization of Bacillus velezensis LB-Y-1 toward selection as a potential probiotic for poultry with multi-enzyme production property. Front Microbiol 2023; 14:1143265. [PMID: 37138616 PMCID: PMC10149742 DOI: 10.3389/fmicb.2023.1143265] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
Bacillus spp. have gained increasing recognition as an option to use as antimicrobial growth promoters, which are characterized by producing various enzymes and antimicrobial compounds. The present study was undertaken to screen and evaluate a Bacillus strain with the multi-enzyme production property for poultry production. LB-Y-1, screened from the intestines of healthy animals, was revealed to be a Bacillus velezensis by the morphological, biochemical, and molecular characterization. The strain was screened out by a specific screening program, possessed excellent multi-enzyme production potential, including protease, cellulase, and phytase. Moreover, the strain also exhibited amylolytic and lipolytic activity in vitro. The dietary LB-Y-1 supplementation improved growth performance and tibia mineralization in chicken broilers, and increased serum albumin and serum total protein at 21 days of age (p < 0.05). Besides, LB-Y-1 enhanced the activity of serum alkaline phosphatase and digestive enzyme in broilers at 21 and 42 days of age (p < 0.05). Analysis of intestinal microbiota showed that a higher community richness (Chao1 index) and diversity (Shannon index) in the LB-Y-1 supplemented compared with the CON group. PCoA analysis showed that the community composition and structure were distinctly different between the CON and LB-Y-1 group. The beneficial genera such as Parasutterella and Rikenellaceae were abundant, while the opportunistic pathogen such as Escherichia-Shigella were reduced in the LB-Y-1 supplemented group (p < 0.05). Collectively, LB-Y-1 can be considered as a potential strain for further utilization in direct-fed microbial or starter culture for fermentation.
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Affiliation(s)
- Chong Li
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agriculture Sciences, Beijing, China
- Precision Livestock and Nutrition Laboratory, Teaching and Research Centre (TERRA), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Shuzhen Li
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Guoqi Dang
- Precision Livestock and Nutrition Laboratory, Teaching and Research Centre (TERRA), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Rui Jia
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Si Chen
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Xuejuan Deng
- National Engineering Research Center of Biological Feed, Beijing, China
| | - Guohua Liu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Yves Beckers
- Precision Livestock and Nutrition Laboratory, Teaching and Research Centre (TERRA), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Huiyi Cai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agriculture Sciences, Beijing, China
- National Engineering Research Center of Biological Feed, Beijing, China
- *Correspondence: Huiyi Cai,
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13
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Szafraniec GM, Szeleszczuk P, Dolka B. Review on skeletal disorders caused by Staphylococcus spp. in poultry. Vet Q 2022; 42:21-40. [PMID: 35076352 PMCID: PMC8843168 DOI: 10.1080/01652176.2022.2033880] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 12/03/2021] [Accepted: 01/21/2022] [Indexed: 12/17/2022] Open
Abstract
Lameness or leg weakness is the main cause of poor poultry welfare and serious economic losses in meat-type poultry production worldwide. Disorders related to the legs are often associated with multifactorial aetiology which makes diagnosis and proper treatment difficult. Among the infectious agents, bacteria of genus Staphylococcus are one of the most common causes of bone infections in poultry and are some of the oldest bacterial infections described in poultry. Staphylococci readily infect bones and joints and are associated with bacterial chondronecrosis with osteomyelitis (BCO), spondylitis, arthritis, tendinitis, tenosynovitis, osteomyelitis, turkey osteomyelitis complex (TOC), bumblefoot, dyschondroplasia with osteomyelitis and amyloid arthropathy. Overall, 61 staphylococcal species have been described so far, and 56% of them (34/61) have been isolated from clinical cases in poultry. Although Staphylococcus aureus is the principal cause of poultry staphylococcosis, other Staphylococcus species, such as S. agnetis, S. cohnii, S. epidermidis, S. hyicus, S. simulans, have also been isolated from skeletal lesions. Antimicrobial treatment of staphylococcosis is usually ineffective due to the location and type of lesion, as well as the possible occurrence of multidrug-resistant strains. Increasing demand for antibiotic-free farming has contributed to the use of alternatives to antibiotics. Other prevention methods, such as better management strategies, early feed restriction or use of slow growing broilers should be implemented to avoid rapid growth rate, which is associated with locomotor problems. This review aims to summarise and address current knowledge on skeletal disorders associated with Staphylococcus spp. infection in poultry.
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Affiliation(s)
- Gustaw M. Szafraniec
- Department of Pathology and Veterinary Diagnostics, Institute of Veterinary Medicine, Warsaw University of Life Sciences – SGGW, Warsaw, Poland
| | - Piotr Szeleszczuk
- Department of Pathology and Veterinary Diagnostics, Institute of Veterinary Medicine, Warsaw University of Life Sciences – SGGW, Warsaw, Poland
| | - Beata Dolka
- Department of Pathology and Veterinary Diagnostics, Institute of Veterinary Medicine, Warsaw University of Life Sciences – SGGW, Warsaw, Poland
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14
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Ramser A, Greene E, Rath N, Dridi S. Primary growth plate chondrocyte isolation, culture, and characterization from the modern broiler. Poult Sci 2022; 102:102254. [PMID: 36370660 PMCID: PMC9660625 DOI: 10.1016/j.psj.2022.102254] [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: 03/18/2022] [Revised: 09/27/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
Lameness is a leading cause of animal welfare and production concerns for the poultry industry as fast-growing, high-yielding broilers seem more susceptible to bone disease and infections. A major limitation to the study of these disorders is the lack of a chicken immortalized chondrocyte cell. Primary cell isolation is a valid and complex method for establishing a relevant in vitro model for diseases. In this study, isolation and high-density culturing of primary chondrocytes form 1-d old chicks was followed by confirmation of cell type, identification of optimal phenotypic expression, and evaluation of cells functionality. mRNA expression, as well as protein production and secretion, of COLI, COLII, Sox9, ACAN, and COLXA1 on day 3 (d3), d7, d11, d14, d18, and d21 in culture showed that avian growth plate chondrocytes under these conditions exhibit optimal phenotypes from d3 to d7. This is evident by a shift from COLII dominant expression in early-culture to COLI dominant expression by late-culture in conjunction with a loss of other chondrocyte markers Sox9, ACAN, and COLXA1. Additionally, morphological changes seen through live cell imaging coincide with the shift of phenotype in mid- to late-culture periods indicating a dedifferentiated phenotype. The functionality of the cultured cells was confirmed using Brefeldin-A treatment which significantly reduced secretion of COLII by d7 chondrocytes. These results provide a foundation for future research utilizing avian primary chondrocytes with optimal phenotypes for disease modeling or passaging.
