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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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2
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Vientós‐Plotts AI, Ericsson AC, Reinero CR. The respiratory microbiota and its impact on health and disease in dogs and cats: A One Health perspective. J Vet Intern Med 2023; 37:1641-1655. [PMID: 37551852 PMCID: PMC10473014 DOI: 10.1111/jvim.16824] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 07/10/2023] [Indexed: 08/09/2023] Open
Abstract
Healthy lungs were long thought of as sterile, with presence of bacteria identified by culture representing contamination. Recent advances in metagenomics have refuted this belief by detecting rich, diverse, and complex microbial communities in the healthy lower airways of many species, albeit at low concentrations. Although research has only begun to investigate causality and potential mechanisms, alterations in these microbial communities (known as dysbiosis) have been described in association with inflammatory, infectious, and neoplastic respiratory diseases in humans. Similar studies in dogs and cats are scarce. The microbial communities in the respiratory tract are linked to distant microbial communities such as in the gut (ie, the gut-lung axis), allowing interplay of microbes and microbial products in health and disease. This review summarizes considerations for studying local microbial communities, key features of the respiratory microbiota and its role in the gut-lung axis, current understanding of the healthy respiratory microbiota, and examples of dysbiosis in selected respiratory diseases of dogs and cats.
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Affiliation(s)
- Aida I. Vientós‐Plotts
- College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
- Department of Veterinary Medicine and Surgery, College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
- Comparative Internal Medicine LaboratoryUniversity of MissouriColumbiaMissouriUSA
| | - Aaron C. Ericsson
- College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
- University of Missouri Metagenomics CenterUniversity of MissouriColumbiaMissouriUSA
- Department of Veterinary Pathobiology, College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
| | - Carol R. Reinero
- College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
- Department of Veterinary Medicine and Surgery, College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
- Comparative Internal Medicine LaboratoryUniversity of MissouriColumbiaMissouriUSA
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3
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Kang S, Lee I, Park SY, Kim JY, Kim Y, Choe JS, Kwon O. Blood Microbiota Profile Is Associated with the Responsiveness of Postprandial Lipemia to Platycodi radix Beverage: A Randomized Controlled Trial in Healthy Subjects. Nutrients 2023; 15:3267. [PMID: 37513685 PMCID: PMC10386470 DOI: 10.3390/nu15143267] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/19/2023] [Accepted: 07/22/2023] [Indexed: 07/30/2023] Open
Abstract
Prolonged postprandial hyperlipidemia may cause the development of cardiovascular diseases. This study explored whether postprandial triglyceride-rich lipoprotein (TRL) clearance responsiveness to Platycodi radix beverage (PR) is associated with changes in blood microbiota profiles. We conducted an 8-week randomized controlled clinical trial involving normolipidemic adults with low fruit and vegetable intakes. Participants underwent an oral fat tolerance test and 16S amplicon sequencing analysis of blood microbiota. Using the Qualitative Interaction Trees, we identified responders as those with higher baseline dietary fat intake (>38.5 g/day) and lipoprotein lipase levels (>150.6 ng/mL), who showed significant reductions in AUC for triglyceride (TG) and chylomicron-TG after the oral fat tolerance test. The LEfSe analysis showed differentially abundant blood microbiota between responders and non-responders. A penalized logistic regression algorithm was employed to predict the responsiveness to intervention on the TRL clearance based on the background characteristics, including the blood microbiome. Our findings suggest that PR intake can modulate postprandial TRL clearance in adults consuming higher fat intake over 38.5 g/day and low fruit and vegetable intake through shared links to systemic microbial signatures.