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Affiliation(s)
- Alison Ramser
- University of Arkansas, Center of Excellence for Poultry Science, Fayetteville, AR 72701, USA,University of Arkansas, Cell and Molecular Biology, Fayetteville, AR 72701, USA
| | - Elizabeth Greene
- University of Arkansas, Center of Excellence for Poultry Science, Fayetteville, AR 72701, USA
| | - Narayan Rath
- University of Arkansas, Center of Excellence for Poultry Science, Fayetteville, AR 72701, USA,Poultry Production and Product Safety Research, USDA/ARS, Fayetteville, AR 72701, USA
| | - Sami Dridi
- University of Arkansas, Center of Excellence for Poultry Science, Fayetteville, AR 72701, USA,University of Arkansas, Cell and Molecular Biology, Fayetteville, AR 72701, USA,Corresponding author:
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15
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Goraya MU, Li R, Mannan A, Gu L, Deng H, Wang G. Human circulating bacteria and dysbiosis in non-infectious diseases. Front Cell Infect Microbiol 2022; 12:932702. [PMID: 36093202 PMCID: PMC9448904 DOI: 10.3389/fcimb.2022.932702] [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: 04/30/2022] [Accepted: 08/01/2022] [Indexed: 02/05/2023] Open
Abstract
Blood microorganisms were once thought to indicate infection. Blood in healthy people appears to be devoid of growing bacteria; nonetheless, intracellular dormant forms of bacteria have been reported previously. With breakthroughs in sequencing and bioinformatics, the presence of bacterial DNA in healthy human blood initiated the controversy of human blood microbiota (HBM). Recently, bacteria-specific DNA and culturable bacteria were found in healthy human blood. Researchers wanted to study the phenomena of a "healthy blood microbiota" by providing a thorough description of bacterially produced nucleic acids using many complementing molecular and traditional microbiological approaches. Because blood is a relatively limited and particular environment, culturability and plate count issues can be overcome using enhanced cultured procedures. However, more evidence is required to confirm that healthy human blood contains normal microbiota. Cavities, mouth and intestinal microbiota, trauma, surgery, and animal/insect bites can introduce bacteria into human blood. All these factors strengthen the concept of transient blood bacteria too. The presence of blood bacteria may be caused by temporary immunological clearance and absorption by dendritic or M cells. This review provides an extensive and comprehensive analysis that suggests that healthy blood bacteria may not be typical microbiota but transient circulatory microorganisms. In this study, we look at how contaminants (Escherichia, Shigella, Pseudomonads, etc.) from the skin, laboratory environments, and reagents can affect the interpretation of blood-derived microbial information and the relationship between the circulating bacteria and non-communicable diseases. Circulating transient bacteria may play a role in the pathogenesis of non-infectious diseases such as diabetes and CVD. Contamination-free hematological studies can aid in understanding the disease mechanisms, therapy, and biomarkers.
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Affiliation(s)
- Mohsan Ullah Goraya
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Rui Li
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Abdul Mannan
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
| | - Liming Gu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Huixiong Deng
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Gefei Wang
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
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16
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Dehau T, Ducatelle R, Immerseel FV, Goossens E. Omics technologies in poultry health and productivity - part 1: current use in poultry research. Avian Pathol 2022; 51:407-417. [PMID: 35675291 DOI: 10.1080/03079457.2022.2086447] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In biology, molecular terms with the suffix "-omics" refer to disciplines aiming at the collective characterization of pools of molecules derived from different layers (DNA, RNA, proteins, metabolites) of living organisms using high-throughput technologies. Such omics analyses have been widely implemented in poultry research in recent years. This first part of a bipartite review on omics technologies in poultry health and productivity examines the use of multiple omics and multi-omics techniques in poultry research. More specific present and future applications of omics technologies, not only for the identification of specific diagnostic biomarkers, but also for potential future integration in the daily monitoring of poultry production, are discussed in part 2. Approaches based on omics technologies are particularly used in poultry research in the hunt for genetic markers of economically important phenotypical traits in the host, and in the identification of key bacterial species or functions in the intestinal microbiome. Integrative multi-omics analyses, however, are still scarce. Host physiology is investigated via genomics together with transcriptomics, proteomics and metabolomics techniques, to understand more accurately complex production traits such as disease resistance and fertility. The gut microbiota, as a key player in chicken productivity and health, is also a main subject of such studies, investigating the association between its composition (16S rRNA gene sequencing) or function (metagenomics, metatranscriptomics, metaproteomics, metabolomics) and host phenotypes. Applications of these technologies in the study of other host-associated microbiota and other host characteristics are still in their infancy.
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Affiliation(s)
- Tessa Dehau
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Richard Ducatelle
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Filip Van Immerseel
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Evy Goossens
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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17
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Meroni G, Tsikopoulos A, Tsikopoulos K, Allemanno F, Martino PA, Soares Filipe JF. A Journey into Animal Models of Human Osteomyelitis: A Review. Microorganisms 2022; 10:1135. [PMID: 35744653 PMCID: PMC9228829 DOI: 10.3390/microorganisms10061135] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 12/24/2022] Open
Abstract
Osteomyelitis is an infection of the bone characterized by progressive inflammatory destruction and apposition of new bone that can spread via the hematogenous route (hematogenous osteomyelitis (HO)), contiguous spread (contiguous osteomyelitis (CO)), and direct inoculation (osteomyelitis associated with peripheral vascular insufficiency (PVI)). Given the significant financial burden posed by osteomyelitis patient management, the development of new preventive and treatment methods is warranted. To achieve this objective, implementing animal models (AMs) of infection such as rats, mice, rabbits, avians, dogs, sheep, goats, and pigs might be of the essence. This review provides a literature analysis of the AMs developed and used to study osteomyelitis. Historical relevance and clinical applicability were taken into account to choose the best AMs, and some study methods are briefly described. Furthermore, the most significant strengths and limitations of each species as AM are discussed, as no single model incorporates all features of osteomyelitis. HO's clinical manifestation results in extreme variability between patients due to multiple variables (e.g., age, sex, route of infection, anatomical location, and concomitant diseases) that could alter clinical studies. However, these variables can be controlled and tested through different animal models.
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Affiliation(s)
- Gabriele Meroni
- One Health Unit, Department of Biomedical, Surgical, and Dental Sciences, University of Milan, Via Pascal 36, 20133 Milan, Italy; (F.A.); (P.A.M.)
| | - Alexios Tsikopoulos
- Department of Pharmacology, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece;
| | | | - Francesca Allemanno
- One Health Unit, Department of Biomedical, Surgical, and Dental Sciences, University of Milan, Via Pascal 36, 20133 Milan, Italy; (F.A.); (P.A.M.)
| | - Piera Anna Martino
- One Health Unit, Department of Biomedical, Surgical, and Dental Sciences, University of Milan, Via Pascal 36, 20133 Milan, Italy; (F.A.); (P.A.M.)
| | - Joel Fernando Soares Filipe
- Department of Veterinary Medicine and Animal Sciences, University of Milan, Via dell’Università 6, 26900 Lodi, Italy;
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18
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Ekesi NS, Hasan A, Parveen A, Shwani A, Rhoads DD. Embryo lethality assay as a tool for assessing virulence of isolates from bacterial chondronecrosis with osteomyelitis in broilers. Poult Sci 2021; 100:101455. [PMID: 34607145 PMCID: PMC8496174 DOI: 10.1016/j.psj.2021.101455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 08/21/2021] [Accepted: 08/26/2021] [Indexed: 11/26/2022] Open
Abstract
We used an embryo lethality assay (ELA) to assess virulence for different isolates from cases of bacterial chondronecrosis with osteomyelitis (BCO) in broilers. Lameness is among the most significant animal welfare issues in the poultry industry. Bacterial infections are a major cause of lameness and different bacterial species have been obtained from lame broilers. Reliable lab-based assays are required to assess relative virulence of bacteria obtained from lame broilers. ELA has been used to assess lethal dosage of Enterococcus faecalis and Enterococcus cecorum. We hypothesized that ELA could substitute for more laborious and costly assessments of BCO isolate pathogenicity using live birds. We evaluated 2 different levels of bacteria injected into eggs from layer and commercial broiler embryos. Significant findings include 1) Escherichia coli from neighboring farms operated by the same integrator had very different embryo lethality, 2) isolate Staphylococcus agnetis 908 had low virulence in ELA, even though this isolate can induce more than 50% BCO lameness, 3) Enterococcus cecorum 1415 also had low pathogenicity; even though it was recovered from severe bilateral tibial dyschondroplasia, 4) human and chicken BCO isolates of S. aureus had significant pathogenicity, 5) virulence for some isolates was highly variable possibly corresponding with quality of the embryos/fertile eggs used, and 6) ELA pathogenicity was much lower for our BCO isolates than previous reports which may reflect maternal environment. Overall, ELA virulence and BCO virulence are not always concordant indicating that ELA may not be an effective measure for assessing virulence with respect to BCO.
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Affiliation(s)
- Nnamdi S Ekesi
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, USA
| | - Amer Hasan
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, USA; Department of Veterinary Public Health, College of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
| | - Alia Parveen
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, USA
| | - Abdulkarim Shwani
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, USA
| | - Douglas D Rhoads
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, USA.
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19
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Chen J, Xiong A, Ma Y, Qin C, Ho CL. Impact of the Host-Microbiome on Osteomyelitis Pathogenesis. Front Mol Biosci 2021; 8:702484. [PMID: 34434965 PMCID: PMC8381018 DOI: 10.3389/fmolb.2021.702484] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/30/2021] [Indexed: 01/04/2023] Open
Abstract
The microbiome is a collection of genomes from microbiota, including all microorganisms in a niche, through direct and indirect interactions with the host. Certain microorganisms can exist in areas conventionally considered to be sterile, such as the bone matrix. Osseous microbiota dysbiosis caused by host-microbiome perturbation or external infections may ultimately lead to osteomyelitis, a bone inflammatory disorder. Our review covers the current discoveries on the impact of host-microbiome on osteomyelitis and some common osseous diseases. Some studies suggest that the microbiotas from both osseous and non-osseous tissues (e.g., blood or gut) impact the pathogenicity of osteomyelitis and other osseous diseases (e.g., rheumatoid arthritis). We believe that this review will provide readers with a better understanding on the role of the microbiome to the host’s bone health.
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Affiliation(s)
- Jun Chen
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Ailin Xiong
- Department of Orthopaedic Trauma, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Yuhao Ma
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Chenghe Qin
- Department of Orthopaedic Trauma, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Chun Loong Ho
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China
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20
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Scarsella E, Zecconi A, Cintio M, Stefanon B. Characterization of Microbiome on Feces, Blood and Milk in Dairy Cows with Different Milk Leucocyte Pattern. Animals (Basel) 2021; 11:ani11051463. [PMID: 34069719 PMCID: PMC8160755 DOI: 10.3390/ani11051463] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 05/17/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Mastitis is an inflammation of the mammary gland caused by microorganisms and associated with an altered immune response. Recently, several studies hypothesized that a translocation of some bacteria from the gastrointestinal tract to the mammary gland can occur and that this bacterial crossing could be the cause of certain mastitis. The aim of this research is to investigate the bacteria translocation from the gut to the mammary gland, the so-called entero-mammary pathway, through the study of the fecal, blood and milk microbiome. Cows were recruited on the basis of their mammary gland health status and classified as healthy, at risk of mastitis and with mastitis. The microbial composition of feces, blood and milk were analyzed through high-throughput sequencing technique and the results were checked through a quantitative real-time PCR analysis. Although small differences were found in the microbiome of these three specimens between the groups of animals, beta biodiversity, that is, the ratio between whole and individual species diversity, highlighted a microbial community change in the milk of cows with different udder health conditions. The three matrices shared a high number of taxa; however, our results do not confirm a bacterial crossing from gut to milk, that still remains hypothetical. Abstract Mastitis is an inflammatory disease of the mammary gland, caused by the invasion of microorganism on this site, associated with an altered immune response. Recent studies in this field hypothesize that the origin of these pathogens can also be from the gastrointestinal tract, through the entero-mammary pathway in relation to an increase in gut permeability. In this study, we wanted to investigate if inflammatory status of the mammary gland is related to an alteration of gut permeability. The microbiome of feces, blood and milk of lactating cows, recruited on the basis of the total somatic cell count and of the percentage of polymorphonuclear neutrophils and lymphocytes, was studied. Cows were divided into healthy (G), at risk of mastitis (Y) and with mastitis (R) classifications. The bacterial DNA was extracted and the V3 and V4 regions of 16S rRNA sequenced. Moreover, the quantification of total bacteria was performed with quantitative real-time PCR. A non-parametric Kruskal–Wallis test was applied at the phylum, family and genera levels and beta biodiversity was evaluated with the unweighted UniFrac distance metric. Significant differences between groups were found for the microbial composition of feces (Clostridiaceae, Turicibacteriaceae for family level and Clostridium, Dorea, SMB53 and Turicibacter for genus level), blood (Tenericutes for phylum level and Mycoplasma for genus level) and milk (OD1 and Proteobacteria for phylum level, Enterobacteriaceae and Moraxallaceae for family level and Olsenella and Rhodococcus for genus level). The beta biodiversity of feces and blood did not change between groups. Significant differences (p < 0.05) were observed between the beta diversity in milk of G group and Y group and between Y group and R group. The number of taxa in common between feces, blood and milk were 8 at a phylum, 19 at a family and 15 at a genus level. From these results, the bacterial crossing from gut to milk in cows was not confirmed but remained hypothetical and deserves further investigation.
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Affiliation(s)
- Elisa Scarsella
- Department of Agriculture, Food, Environmental and Animal Science, University of Udine, 33100 Udine, Italy; (E.S.); (M.C.)
| | - Alfonso Zecconi
- Department of Biomedical, Surgical and Dental Sciences–One Health Unit, University of Milan, 20100 Milan, Italy;
| | - Michela Cintio
- Department of Agriculture, Food, Environmental and Animal Science, University of Udine, 33100 Udine, Italy; (E.S.); (M.C.)
| | - Bruno Stefanon
- Department of Agriculture, Food, Environmental and Animal Science, University of Udine, 33100 Udine, Italy; (E.S.); (M.C.)
- Correspondence:
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21
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Peña-Cearra A, Belanche A, Gonzalez-Lopez M, Lavín JL, Pascual-Itoiz MÁ, Jiménez E, Rodríguez H, Aransay AM, Anguita J, Yáñez-Ruiz DR, Abecia L. Peripheral blood mononuclear cells (PBMC) microbiome is not affected by colon microbiota in healthy goats. Anim Microbiome 2021; 3:28. [PMID: 33853683 PMCID: PMC8048065 DOI: 10.1186/s42523-021-00091-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 03/30/2021] [Indexed: 12/15/2022] Open
Abstract
Background The knowledge about blood circulating microbiome and its functional relevance in healthy individuals remains limited. An assessment of changes in the circulating microbiome was performed by sequencing peripheral blood mononuclear cells (PBMC) bacterial DNA from goats supplemented or not in early life with rumen liquid transplantation. Results Most of the bacterial DNA associated to PBMC was identified predominantly as Proteobacteria (55%) followed by Firmicutes (24%), Bacteroidetes (11%) and Actinobacteria (8%). The predominant genera found in PBMC samples were Pseudomonas, Prevotella, Sphingomonas, Acinetobacter, Corynebacterium and Ruminococcus. Other genera such as Butyrivibrivio, Bifidobacterium, Dorea and Coprococcus were also present in lower proportions. Several species known as blood pathogens or others involved in gut homeostasis such as Faecalibacterium prausnitzii were also identified. However, the PBMC microbiome phylum composition differed from that in the colon of goats (P ≤ 0.001), where Firmicutes was the predominant phylum (83%). Although, rumen liquid administration in early-life altered bacterial community structure and increased Tlr5 expression (P = 0.020) in colon pointing to higher bacterial translocation, less than 8% of OTUs in colon were also observed in PBMCs. Conclusions Data suggest that in physiological conditions, PBMC microbiome differs from and is not affected by colon gut microbiota in small ruminants. Although, further studies with larger number of animals and covering other animal tissues are required, results point to a common circulating bacterial profile on mammals being phylum Proteobacteria, and genera Pseudomonas and Prevotella the most abundants. All suggest that PBMC microbiome in healthy ruminants could be implicated in homeostatic condition. This study expands our knowledge about PBMC microbiome contribution to health in farm animals. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00091-7.