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Affiliation(s)
| | - Inhye Lee
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Soo-Yeon Park
- Department of Nutritional Science and Food Management, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Ji Yeon Kim
- Department of Food Science and Technology, Seoul National University of Science and Technology, 232 Gongneung-ro, Nowon-gu, Seoul 01811, Republic of Korea
| | - Youjin Kim
- Logme Inc., Seoul 03182, Republic of Korea
| | - Jeong-Sook Choe
- Department of Agrofood Resources, National Institute of Agricultural Sciences, Rural Development Administration, Jeonbuk 55365, Republic of Korea
| | - Oran Kwon
- Logme Inc., Seoul 03182, Republic of Korea
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03760, Republic of Korea
- Department of Nutritional Science and Food Management, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
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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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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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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] [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,*Correspondence: Stefan Panaiotov,
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Arnold HK, Hanselmann R, Duke SM, Sharpton TJ, Beechler BR. Chronic clinical signs of upper respiratory tract disease associate with gut and respiratory microbiomes in a cohort of domestic felines. PLoS One 2022; 17:e0268730. [PMID: 36454958 PMCID: PMC9714858 DOI: 10.1371/journal.pone.0268730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022] Open
Abstract
Feline upper respiratory tract disease (FURTD), often caused by infections etiologies, is a multifactorial syndrome affecting feline populations worldwide. Because of its highly transmissible nature, infectious FURTD is most prevalent anywhere cats are housed in groups such as animal shelters, and is associated with negative consequences such as decreasing adoption rates, intensifying care costs, and increasing euthanasia rates. Understanding the etiology and pathophysiology of FURTD is thus essential to best mitigate the negative consequences of this disease. Clinical signs of FURTD include acute respiratory disease, with a small fraction of cats developing chronic sequelae. It is thought that nasal mucosal microbiome changes play an active role in the development of acute clinical signs, but it remains unknown if the microbiome may play a role in the development and progression of chronic clinical disease. To address the knowledge gap surrounding how microbiomes link to chronic FURTD, we asked if microbial community structure of upper respiratory and gut microbiomes differed between cats with chronic FURTD signs and clinically normal cats. We selected 8 households with at least one cat exhibiting chronic clinical FURTD, and simultaneously collected samples from cohabitating clinically normal cats. Microbial community structure was assessed via 16S rDNA sequencing of both gut and nasal microbiome communities. Using a previously described ecophylogenetic method, we identified 136 and 89 microbial features within gut and nasal microbiomes respectively that significantly associated with presence of active FURTD clinical signs in cats with a history of chronic signs. Overall, we find that nasal and gut microbial community members associate with the presence of chronic clinical course, but more research is needed to confirm our observations.
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Affiliation(s)
- Holly Kristin Arnold
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
| | - Rhea Hanselmann
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, United States of America
| | - Sarah M. Duke
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
| | - Thomas J. Sharpton
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
| | - Brianna R. Beechler
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon, United States of America
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Li Z, Di D, Sun Q, Yao X, Wei J, Li B, Liu K, Shao D, Qiu Y, Liu H, Cheng Z, Ma Z. Comparative Analyses of the Gut Microbiota in Growing Ragdoll Cats and Felinae Cats. Animals (Basel) 2022; 12:ani12182467. [PMID: 36139326 PMCID: PMC9494971 DOI: 10.3390/ani12182467] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/03/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Accumulating studies have revealed that the gut microbiota had intimate relations with the animal gastrointestinal tract diseases. Through regulating the development of the host’s intestinal immune system, the gut microbiota could directly influence the host’s intestinal function. In the current study, the gut microbiota of Ragdoll cats and Felinae cats were investigated and compared. Results demonstrated the diversity and richness of the gut microbiota in the Felinae cats were much higher than in the Ragdoll cats. However, the relative abundances of beneficial microbes in the Ragdoll cats were much higher than those in the Felinae cats. In all, different genetic portraits determined the different microbial communities in the feline gut. The candidate probiotics isolated in the growing cat’s gut might be applied to treat the gastrointestinal tract diseases. Abstract Today, domestic cats are important human companion animals for their appearance and favorable personalities. During the history of their domestication, the morphological and genetic portraits of domestic cats changed significantly from their wild ancestors, and the gut microbial communities of different breeds of cats also apparently differ. In the current study, the gut microbiota of Ragdoll cats and Felinae cats were analyzed and compared. Our data indicated that the diversity and richness of the gut microbiota in the Felinae cats were much higher than in the Ragdoll cats. The taxonomic analyses revealed that the most predominant phyla of the feline gut microbiota were Firmicutes, Bacteroidota, Fusobacteriota, Proteobacteria, Actinobacteriota, Campilobacterota, and others, while the most predominant genera were Anaerococcus, Fusobacterium, Bacteroides, Escherichia-Shigella, Finegoldia, Porphyromonas, Collinsella, Lactobacillus, Ruminococcus_gnavus_group, Prevotella, and others. Different microbial communities between the Ragdoll group and the Felinae group were observed, and the compared results demonstrated that the relative abundances of beneficial microbes (such as Lactobacillus, Enterococcus, Streptococcus, Blautia, Roseburia, and so on) in the Ragdoll group were much higher than in the Felinae group. The co-occurrence network revealed that the number of nodes and links in the Felinae group was significantly higher than the Ragdoll group, which meant that the network of the Felinae group was larger and more complex than that of the Ragdoll group. PICRUSt function analyses indicated that the differences in microbial genes might influence the energy metabolism and immune functions of the host. In all, our data demonstrated that the richness and diversity of beneficial microbes in the Ragdoll group were much higher than the Felinae group. Therefore, it is possible to isolate and identify more candidate probiotics in the gut microbiota of growing Ragdoll cats.
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Affiliation(s)
- Zongjie Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Di Di
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Qing Sun
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Xiaohui Yao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Beibei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Ke Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Donghua Shao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Haixia Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Zhanjun Cheng
- Nanjing Policedog Insitute of the Ministry of Public Security, Nanjing 210012, China
- Correspondence: (Z.C.); (Z.M.); Tel.: +86-21-3429-3139 (Z.M.); Fax: +86-21-5408-1818 (Z.M.)