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Affiliation(s)
- Ainize Peña-Cearra
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain.,Departamento de Inmunología, Microbiología y Parasitología, Facultad de Medicina y Enfermería, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Apartado 699, 48080, Bilbao, Spain
| | | | - Monika Gonzalez-Lopez
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain
| | - José Luis Lavín
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain.,Present Address: NEIKER Instituto Vasco de Investigación y Desarrollo Agrario, Parque Tecnológico Bizkaia Ed. 812, 48160, Derio, Spain
| | | | | | - Héctor Rodríguez
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain
| | - Ana Mª Aransay
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain.,CIBERehd, ISCIII, Madrid, Spain
| | - Juan Anguita
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | | | - Leticia Abecia
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain. .,Departamento de Inmunología, Microbiología y Parasitología, Facultad de Medicina y Enfermería, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Apartado 699, 48080, Bilbao, Spain.
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22
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Ferver A, Greene E, Wideman R, Dridi S. Evidence of Mitochondrial Dysfunction in Bacterial Chondronecrosis With Osteomyelitis-Affected Broilers. Front Vet Sci 2021; 8:640901. [PMID: 33634182 PMCID: PMC7902039 DOI: 10.3389/fvets.2021.640901] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 01/08/2021] [Indexed: 11/13/2022] Open
Abstract
A leading cause of lameness in modern broilers is bacterial chondronecrosis with osteomyelitis (BCO). While it is known that the components of BCO are bacterial infection, necrosis, and inflammation, the mechanism behind BCO etiology is not yet fully understood. In numerous species, including chicken, mitochondrial dysfunction has been shown to have a role in the pathogenicity of numerous diseases. The mitochondria is a known target for intracellular bacterial infections, similar to that of common causative agents in BCO, as well as a known regulator of cellular metabolism, stress response, and certain types of cell death. This study aimed to determine the expression profile of genes involved in mitochondrial biogenesis, dynamics, and function. RNA was isolated form the tibias from BCO-affected and healthy broilers and used to measure target gene expression via real-time qPCR. Mitochondrial biogenesis factors PGC-1α and PGC-1β were both significantly upregulated in BCO along with mitochondrial fission factors OMA1, MTFR1, MTFP1, and MFF1 as well as cellular respiration-related genes FOXO3, FOXO4, and av-UCP. Conversely, genes involved in mitochondrial function, ANT, COXIV, and COX5A showed decreased mRNA levels in BCO-affected tibia. This study is the first to provide evidence of potential mitochondrial dysfunction in BCO bone and warrants further mechanistic investigation into how this dysfunction contributes to BCO etiology.
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Affiliation(s)
- Alison Ferver
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Elizabeth Greene
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Robert Wideman
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Sami Dridi
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, United States
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23
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Scarsella E, Sandri M, Monego SD, Licastro D, Stefanon B. Blood Microbiome: A New Marker of Gut Microbial Population in Dogs? Vet Sci 2020; 7:vetsci7040198. [PMID: 33291629 PMCID: PMC7761930 DOI: 10.3390/vetsci7040198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022] Open
Abstract
The characterization of the microbial population in different compartments of the organism, such as the gastrointestinal tract, is now possible thanks to the use of high-throughput DNA sequencing technique. Several studies in the companion animals field have already investigated the fecal microbiome in healthy or sick subjects; however, the methodologies used in the different laboratories and the limited number of animals recruited in each experiment do not allow a straight comparison among published results. Previously, our research focused on the characterization of the microbial taxa variability in 340 fecal samples from 132 healthy dogs, collected serially from several in-house experiments. The results supported the responsiveness of microbiota to dietary and sex factors and allowed us to cluster dogs with high accuracy. For the present study, intestinal and blood microbiota of healthy dogs from different breeds, genders, ages and food habits were collected, with three principal aims: firstly, to confirm the results of our previous study regarding the fecal microbiome affected by the different type of diet; secondly, to investigate the existence of a blood microbial population, even in heathy subjects; and thirdly, to seek for a possible connection between the fecal and the blood microbiota. Limited researches have been published on blood microbiota in humans, and this is the first evidence of the presence of a bacterial population in the blood of dogs. Moreover, gut and blood microbiota can discriminate the animals by factors such as diet, suggesting some relationship between them. These preliminary results make us believe in the use of the blood microbiome for diagnostic purposes, such as researching and preventing gut inflammatory diseases.
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Affiliation(s)
- Elisa Scarsella
- Department of Agriculture, Food, Environmental and Animal Science, University of Udine, 33100 Udine, Italy; (E.S.); (M.S.)
| | - Misa Sandri
- Department of Agriculture, Food, Environmental and Animal Science, University of Udine, 33100 Udine, Italy; (E.S.); (M.S.)
| | - Simeone Dal Monego
- ARGO Open Lab Platform for Genome Sequencing, AREA Science Park, Padriciano, 34149 Trieste, Italy; (S.D.M.); (D.L.)
| | - Danilo Licastro
- ARGO Open Lab Platform for Genome Sequencing, AREA Science Park, Padriciano, 34149 Trieste, Italy; (S.D.M.); (D.L.)
| | - Bruno Stefanon
- Department of Agriculture, Food, Environmental and Animal Science, University of Udine, 33100 Udine, Italy; (E.S.); (M.S.)
- Correspondence: ; Tel.: +39-0432-55-8581
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24
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Abdelhamid MK, Quijada NM, Dzieciol M, Hatfaludi T, Bilic I, Selberherr E, Liebhart D, Hess C, Hess M, Paudel S. Co-infection of Chicken Layers With Histomonas meleagridis and Avian Pathogenic Escherichia coli Is Associated With Dysbiosis, Cecal Colonization and Translocation of the Bacteria From the Gut Lumen. Front Microbiol 2020; 11:586437. [PMID: 33193238 PMCID: PMC7661551 DOI: 10.3389/fmicb.2020.586437] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022] Open
Abstract
Histomonosis in chickens often appears together with colibacillosis in the field. Thus, we have experimentally investigated consequences of the co-infection of birds with Histomonas meleagridis and avian pathogenic Escherichia coli (APEC) on the pathology, host microbiota and bacterial translocation from the gut. Commercial chicken layers were infected via oral and cloacal routes with lux-tagged APEC with or without H. meleagridis whereas negative controls were left uninfected. Except one bird, which died due to colibacillosis, no clinical signs were recorded in birds infected with bioluminescence lux gene tagged E. coli. In co-infected birds, depression and ruffled feathers were observed in 4 birds and average body weight gain significantly decreased. Typhlitis caused by H. meleagridis was present only in co-infected birds, which also had pronounced microscopic lesions in systemic organs such as liver, heart and spleen. The 16S rRNA gene amplicon sequencing showed that in co-infected birds, corresponding to the severity of cecal lesions, microbial species richness and diversity in caeca greatly decreased and the abundance of the Escherichia group, Helicobacter and Bacteroides was relatively higher with a reduction of commensals. Most of the shared Amplicon Sequencing Variants between cecum and blood in co-infected birds belonged to Pseudomonas, Staphylococcus, and members of Enterobacteriaceae while those assigned as Lactobacillus and members of Ruminococcaceae and Lachnospiraceae were found mainly in negative controls. In infected birds, E. coli in the cecal lumen penetrated into deeper layers, a phenomenon noticed with higher incidence in the dead and co-infected birds. Furthermore, numbers of lux-tagged E. coli in caeca were significantly higher at every sampling date in co-infected birds. Altogether, infection of layers with H. meleagridis and E. coli resulted in more severe pathological changes, dramatic shift in the cecal mucosa-associated microbiota, higher tissue colonization of pathogenic bacteria such as avian pathogenic E. coli in the gut and increased penetration of E. coli from the cecal lumen toward peritoneum. This study provides novel insights into the parasite-bacteria interaction in vivo highlighting the role of H. meleagridis to support E. coli in the pathogenesis of colibacillosis in chickens.
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Affiliation(s)
- Mohamed Kamal Abdelhamid
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria.,Department of Pathology, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Narciso M Quijada
- Department for Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria.,Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Monika Dzieciol
- Department for Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Tamas Hatfaludi
- Christian Doppler Laboratory for Innovative Poultry Vaccines (IPOV), University of Veterinary Medicine Vienna, Vienna, Austria
| | - Ivana Bilic
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Evelyne Selberherr
- Department for Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Dieter Liebhart
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Claudia Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Michael Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria.,Christian Doppler Laboratory for Innovative Poultry Vaccines (IPOV), University of Veterinary Medicine Vienna, Vienna, Austria
| | - Surya Paudel
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
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25
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Mandal RK, Jiang T, Wideman RF, Lohrmann T, Kwon YM. Microbiota Analysis of Chickens Raised Under Stressed Conditions. Front Vet Sci 2020; 7:482637. [PMID: 33134343 PMCID: PMC7575692 DOI: 10.3389/fvets.2020.482637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/21/2020] [Indexed: 01/12/2023] Open
Abstract
A substantial progress has been made toward understanding stress-associated gut and extraintestinal microbiota. However, a comprehensive understanding of the extraintestinal microbiota of chickens raised under stressed conditions is lacking. In this study, chickens were raised on a wire-floor model to induce stress, and the microbiota in the gut (ceca) and extraintestinal sites (blood, femur, and tibia) were characterized at different ages (1, 17, and 56 days) using 16S rRNA gene microbiota profiling. Open reference OTU picking showed extraintestinal sites had a significantly higher number of unassigned OTUs compared to ceca across all ages of chickens. Extraintestinal sites of all ages, irrespective of body sites, as well as ceca of 1 day-old chickens had significantly lower alpha diversity than ceca of older chickens. Intriguingly, bacterial diversity (alpha and beta) and OTU interaction network analysis showed relatively stable bacterial composition within the extraintestinal sites of chickens regardless of age and sites compared to ceca. Furthermore, assessment using UniFrac distance suggested the gut as a possible source of extraintestinal bacteria. Lastly, LEfSe analysis showed that both commensal and pathogenic bacteria were translocated into the extraintestinal tissues and organs under the stress. Extraintestinal sites have highly abundant novel taxa that need to be further explored. In ovo microbiota colonization and/or translocation of circulating maternal blood microbiota into ovarian follicles might be the source of intestinal and extraintestinal microbiota in 1 day-old chickens. Our comprehensive microbiota data including extraintestinal sites in reference to gut provide unique insights into microbiota of chickens raised under stressed conditions, which may be relevant in other animal species as well.
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Affiliation(s)
- Rabindra K Mandal
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Tieshan Jiang
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Robert F Wideman
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Troy Lohrmann
- Quality Technology International, Inc., Elgin, IL, United States
| | - Young Min Kwon
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States.,Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
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26
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Adhikari B, Kwon YM. Cell density alters bacterial community structure in culture-enriched 16S rRNA gene microbiota profiling. BMC Res Notes 2020; 13:269. [PMID: 32493423 PMCID: PMC7268277 DOI: 10.1186/s13104-020-05113-2] [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: 03/16/2020] [Accepted: 05/26/2020] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Microbial community profiling using 16S rRNA gene has provided invaluable insights into diverse microbial communities. Recently a few studies have attempted to use 16S rRNA gene microbiota profiling in combination with the conventional culture methods to explore bacterial communities. In this "culture-enriched microbiota profiling" approach, microbes in a sample are cultured on solid media, and the resulting colonies are combined and subjected to 16S rRNA gene microbiota profiling. Here we investigated the effect of cell densities as determined by varying levels of sample dilution on the culture-enriched microbiota profiles using De Man, Rogosa and Sharpe (MRS) agar medium as a model system. RESULTS Cecal samples collected from 10 healthy chickens were serially diluted to 102 fold (M-LOW), 104 fold (M-MEDIUM), and 106 fold (M-HIGH), and the dilutions were plated on MRS agar. 16S rRNA gene profiling showed that the relative abundance of certain genera showed gradual increase (Pediococcus and Enterococcus) or decrease (Lactobacillus and Turicibacter) with higher dilutions, though it was significant only for Pediococcus (p < 0.05). The result indicates that the dilution levels of the samples can alter the resulting microbiota profiles via unknown density-dependent mechanisms and thus should be considered for designing experiments using culture-enriched microbiota profiling.
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Affiliation(s)
- Bishnu Adhikari
- Department of Poultry Science, College of Agricultural, Food and Life Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Young Min Kwon
- Department of Poultry Science, College of Agricultural, Food and Life Sciences, University of Arkansas, Fayetteville, AR, 72701, USA. .,Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA.
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27
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RNA-seq reveals downregulated osteochondral genes potentially related to tibia bacterial chondronecrosis with osteomyelitis in broilers. BMC Genet 2020; 21:58. [PMID: 32493207 PMCID: PMC7271470 DOI: 10.1186/s12863-020-00862-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/18/2020] [Indexed: 12/14/2022] Open
Abstract
Background Bacterial chondronecrosis with osteomyelitis (BCO) develops in the growth plate (GP) of the proximal femur and tibia and is initiated by damage to the less mineralized chondrocytes followed by colonization of opportunistic bacteria. This condition affects approximately 1% of all birds housed, being considered one of the major causes of lameness in fast growing broilers. Although several studies have been previously performed aiming to understand its pathogenesis, the molecular mechanisms involved with BCO remains to be elucidated. Therefore, this study aimed to generate a profile of global differential gene expression involved with BCO in the tibia of commercial broilers, through RNA sequencing analysis to identity genes and molecular pathways involved with BCO in chickens. Results Our data showed 192 differentially expressed (DE) genes: 63 upregulated and 129 downregulated in the GP of the tibia proximal epiphysis of BCO-affected broilers. Using all DE genes, six Biological Processes (BP) were associated with bone development (connective tissue development, cartilage development, skeletal system development, organ morphogenesis, system development and skeletal system morphogenesis). The analyses of the upregulated genes did not indicate any significant BP (FDR < 0.05). However, with the downregulated genes, the same BP were identified when using all DE genes in the analysis, with a total of 26 coding genes explaining BCO in the tibia: ACAN, ALDH1A2, CDH7, CHAD, CHADL, COL11A1, COMP, CSGALNACT1, CYR61, FRZB, GAL3ST1, HAPLN1, IHH, KIF26B, LECT1, LPPR1, PDE6B, RBP4A, SERINC5, SFRP1, SOX8, SOX9, TENM2, THBS1, UCHL1 and WFIKKN2. In addition, seven transcription factors were also associated to BCO: NFATC2, MAFB, HIF1A-ARNT, EWSR1-FLI1, NFIC, TCF3 and NF-KAPPAB. Conclusions Our data show that osteochondral downregulated genes are potential molecular causes of BCO in broilers, and the bacterial process seems to be, in fact, a secondary condition. Sixteen genes responsible for bone and cartilage formation were downregulated in BCO-affected broilers being strong candidate genes to trigger this disorder.
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28
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Whole-Genome Comparisons of Staphylococcus agnetis Isolates from Cattle and Chickens. Appl Environ Microbiol 2020; 86:AEM.00484-20. [PMID: 32245765 DOI: 10.1128/aem.00484-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/30/2020] [Indexed: 12/12/2022] Open
Abstract
Staphylococcus agnetis has been previously associated with subclinical or clinically mild cases of mastitis in dairy cattle and is one of several staphylococcal species that have been isolated from the bones and blood of lame broilers. We reported that S. agnetis could be obtained frequently from bacterial chondronecrosis with osteomyelitis (BCO) lesions of lame broilers (A. Al-Rubaye et al., PLoS One 10:e0143336, 2015 [https://doi.org/10.1371/journal.pone.0143336]). A particular isolate, S. agnetis 908, can induce lameness in over 50% of exposed chickens, exceeding normal BCO incidences in broiler operations. We reported the assembly and annotation of the genome of isolate 908. To better understand the relationship between dairy cattle and broiler isolates, we assembled 11 additional genomes for S. agnetis isolates, an additional chicken BCO strain, and ten isolates from cattle milk, mammary gland secretions, or udder skin from the collection at the University of Missouri. To trace phylogenetic relationships, we constructed phylogenetic trees based on multilocus sequence typing and genome-to-genome distance comparisons. Chicken isolate 908 clustered with two of the cattle isolates, along with three isolates from chickens in Denmark and an isolate of S. agnetis we isolated from a BCO lesion on a commercial broiler farm in Arkansas. We used a number of BLAST tools to compare the chicken isolates to those from cattle and identified 98 coding sequences distinguishing isolate 908 from the cattle isolates. None of the identified genes explain the differences in host or tissue tropism. These analyses are critical to understanding how staphylococci colonize and infect different hosts and potentially how they can transition to alternative niches (bone versus dermis).IMPORTANCE Staphylococcus agnetis has been recently recognized as associated with disease in dairy cattle and meat-type chickens. The infections appear to be limited in cattle and systemic in broilers. This report details the molecular relationships between cattle and chicken isolates in order to understand how this recently recognized species infects different hosts with different disease manifestations. The data show that the chicken and cattle isolates are very closely related, but the chicken isolates all cluster together, suggesting a single jump from cattle to chickens.