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
- Correspondence: (Z.C.); (Z.M.); Tel.: +86-21-3429-3139 (Z.M.); Fax: +86-21-5408-1818 (Z.M.)
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10
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Vientós-Plotts AI, Ericsson AC, McAdams ZL, Rindt H, Reinero CR. Respiratory dysbiosis in cats with spontaneous allergic asthma. Front Vet Sci 2022; 9:930385. [PMID: 36157187 PMCID: PMC9492960 DOI: 10.3389/fvets.2022.930385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/04/2022] [Indexed: 12/31/2022] Open
Abstract
Deviations from a core airway microbiota have been associated with the development and progression of asthma as well as disease severity. Pet cats represent a large animal model for allergic asthma, as they spontaneously develop a disease similar to atopic childhood asthma. This study aimed to describe the lower airway microbiota of asthmatic pet cats and compare it to healthy cats to document respiratory dysbiosis occurring with airway inflammation. We hypothesized that asthmatic cats would have lower airway dysbiosis characterized by a decrease in richness, diversity, and alterations in microbial community composition including identification of possible pathobionts. In the current study, a significant difference in airway microbiota composition was documented between spontaneously asthmatic pet cats and healthy research cats mirroring the finding of dysbiosis in asthmatic humans. Filobacterium and Acinetobacter spp. were identified as predominant taxa in asthmatic cats without documented infection based on standard culture and could represent pathobionts in the lower airways of cats. Mycoplasma felis, a known lower airway pathogen of cats, was identified in 35% of asthmatic but not healthy cats. This article has been published alongside "Temporal changes of the respiratory microbiota as cats transition from health to experimental acute and chronic allergic asthma" (1).
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Affiliation(s)
- Aida I. Vientós-Plotts
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
- Comparative Internal Medicine Laboratory, College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Aaron C. Ericsson
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
- University of Missouri Metagenomics Center, University of Missouri, Columbia, MO, United States
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Zachary L. McAdams
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Hansjorg Rindt
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
- Comparative Internal Medicine Laboratory, College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Carol R. Reinero
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
- Comparative Internal Medicine Laboratory, College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
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Mtshali K, Khumalo ZTH, Kwenda S, Arshad I, Thekisoe OMM. Exploration and comparison of bacterial communities present in bovine faeces, milk and blood using 16S rRNA metagenomic sequencing. PLoS One 2022; 17:e0273799. [PMID: 36044481 PMCID: PMC9432762 DOI: 10.1371/journal.pone.0273799] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 08/15/2022] [Indexed: 11/23/2022] Open
Abstract
Cattle by-products like faeces, milk and blood have many uses among rural communities; aiding to facilitate everyday household activities and occasional rituals. Ecologically, the body sites from which they are derived consist of distinct microbial communities forming a complex ecosystem of niches. We aimed to explore and compare the faecal, milk and blood microbiota of cows through 16S rRNA sequencing. All downstream analyses were performed using applications in R Studio (v3.6.1). Alpha-diversity metrics showed significant differences between faeces and blood; faeces and milk; but non-significant between blood and milk using Kruskal-Wallis test, P < 0,05. The beta-diversity metrics on Principal Coordinate Analysis and Non-Metric Dimensional Scaling significantly clustered samples by type (PERMANOVA test, P < 0,05). The overall analysis revealed a total of 30 phyla, 74 classes, 156 orders, 243 families and 408 genera. Firmicutes, Bacteroidota and Proteobacteria were the most abundant phyla overall. A total of 58 genus-level taxa occurred concurrently between the body sites. The important taxa could be categorized into four potentially pathogenic clusters i.e. arthropod-borne; food-borne and zoonotic; mastitogenic; and metritic and abortigenic. A number of taxa were significantly differentially abundant (DA) between sites based on the Wald test implemented in DESeq2 package. Majority of the DA taxa (i.e. Romboutsia, Paeniclostridium, Monoglobus, Akkermansia, Turicibacter, Bacteroides, Candidatus_Saccharimonas, UCG-005 and Prevotellaceae_UCG-004) were significantly enriched in faeces in comparison to milk and blood, except for Anaplasma which was greatly enriched in blood and was in turn the largest microbial genus in the entire analysis. This study provides insights into the microbial community composition of the sampled body sites and its extent of overlapping. It further highlights the potential risk of disease occurrence and transmission between the animals and the community of Waaihoek in KwaZulu-Natal, Republic of South Africa pertaining to their unsanitary practices associated with the use of cattle by-products.
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Affiliation(s)
- Khethiwe Mtshali
- Biomedical Sciences Department, Tshwane University of Technology, Pretoria, South Africa
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
- * E-mail: ,
| | - Zamantungwa Thobeka Happiness Khumalo
- Faculty of Veterinary Science, Department of Veterinary Tropical Diseases, University of Pretoria, Onderstepoort, South Africa
- Study Management, ClinVet International, Bainsvlei, Bloemfontein, South Africa
| | - Stanford Kwenda
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Ismail Arshad
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- Faculty of Science, Department of Biochemistry and Microbiology, Engineering and Agriculture, University of Venda, Thohoyandou, South Africa
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12
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Vientós-Plotts AI, Ericsson AC, McAdams ZL, Rindt H, Reinero CR. Temporal changes of the respiratory microbiota as cats transition from health to experimental acute and chronic allergic asthma. Front Vet Sci 2022; 9:983375. [PMID: 36090168 PMCID: PMC9453837 DOI: 10.3389/fvets.2022.983375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/08/2022] [Indexed: 01/04/2023] Open
Abstract
In humans, deviation from a core airway microbiota may predispose to development, exacerbation, or progression of asthma. We proposed to describe microbiota changes using 16 rRNA sequencing in samples from the upper and lower airways, and rectal swabs of 8 cats after experimental induction of asthma using Bermuda grass allergen, in acute (6 weeks) and chronic (36 weeks) stages. We hypothesized that asthma induction would decrease richness and diversity and alter microbiota composition and structure in the lower airways, without significantly impacting other sites. After asthma induction, richness decreased in rectal (p = 0.014) and lower airway (p = 0.016) samples. B diversity was significantly different between health and chronic asthma in all sites, and between all time points for lower airways. In healthy lower airways Pseudomonadaceae comprised 80.4 ± 1.3% whereas Sphingobacteriaceae and Xanthobacteraceae predominated (52.4 ± 2.2% and 33.5 ± 2.1%, respectively), and Pseudomonadaceae was absent, in 6/8 cats with chronic asthma. This study provides evidence that experimental induction of asthma leads to dysbiosis in the airways and distant sites in both the acute and chronic stages of disease. This article has been published alongside "Respiratory dysbiosis in cats with spontaneous allergic asthma" (1).
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Affiliation(s)
- Aida I. Vientós-Plotts
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
- Comparative Internal Medicine Laboratory, University of Missouri, Columbia, MO, United States
| | - Aaron C. Ericsson
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
- University of Missouri Metagenomics Center, University of Missouri, Columbia, MO, United States
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Zachary L. McAdams
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Hansjorg Rindt
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
- Comparative Internal Medicine Laboratory, University of Missouri, Columbia, MO, United States
| | - Carol R. Reinero
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
- Comparative Internal Medicine Laboratory, University of Missouri, Columbia, MO, United States
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13
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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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14
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Bugrov N, Rudenko P, Lutsay V, Gurina R, Zharov A, Khairova N, Molchanova M, Krotova E, Shopinskaya M, Bolshakova M, Popova I. Fecal Microbiota Analysis in Cats with Intestinal Dysbiosis of Varying Severity. Pathogens 2022; 11:pathogens11020234. [PMID: 35215175 PMCID: PMC8875498 DOI: 10.3390/pathogens11020234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 01/27/2023] Open
Abstract
Recent studies have shown that the gut microbiota plays an important role in the pathogenesis of gastrointestinal diseases in various animal species. There are only limited data on the microbiome in cats with varying grades of dysbiosis. The purpose of the study was a detailed analysis of the quantitative and qualitative fecal microbiota spectrum in cats with intestinal dysbiosis of varying severity. The data obtained indicate that, depending on the dysbiosis severity in cats, the intestinal microbiome landscape changes significantly. It has been established that, depending on the dysbiosis severity, there is a shift in the balance between the Gram-positive and Gram-negative bacterial pools and in the nature of the isolation of specific bacteria forms, in the amount of obligate microbiota isolation, as well as individual facultative strains. When analyzing the serotyping of E. coli cultures isolated at various grades of intestinal dysbiosis severity, differences were found both in the isolation amount of various serotypes from one animal and in the prevalence of certain serotypes for each disease severity. A retrospective analysis of the fecal microbiota sensitivity in cats with dysbiosis to antibacterial drugs showed that, depending on the disease severity, the number of isolates sensitive to antibiotics increases significantly.
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Affiliation(s)
- Nikolay Bugrov
- Department of Veterinary Medicine, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia; (N.B.); (P.R.); (V.L.); (E.K.); (M.S.); (M.B.)
| | - Pavel Rudenko
- Department of Veterinary Medicine, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia; (N.B.); (P.R.); (V.L.); (E.K.); (M.S.); (M.B.)