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29
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Castillo DJ, Rifkin RF, Cowan DA, Potgieter M. The Healthy Human Blood Microbiome: Fact or Fiction? Front Cell Infect Microbiol 2019; 9:148. [PMID: 31139578 PMCID: PMC6519389 DOI: 10.3389/fcimb.2019.00148] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
The blood that flows perpetually through our veins and arteries performs numerous functions essential to our survival. Besides distributing oxygen, this vast circulatory system facilitates nutrient transport, deters infection and dispenses heat throughout our bodies. Since human blood has traditionally been considered to be an entirely sterile environment, comprising only blood-cells, platelets and plasma, the detection of microbes in blood was consistently interpreted as an indication of infection. However, although a contentious concept, evidence for the existence of a healthy human blood-microbiome is steadily accumulating. While the origins, identities and functions of these unanticipated micro-organisms remain to be elucidated, information on blood-borne microbial phylogeny is gradually increasing. Given recent advances in microbial-hematology, we review current literature concerning the composition and origin of the human blood-microbiome, focusing on bacteria and their role in the configuration of both the diseased and healthy human blood-microbiomes. Specifically, we explore the ways in which dysbiosis in the supposedly innocuous blood-borne bacterial microbiome may stimulate pathogenesis. In addition to exploring the relationship between blood-borne bacteria and the development of complex disorders, we also address the matter of contamination, citing the influence of contaminants on the interpretation of blood-derived microbial datasets and urging the routine analysis of laboratory controls to ascertain the taxonomic and metabolic characteristics of environmentally-derived contaminant-taxa.
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Affiliation(s)
- Diego J Castillo
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Riaan F Rifkin
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa.,Human Origins and Palaeo Environmental Research Group, Department of Anthropology and Geography, Oxford Brookes University, Oxford, United Kingdom
| | - Don A Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Marnie Potgieter
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
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30
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Wells PM, Williams FMK, Matey-Hernandez ML, Menni C, Steves CJ. 'RA and the microbiome: do host genetic factors provide the link? J Autoimmun 2019; 99:104-115. [PMID: 30850234 PMCID: PMC6470121 DOI: 10.1016/j.jaut.2019.02.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 12/29/2022]
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disease, characterised by painful synovium inflammation, bony erosions, immune activation and the circulation of autoantibodies. Despite recent advances in therapeutics enabling disease suppression, there is a considerable demand for alternative therapeutic strategies as well as optimising those available at present. The relatively low concordance rate between monozygotic twins, 20–30% contrasts with heritability estimates of ∼65%, indicating a substantive role of other risk factors in RA pathogenesis. There is established evidence that RA has an infective component to its aetiology. More recently, differences in the commensal microbiota in RA compared to controls have been identified. Studies have shown that the gut, oral and lung microbiota is different in new onset treatment naïve, and established RA patients, compared to controls. Key taxonomic associations are an increase in abundance of Porphyromonas gingivalis and Prevotella copri in RA patients, compared to healthy controls. Host genetics may provide the link between disease and the microbiome. Genetic influence may be mediated by the host immune system; a differential response to RA associated taxa is suggested. The gut microbiome contains elements which are as much as 30% heritable. A better understanding of the influence of host genetics will shed light onto the role of the microbiome in RA. Here we review the role of the microbiome in RA through the lens of host genetics, and consider future research areas addressing microbiome study design and bioinformatics approaches. Rheumatoid arthritis (RA) affects 1% of the population and is highly debilitating. RA is ~65% heritable, yet the concordance rate between monozygotic twins is just 20–30%, indicating a substantive role of other risk factors. Studies have shown that the gut, oral and lung microbiome is different in treatment naïve and established RA patients, compared to controls. Current findings suggest an important influence of host genetics on the microbiome, which may contribute to RA via the host immune system. Associations of the microbiome with RA described thus far are confounded by host genetics, and future studies need to take account of this.
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Affiliation(s)
- Philippa M Wells
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK.
| | - Frances M K Williams
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK
| | - M L Matey-Hernandez
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK
| | - Cristina Menni
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK
| | - Claire J Steves
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK; Clinical Age Research Unit, Kings College Hospital Foundation Trust, London, UK
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31
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Shi YC, Wang ZK, Yang YS. Consensus on standard biobanking of gut microbiota. J Dig Dis 2019; 20:114-121. [PMID: 30677249 DOI: 10.1111/1751-2980.12705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Yi Chao Shi
- Department of Gastroenterology and Hepatology, Institute of Digestive Diseases, Chinese PLA General Hospital, Beijing, China
| | - Zi Kai Wang
- Department of Gastroenterology and Hepatology, Institute of Digestive Diseases, Chinese PLA General Hospital, Beijing, China
| | - Yun Sheng Yang
- Department of Gastroenterology and Hepatology, Institute of Digestive Diseases, Chinese PLA General Hospital, Beijing, China
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32
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Whittle E, Leonard MO, Harrison R, Gant TW, Tonge DP. Multi-Method Characterization of the Human Circulating Microbiome. Front Microbiol 2019; 9:3266. [PMID: 30705670 PMCID: PMC6345098 DOI: 10.3389/fmicb.2018.03266] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/17/2018] [Indexed: 01/14/2023] Open
Abstract
The term microbiome describes the genetic material encoding the various microbial populations that inhabit our body. Whilst colonization of various body niches (e.g., the gut) by dynamic communities of microorganisms is now universally accepted, the existence of microbial populations in other "classically sterile" locations, including the blood, is a relatively new concept. The presence of bacteria-specific DNA in the blood has been reported in the literature for some time, yet the true origin of this is still the subject of much deliberation. The aim of this study was to investigate the phenomenon of a "blood microbiome" by providing a comprehensive description of bacterially derived nucleic acids using a range of complementary molecular and classical microbiological techniques. For this purpose we utilized a set of plasma samples from healthy subjects (n = 5) and asthmatic subjects (n = 5). DNA-level analyses involved the amplification and sequencing of the 16S rRNA gene. RNA-level analyses were based upon the de novo assembly of unmapped mRNA reads and subsequent taxonomic identification. Molecular studies were complemented by viability data from classical aerobic and anaerobic microbial culture experiments. At the phylum level, the blood microbiome was predominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key phyla detected were consistent irrespective of molecular method (DNA vs. RNA), and consistent with the results of other published studies. In silico comparison of our data with that of the Human Microbiome Project revealed that members of the blood microbiome were most likely to have originated from the oral or skin communities. To our surprise, aerobic and anaerobic cultures were positive in eight of out the ten donor samples investigated, and we reflect upon their source. Our data provide further evidence of a core blood microbiome, and provide insight into the potential source of the bacterial DNA/RNA detected in the blood. Further, data reveal the importance of robust experimental procedures, and identify areas for future consideration.