- Biological Testing Laboratory, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences (BIBCh RAS), 142290 Pushchino, Russia
| | - Vladimir Lutsay
- Department of Veterinary Medicine, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia; (N.B.); (P.R.); (V.L.); (E.K.); (M.S.); (M.B.)
| | - Regina Gurina
- Department of Technosphere Safety, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia; (R.G.); (A.Z.); (N.K.)
| | - Andrey Zharov
- Department of Technosphere Safety, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia; (R.G.); (A.Z.); (N.K.)
| | - Nadiya Khairova
- Department of Technosphere Safety, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia; (R.G.); (A.Z.); (N.K.)
| | - Maria Molchanova
- Department of Foreign Languages, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia;
| | - Elena Krotova
- Department of Veterinary Medicine, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia; (N.B.); (P.R.); (V.L.); (E.K.); (M.S.); (M.B.)
| | - Marina Shopinskaya
- Department of Veterinary Medicine, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia; (N.B.); (P.R.); (V.L.); (E.K.); (M.S.); (M.B.)
| | - Marina Bolshakova
- Department of Veterinary Medicine, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia; (N.B.); (P.R.); (V.L.); (E.K.); (M.S.); (M.B.)
| | - Irina Popova
- Department of Veterinary Medicine, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia; (N.B.); (P.R.); (V.L.); (E.K.); (M.S.); (M.B.)
- Correspondence:
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15
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The role of microbiota in respiratory health and diseases, particularly in tuberculosis. Biomed Pharmacother 2021; 143:112108. [PMID: 34560539 DOI: 10.1016/j.biopha.2021.112108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/11/2021] [Accepted: 08/23/2021] [Indexed: 12/11/2022] Open
Abstract
Trillions of beneficial and hostile microorganisms live in the human respiratory and gastrointestinal tracts, which act as gatekeepers in maintaining human health, i.e., protecting the body from pathogens by colonizing mucosal surfaces with microbiota-derived antimicrobial metabolites such as short-chain fatty acids or host-derived cytokines and chemokines. It is widely accepted that the microbiome interacts with each other and with the host in a mutually beneficial relationship. Microbiota in the respiratory tract may also play a crucial role in immune homeostasis, maturation, and maintenance of respiratory physiology. Anti-TB antibiotics may cause dysbiosis in the lung and intestinal microbiota, affecting colonization resistance and making the host more susceptible to Mycobacterium tuberculosis (M. tuberculosis) infection. This review discusses recent advances in our understanding of the lung microbiota composition, the lungs and intestinal microbiota related to respiratory health and diseases, microbiome sequencing and analysis, the bloodstream, and the lymphatic system that underpin the gut-lung axis in M. tuberculosis-infected humans and animals. We also discuss the gut-lung axis interactions with the immune system, the role of the microbiome in TB pathogenesis, and the impact of anti-TB antibiotic therapy on the microbiota in animals, humans, and drug-resistant TB individuals.
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16
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D'Aquila P, Giacconi R, Malavolta M, Piacenza F, Bürkle A, Villanueva MM, Dollé MET, Jansen E, Grune T, Gonos ES, Franceschi C, Capri M, Grubeck-Loebenstein B, Sikora E, Toussaint O, Debacq-Chainiaux F, Hervonen A, Hurme M, Slagboom PE, Schön C, Bernhardt J, Breusing N, Passarino G, Provinciali M, Bellizzi D. Microbiome in Blood Samples From the General Population Recruited in the MARK-AGE Project: A Pilot Study. Front Microbiol 2021; 12:707515. [PMID: 34381434 PMCID: PMC8350766 DOI: 10.3389/fmicb.2021.707515] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/29/2021] [Indexed: 01/12/2023] Open
Abstract
The presence of circulating microbiome in blood has been reported in both physiological and pathological conditions, although its origins, identities and function remain to be elucidated. This study aimed to investigate the presence of blood microbiome by quantitative real-time PCRs targeting the 16S rRNA gene. To our knowledge, this is the first study in which the circulating microbiome has been analyzed in such a large sample of individuals since the study was carried out on 1285 Randomly recruited Age-Stratified Individuals from the General population (RASIG). The samples came from several different European countries recruited within the EU Project MARK-AGE in which a series of clinical biochemical parameters were determined. The results obtained reveal an association between microbial DNA copy number and geographic origin. By contrast, no gender and age-related difference emerged, thus demonstrating the role of the environment in influencing the above levels independent of age and gender at least until the age of 75. In addition, a significant positive association was found with Free Fatty Acids (FFA) levels, leukocyte count, insulin, and glucose levels. Since these factors play an essential role in both health and disease conditions, their association with the extent of the blood microbiome leads us to consider the blood microbiome as a potential biomarker of human health.