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Affiliation(s)
- Emma Whittle
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Keele, United Kingdom
| | - Martin O. Leonard
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, United Kingdom
| | - Rebecca Harrison
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Keele, United Kingdom
| | - Timothy W. Gant
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, United Kingdom
| | - Daniel Paul Tonge
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Keele, United Kingdom
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Tarnecki AM, Rhody NR, Walsh CJ. Health Characteristics and Blood Bacterial Assemblages of Healthy Captive Red Drum: Implications for Aquaculture and Fish Health Management. JOURNAL OF AQUATIC ANIMAL HEALTH 2018; 30:339-353. [PMID: 30269412 DOI: 10.1002/aah.10047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 09/21/2018] [Indexed: 06/08/2023]
Abstract
The newly emerging tissue microbiota hypothesis suggests that bacteria found in blood and tissues play a role in host health, as these bacterial communities have been associated with various noncommunicable diseases such as obesity, liver disease, and cardiovascular disease. Numerous reports have identified bacteria in the blood of healthy finfish, indicating bacteremia may not always indicate disease. Current research priorities in aquaculture include the development of technologies and practices that will allow for an effective reduction in antibiotic use for the prevention and treatment of disease. Overall, a better understanding of fish health is needed, particularly among species selected for commercial-scale production. This study investigated blood characteristics of cultured Red Drum Sciaenops ocellatus with the tissue microbiota hypothesis in mind. Bacterial assemblages within the blood were characterized using next-generation sequencing and compared with other various blood characteristics, including innate immune function enzymes, between two fish cohorts reared in aquaculture. A total of 137 prokaryotic operational taxonomic units (OTUs) were identified from the blood of Red Drum. Microbiota diversity and structure varied greatly among individuals, for which the number of OTUs ranged from 4 to 58; however, predicted metagenomic function was highly similar between individuals and was dominated by the metabolism of carbohydrates and amino acids and membrane transport. Communities were dominated by Proteobacteria, followed by Bacteroidetes, Firmicutes, and Actinobacteria. The most commonly identified genera included Acinetobacter, Bacillus, Corynebacterium, and Pseudomonas. Three genera previously identified as containing marine fish pathogens were detected: Corynebacterium, Pantoea, and Chryseobacterium. A subset of bacterial OTUs were positively correlated with superoxide dismutase activity and negatively correlated with lysozyme activity, indicating a relationship between blood microbiota and the innate immune system. The results of this study provide further evidence for the tissue microbiota hypothesis and demonstrate the potential for these bacterial communities to be linked to immunological characteristics often used as biomarkers for fish health.
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Affiliation(s)
- Andrea M Tarnecki
- Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, Florida, 34236, USA
| | - Nicole R Rhody
- Mote Aquaculture Research Park, 874 WR Mote Way, Sarasota, Florida, 34240, USA
| | - Catherine J Walsh
- Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, Florida, 34236, USA
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Gaußmann B, Hess C, Grafl B, Kovacs M, Troxler S, Stessl B, Hess M, Paudel S. Escherichia coli isolates from femoral bone marrow of broilers exhibit diverse pheno- and genotypic characteristics that do not correlate with macroscopic lesions of bacterial chondronecrosis with osteomyelitis. Avian Pathol 2018; 47:271-280. [DOI: 10.1080/03079457.2018.1440065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Barbara Gaußmann
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Claudia Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Beatrice Grafl
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Mercedes Kovacs
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Salome Troxler
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Beatrix Stessl
- Institute of Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Michael Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Surya Paudel
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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Hornok S, Ágh N, Takács N, Kontschán J, Hofmann-Lehmann R. Haematospirillum and insect Wolbachia DNA in avian blood. Antonie van Leeuwenhoek 2017; 111:479-483. [PMID: 29063344 DOI: 10.1007/s10482-017-0961-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/10/2017] [Indexed: 10/18/2022]
Abstract
In this study, blood samples of 259 Acrocephalus sp. warblers were molecularly analysed for Anaplasmataceae and Rhodospirillaceae based on PCR amplification of 16S rRNA gene fragments. One bird blood sample (from Reed Warbler, Acrocephalus scirpaceus) yielded a sequence with 99.8% identity to Haematospirillum jordaniae. This is the first molecular evidence for the occurrence of this species in the blood of any vertebrate other than human. Another bird blood sample (from Marsh Warbler: Acrocephalus palustris) yielded a Wolbachia sequence, closely related to a moth endosymbiont with 99.8% identity. A nematode origin of Wolbachia DNA detected here in avian blood can be excluded, because results of phylogenetic analysis showed its closest alignment with insect wolbachiae. This is the first finding of insect Wolbachia DNA in the circulatory system of birds, which can be explained either by the inoculation of wolbachiae by blood-sucking vectors, or passing of Wolbachia DNA from the gut into the blood of this insectivorous bird species.
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Affiliation(s)
- Sándor Hornok
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, 1078, Hungary.
| | - Nóra Ágh
- Department of Biomathematics and Informatics, University of Veterinary Medicine, Budapest, 1078, Hungary
| | - Nóra Takács
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, 1078, Hungary
| | - Jenő Kontschán
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, 1022, Hungary
| | - Regina Hofmann-Lehmann
- Vetsuisse Faculty, Clinical Laboratory and Center for Clinical Studies, University of Zürich, 8057, Zurich, Switzerland
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Wijesurendra DS, Chamings AN, Bushell RN, Rourke DO, Stevenson M, Marenda MS, Noormohammadi AH, Stent A. Pathological and microbiological investigations into cases of bacterial chondronecrosis and osteomyelitis in broiler poultry. Avian Pathol 2017; 46:683-694. [DOI: 10.1080/03079457.2017.1349872] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Dinidu S. Wijesurendra
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Australia
| | | | - Rhys Nathan Bushell
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Australia
| | - Denise O’ Rourke
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Australia
| | - Mark Stevenson
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
| | - Marc Serge Marenda
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Australia
| | - Amir H. Noormohammadi
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Australia
| | - Andrew Stent
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Australia
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Adhikari B, Kwon YM. Characterization of the Culturable Subpopulations of Lactobacillus in the Chicken Intestinal Tract as a Resource for Probiotic Development. Front Microbiol 2017; 8:1389. [PMID: 28798730 PMCID: PMC5526839 DOI: 10.3389/fmicb.2017.01389] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/10/2017] [Indexed: 01/29/2023] Open
Abstract
To gain better understanding of the distributions of the culturable Lactobacillus species in the chicken intestinal tract, we collected ceca, and distal ileum from 10 3-weeks-old broiler chickens. Lactobacillus strains from cecal lumen contents (M-CL), and those associated with mucosa of ceca (M-CM) and ileum (M-IM) were recovered on de Man, Rogosa and Sharpe (MRS) agar plates, and used for microbiota analysis. The total cecal content (T-CL) was also used directly for microbiota analysis. We purposefully focused on MRS-recovered populations to gain understanding of the culturable subpopulations of Lactobacillus, since the culturability is an important phenotype in order to exploit the chicken gut microbiota as a resource for development of probiotics. The V1–V3 regions of 16S rRNA gene was amplified from genomic DNA samples, and the pooled amplicons were analyzed by MiSeq sequencing with paired-end read 300 cycle option. Among MRS groups, Firmicutes were significantly higher in M-IM and M-CL as compared to M-CM, whereas Proteobacteria were significantly higher in M-CM as compared to M-IM and M-CL at p < 0.05. Among Lactobacillus, L. salivarius (36%) and L. johnsonii (21%) were higher in M-IM as compared to M-CL (L. salivarius, 28%; L. johnsonii, 15%), and M-CM (L. salivarius, 20%; L. johnsonii, 11%). L. crispatus was found significantly higher in M-CL as compared to M-IM (p < 0.01) whereas L. gasseri was found significantly higher in M-IM as compared to M-CM (p < 0.05). L. aviarius, and L. fornicalis were only observed in T-CL. In summary, Lactobacillus populations recovered on MRS vary with different regions and locations in chicken GIT, which might indicate their distinct functional roles in different gastrointestinal tract (GIT) niches, and some species of Lactobacillus are not culturable on MRS agar media. This study is the first attempt to define culturable Lactobacillus subpopulations in the chicken intestinal tract comprehensively using 16S rRNA gene profiling, and the findings of this study will be used as a platform to develop a new strategy for isolation of effective Lactobacillus probiotic candidates based on comparative analyses of chicken gut microbiota.