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Affiliation(s)
- Patrizia D'Aquila
- Department of Biology, Ecology and Earth Sciences (DIBEST), University of Calabria, Rende, Italy
| | - Robertina Giacconi
- Advanced Technology Center for Aging Research, IRCCS (Scientific Institute for Research, Hospitalization and Healthcare) INRCA National Institute on Health and Science on Ageing, Ancona, Italy
| | - Marco Malavolta
- Advanced Technology Center for Aging Research, IRCCS (Scientific Institute for Research, Hospitalization and Healthcare) INRCA National Institute on Health and Science on Ageing, Ancona, Italy
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research, IRCCS (Scientific Institute for Research, Hospitalization and Healthcare) INRCA National Institute on Health and Science on Ageing, Ancona, Italy
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - María Moreno Villanueva
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Sport Science, Human Performance Research Centre, University of Konstanz, Konstanz, Germany
| | - Martijn E T Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Eugène Jansen
- Centre for Health Protection, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Tilman Grune
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany.,NutriAct-Competence Cluster Nutrition Research Berlin-Potsdam, Nuthetal, Germany
| | - Efstathios S Gonos
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, Athens, Greece
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy.,Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy.,Interdepartmental Center, Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy
| | | | - Ewa Sikora
- Laboratory of the Molecular Bases of Ageing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Olivier Toussaint
- Research Unit of Cellular Biology (URBC) Namur Research Institute for Life Sciences (Narilis), University of Namur, Namur, Belgium
| | - Florence Debacq-Chainiaux
- Research Unit of Cellular Biology (URBC) Namur Research Institute for Life Sciences (Narilis), University of Namur, Namur, Belgium
| | | | - Mikko Hurme
- Medical School, University of Tampere, Tampere, Finland
| | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Centre, Leiden, Netherlands
| | | | | | - Nicolle Breusing
- Department of Applied Nutritional Science/Dietetics, Institute of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences (DIBEST), University of Calabria, Rende, Italy
| | - Mauro Provinciali
- Advanced Technology Center for Aging Research, IRCCS (Scientific Institute for Research, Hospitalization and Healthcare) INRCA National Institute on Health and Science on Ageing, Ancona, Italy
| | - Dina Bellizzi
- Department of Biology, Ecology and Earth Sciences (DIBEST), University of Calabria, Rende, Italy
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17
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A novel Filobacterium sp can cause chronic bronchitis in cats. PLoS One 2021; 16:e0251968. [PMID: 34106938 PMCID: PMC8189514 DOI: 10.1371/journal.pone.0251968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/06/2021] [Indexed: 11/19/2022] Open
Abstract
Background Cilia-associated respiratory bacillus (CARB; now known as Filobacterium rodentium gen. nov., sp. nov.) is a primary pathogen of rodents. A CARB-like organism was reported in post-mortem lung samples of cats using light and electron microscopy. Here we explore by molecular procedures if a Filobacterium sp. is a part of the normal feline lower respiratory microbiome and whether it could in some cats contribute to the development of chronic bronchial disease. Methodology A Filobacterium sp. was identified in three Czech cats clinically diagnosed as having chronic neutrophilic bronchitis. Bronchoalveolar lavage fluid (BALF) specimens obtained from these cats were subjected to panbacterial 16S rDNA PCR followed by Sanger sequencing of the V5 to V8 region. After these cats were treated with specific antimicrobials, their clinical signs resolved promptly, without recurrence. Next, BALF specimens from 13 Australian and 11 Italian cats with lower respiratory disease and an additional 16 lung samples of Italian cats who died of various causes were examined using next generation sequencing (NGS). Subsequently, a Filobacterium-specific qPCR assay was developed and used to re-test BALF specimens from the 11 Italian cats and lung tissue homogenates from the additional 16 deceased cats. Principal findings An amplicon of 548 bp with 91.24% sequence agreement with Filobacterium rodentium was obtained from all three patients, suggesting the novel Filobacterium sp. was the cause of their lower respiratory disease. The novel Filobacterium sp., which we propose to call F. felis, was detected in 3/3 Czech cats with chronic neutrophilic bronchitis, 13/13 Australian cats and 6/11 Italian cats with chronic lower respiratory disease, and 14/16 necropsy lung specimens from Italian cats. NGS and qPCR results all showed identical sequences. The Filobacterium sp. was sometimes the preponderant bacterial species in BALF specimens from cats with lower airway disease. There was an association between the presence of large numbers (greater than 105 organisms/mL) of Filobacterium and the presence of neutrophilic and/or histiocytic inflammation, although only a subset of inflammatory BALF specimens had F. felis as the preponderant organism. Conclusion The novel Filobacterium sp. comprises a finite part of the normal feline lower respiratory microbiome. Under certain circumstances it can increase in absolute and relative abundance and give rise to neutrophilic and/or histiocytic bronchitis, bronchiolitis and bronchopneumonia. These findings strongly suggest that F. felis could be an underdiagnosed cause of feline bronchial disease.
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18
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Bacterial DNAemia is associated with serum zonulin levels in older subjects. Sci Rep 2021; 11:11054. [PMID: 34040086 PMCID: PMC8154904 DOI: 10.1038/s41598-021-90476-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
The increased presence of bacteria in blood is a plausible contributing factor in the development and progression of aging-associated diseases. In this context, we performed the quantification and the taxonomic profiling of the bacterial DNA in blood samples collected from forty-three older subjects enrolled in a nursing home. Quantitative PCR targeting the 16S rRNA gene revealed that all samples contained detectable amounts of bacterial DNA with a concentration that varied considerably between subjects. Correlation analyses revealed that the bacterial DNAemia (expressed as concentration of 16S rRNA gene copies in blood) significantly associated with the serum levels of zonulin, a marker of intestinal permeability. This result was confirmed by the analysis of a second set of blood samples collected from the same subjects. 16S rRNA gene profiling revealed that most of the bacterial DNA detected in blood was ascribable to the phylum Proteobacteria with a predominance of the genus Pseudomonas. Several control samples were also analyzed to assess the influence of contaminant bacterial DNA potentially originating from reagents and materials. The data reported here suggest that para-cellular permeability of epithelial (and, potentially, endothelial) cell layers may play an important role in bacterial migration into the bloodstream. Bacterial DNAemia is likely to impact on several aspects of host physiology and could underpin the development and prognosis of various diseases in older subjects.
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19
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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: 3] [Impact Index Per Article: 1.0] [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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20
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Mach N, Baranowski E, Nouvel LX, Citti C. The Airway Pathobiome in Complex Respiratory Diseases: A Perspective in Domestic Animals. Front Cell Infect Microbiol 2021; 11:583600. [PMID: 34055660 PMCID: PMC8160460 DOI: 10.3389/fcimb.2021.583600] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 04/30/2021] [Indexed: 12/19/2022] Open
Abstract
Respiratory infections in domestic animals are a major issue for veterinary and livestock industry. Pathogens in the respiratory tract share their habitat with a myriad of commensal microorganisms. Increasing evidence points towards a respiratory pathobiome concept, integrating the dysbiotic bacterial communities, the host and the environment in a new understanding of respiratory disease etiology. During the infection, the airway microbiota likely regulates and is regulated by pathogens through diverse mechanisms, thereby acting either as a gatekeeper that provides resistance to pathogen colonization or enhancing their prevalence and bacterial co-infectivity, which often results in disease exacerbation. Insight into the complex interplay taking place in the respiratory tract between the pathogens, microbiota, the host and its environment during infection in domestic animals is a research field in its infancy in which most studies are focused on infections from enteric pathogens and gut microbiota. However, its understanding may improve pathogen control and reduce the severity of microbial-related diseases, including those with zoonotic potential.
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Affiliation(s)
- Núria Mach
- Université Paris-Saclay, Institut National de Recherche Pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), AgroParisTech, Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - Eric Baranowski
- Interactions Hôtes-Agents Pathogènes (IHAP), Université de Toulouse, INRAE, ENVT, Toulouse, France
| | - Laurent Xavier Nouvel
- Interactions Hôtes-Agents Pathogènes (IHAP), Université de Toulouse, INRAE, ENVT, Toulouse, France
| | - Christine Citti
- Interactions Hôtes-Agents Pathogènes (IHAP), Université de Toulouse, INRAE, ENVT, Toulouse, France
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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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Vientós-Plotts AI, Ericsson AC, Rindt H, Reinero CR. Blood cultures and blood microbiota analysis as surrogates for bronchoalveolar lavage fluid analysis in dogs with bacterial pneumonia. BMC Vet Res 2021; 17:129. [PMID: 33757515 PMCID: PMC7988943 DOI: 10.1186/s12917-021-02841-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/10/2021] [Indexed: 11/10/2022] Open
Abstract
Background Diagnosis of canine bacterial pneumonia relies on airway lavage to confirm septic, suppurative inflammation, and a positive bacterial culture. Considering risks of bronchoalveolar lavage fluid (BALF) collection, minimally invasive methods like culture or next generation sequencing of blood would be appealing. In dogs with bacterial pneumonia, our study aims included (1): determining proportion of agreement between cultivable bacteria in BALF and blood (2); characterizing BALF, blood, and oropharyngeal (OP) microbiota and determining if bacteria cultured from BALF were present in these communities; and (3) comparing relatedness of microbial community composition at all three sites. Bacterial cultures were performed on BALF and blood. After DNA extraction of BALF, blood and OP, 16S rRNA amplicon libraries were generated, sequenced, and compared to a bacterial gene sequence database. Results Disregarding one false positive, blood cultures were positive in 2/9 dogs (5 total isolates), all 5 isolates were present in BALF cultures (16 total isolates). Based on sequencing data, all sites had rich and diverse microbial communities. Comparing cultured BALF bacterial genera with sequenced taxa, all dogs had ≥1 cultured isolate present in their microbiota: cultured BALF isolates were found in microbiota of BALF (12/16), blood (7/16), and OP (6/11; only 7 dogs had OP swabs). Of 394 distinct taxa detected in BALF, these were present in 75% OP and 45% blood samples. BALF community composition was significantly different than OP (p = 0.0059) and blood (p = 0.0009). Conclusions Blood cultures are insensitive but specific for cultured BALF bacteria in canine bacterial pneumonia. Cultivable BALF bacteria were present in BALF, blood and OP microbiota to differing degrees.