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Affiliation(s)
- Bishnu Adhikari
- Department of Poultry Science, College of Agricultural, Food and Life Sciences, University of Arkansas, FayettevilleAR, United States
| | - Young M Kwon
- Department of Poultry Science, College of Agricultural, Food and Life Sciences, University of Arkansas, FayettevilleAR, United States.,Cell and Molecular Biology Program, University of Arkansas, FayettevilleAR, United States
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Liu H, Smith TPL, Nonneman DJ, Dekkers JCM, Tuggle CK. A high-quality annotated transcriptome of swine peripheral blood. BMC Genomics 2017. [PMID: 28646867 PMCID: PMC5483264 DOI: 10.1186/s12864-017-3863-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background High throughput gene expression profiling assays of peripheral blood are widely used in biomedicine, as well as in animal genetics and physiology research. Accurate, comprehensive, and precise interpretation of such high throughput assays relies on well-characterized reference genomes and/or transcriptomes. However, neither the reference genome nor the peripheral blood transcriptome of the pig have been sufficiently assembled and annotated to support such profiling assays in this emerging biomedical model organism. We aimed to assemble published and novel RNA-seq data to provide a comprehensive, well-annotated blood transcriptome for pigs by integrating a de novo assembly with a genome-guided assembly. Results A de novo and a genome-guided transcriptome of porcine whole peripheral blood was assembled with ~162 million pairs of paired-end and ~183 million single-end, trimmed and normalized Illumina RNA-seq reads (~6 billion initial reads from 146 RNA-seq libraries) from five independent studies by using the Trinity and Cufflinks software, respectively. We then removed putative transcripts (PTs) of low confidence from both assemblies and merged the remaining PTs into an integrated transcriptome consisting of 132,928 PTs, with 126,225 (~95%) PTs from the de novo assembly and more than 91% of PTs spliced. In the integrated transcriptome, ~90% and 63% of PTs had significant sequence similarity to sequences in the NCBI NT and NR databases, respectively; 68,754 (~52%) PTs were annotated with 15,965 unique gene ontology (GO) terms; and 7618 PTs annotated with Enzyme Commission codes were assigned to 134 pathways curated by the Kyoto Encyclopedia of Genes and Genomes (KEGG). Full exon-intron junctions of 17,528 PTs were validated by PacBio IsoSeq full-length cDNA reads from 3 other porcine tissues, NCBI pig RefSeq mRNAs and transcripts from Ensembl Sscrofa10.2 annotation. Completeness of the 5’ termini of 37,569 PTs was validated by public cap analysis of gene expression (CAGE) data. By comparison to the Ensembl transcripts, we found that (1) the deduced precursors of 54,402 PTs shared at least one intron or exon with those of 18,437 Ensembl transcripts; (2) 12,262 PTs had both longer 5’ and 3’ termini than their maximally overlapping Ensembl transcripts; and (3) 41,838 spliced PTs were totally missing from the Sscrofa10.2 annotation. Similar results were obtained when the PTs were compared to the pig NCBI RefSeq mRNA collection. Conclusions We built, validated and annotated a comprehensive porcine blood transcriptome with significant improvement over the annotation of Ensembl Sscrofa10.2 and the pig NCBI RefSeq mRNAs, and laid a foundation for blood-based high throughput transcriptomic assays in pigs and for advancing annotation of the pig genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3863-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haibo Liu
- Bioinformatics and Computational Biology Program, Department of Animal Science, Iowa State University, 2258 Kildee Hall, Ames, IA, 50011, USA
| | - Timothy P L Smith
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Dan J Nonneman
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, 239 Kildee Hall, Ames, IA, 50011, USA
| | - Christopher K Tuggle
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011, USA.
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The involvement of RUNX2 and SPARC genes in the bacterial chondronecrosis with osteomyelitis in broilers. Animal 2016; 11:1063-1070. [PMID: 27881195 DOI: 10.1017/s1751731116002433] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Economic losses due to an increase of leg disorders in broilers have become a major concern of the poultry industry. Despite the efforts to reduce skeletal abnormalities in chickens, insufficient progress has been made. Bacterial chondronecrosis with osteomyelitis (BCO) is one of the main disorders that affect bone integrity in broilers. However, the genetic pathways and genes involved in most bone problems, including BCO, remains unclear. In this study, femoral samples from male broilers with 45 days of age affected or not with BCO were used to compare the relative expression with a reverse transcription real time PCR approach of 13 candidate genes: SPP1 (osteopontin), TNFRSF11B (osteoprotegerin), SPARC (osteonectin), CALB1 (calbidin 1), CALM (Calmodulin 2), IBSP (sialoprotein), COL1A2 (collagen, type I, α 2), BMP2 (bone morphogenetic protein 2), BMP3 (bone morphogenetic protein 3), RANKL (κ-B nuclear factor ligand), SMAD1 (SMAD family member 1), LEPR (leptin receptor) and RUNX2 (related transcription factor Runt 2). Differential expression test between affected and non-affected groups was performed using the REST software. The RUNX2 and SPARC genes were downregulated (P<0.05) in the affected group, with reduced expression of fourfold when compared with the non-affected group. This result indicates that the downregulation of RUNX2 and SPARC can contribute to an increased incidence of BCO in broilers.
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40
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Budachetri K, Williams J, Mukherjee N, Sellers M, Moore F, Karim S. The microbiome of neotropical ticks parasitizing on passerine migratory birds. Ticks Tick Borne Dis 2016; 8:170-173. [PMID: 27802919 DOI: 10.1016/j.ttbdis.2016.10.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 10/17/2016] [Accepted: 10/24/2016] [Indexed: 02/01/2023]
Abstract
Seasonal migration of passerine birds between temperate North America and tropical Central and South America is an ecological phenomenon. Migration of birds has been associated with the introduction of ectoparasites like ticks or tick-borne pathogens across the avian migration routes. In this study, the microbial diversity was determined in the ticks and bird DNA samples using 454 pyrosequencing of bacterial 16S rRNA gene. Tick DNA samples showed the dominance of genera Lactococcus, Francisella, Raoultella, Wolbachia and Rickettsia across all the ticks, but birds DNA did not share common microbial diversity with ticks. Furthermore, "Candidatus Rickettsia amblyommii" infection in the 91 ticks collected off the songbirds was also quantified by qPCR assay. Interestingly, "Candidatus R. amblyommii" was tested positive in 24 ticks (26% infection), and infection varied from as low as three copies to thousands of copies, but bird blood samples showed no amplification. Our results provide evidence that songbirds serve as transport carrier for immature ticks, and less likely to be a reservoir for "Candidatus R. amblyommii".
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Affiliation(s)
- Khemraj Budachetri
- Department of Biological Sciences, University of Southern Mississippi, 118 College Drive #5018, Hattiesburg, MS 39406, USA
| | - Jaclyn Williams
- Department of Biological Sciences, University of Southern Mississippi, 118 College Drive #5018, Hattiesburg, MS 39406, USA
| | - Nabanita Mukherjee
- Department of Biological Sciences, University of Southern Mississippi, 118 College Drive #5018, Hattiesburg, MS 39406, USA
| | - Michael Sellers
- Department of Biological Sciences, University of Southern Mississippi, 118 College Drive #5018, Hattiesburg, MS 39406, USA
| | - Frank Moore
- Department of Biological Sciences, University of Southern Mississippi, 118 College Drive #5018, Hattiesburg, MS 39406, USA
| | - Shahid Karim
- Department of Biological Sciences, University of Southern Mississippi, 118 College Drive #5018, Hattiesburg, MS 39406, USA.
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