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Affiliation(s)
- A I Vientós-Plotts
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.,Comparative Internal Medicine Laboratory, University of Missouri, Columbia, MO, 65211, USA
| | - A C Ericsson
- University of Missouri Metagenomics Center, University of Missouri, Columbia, MO, 65211, USA.,Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - H Rindt
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.,Comparative Internal Medicine Laboratory, University of Missouri, Columbia, MO, 65211, USA
| | - C R Reinero
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA. .,Comparative Internal Medicine Laboratory, University of Missouri, Columbia, MO, 65211, USA.
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23
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Exploring Prokaryotic and Eukaryotic Microbiomes Helps in Detecting Tick-Borne Infectious Agents in the Blood of Camels. Pathogens 2021; 10:pathogens10030351. [PMID: 33809738 PMCID: PMC8002256 DOI: 10.3390/pathogens10030351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 12/22/2022] Open
Abstract
Dromedary camels (Camelus dromedarius) are widely distributed in Africa, the Middle East and northern India. In this study, we aimed to detect tick-borne pathogens through investigating prokaryotic and eukaryotic microorganisms in camel blood based on a metagenomic approach and then to characterize potentially pathogenic organisms using traditional molecular techniques. We showed that the bacteria circulating in the blood of camels is dominated by Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria. At the genus level, Sediminibacterium, Hydrotalea, Bradyrhizobium and Anaplasma were the most abundant taxa. Eukaryotic profile was dominated by Fungi, Charophyta and Apicomplexa. At the genus level, Theileria was detected in 10 out of 18 samples, while Sarcocystis, Hoplorhynchus and Stylocephalus were detected in one sample each. Our metagenomic approach was successful in the detection of several pathogens or potential pathogens including Anaplasma sp., Theileria ovis, Th. separata, Th. annulate, Th. mutans-like and uncharacterized Theileria sp. For further characterization, we provided the partial sequences of citrate synthase (gltA) and heat-shock protein (groEL) genes of Candidatus Anaplasma camelii. We also detected Trypanosoma evansi type A using polymerase chain reaction (PCR) targeting the internal transcribed spacer 1 (ITS1) region. This combined metagenomic and traditional approach will contribute to a better understanding of the epidemiology of pathogens including tick-borne bacteria and protozoa in animals.
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24
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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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25
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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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26
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Pet-Human Gut Microbiome Host Classifier Using Data from Different Studies. Microorganisms 2020; 8:microorganisms8101591. [PMID: 33076521 PMCID: PMC7602744 DOI: 10.3390/microorganisms8101591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 12/30/2022] Open
Abstract
(1) Background: microbiome host classification can be used to identify sources of contamination in environmental data. However, there is no ready-to-use host classifier. Here, we aimed to build a model that would be able to discriminate between pet and human microbiomes samples. The challenge of the study was to build a classifier using data solely from publicly available studies that normally contain sequencing data for only one type of host. (2) Results: we have developed a random forest model that distinguishes human microbiota from domestic pet microbiota (cats and dogs) with 97% accuracy. In order to prevent overfitting, samples from several (at least four) different projects were necessary. Feature importance analysis revealed that the model relied on several taxa known to be key components in domestic cat and dog microbiomes (such as Fusobacteriaceae and Peptostreptococcaeae), as well as on some taxa exclusively found in humans (as Akkermansiaceae). (3) Conclusion: we have shown that it is possible to make a reliable pet/human gut microbiome classifier on the basis of the data collected from different studies.
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27
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Respiratory microbiota of humpback whales may be reduced in diversity and richness the longer they fast. Sci Rep 2020; 10:12645. [PMID: 32724137 PMCID: PMC7387350 DOI: 10.1038/s41598-020-69602-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 07/08/2020] [Indexed: 12/31/2022] Open
Abstract
Humpback whales endure several months of fasting while undertaking one of the longest annual migrations of any mammal, which depletes the whales’ energy stores and likely compromises their physiological state. Airway microbiota are linked to respiratory health in mammals. To illuminate the dynamics of airway microbiota in a physiologically challenged mammal, we investigated the bacterial communities in the blow of East Australian humpback whales at two stages of their migration: at the beginning (n = 20) and several months into their migration (n = 20), using barcoded tag sequencing of the bacterial 16S rRNA gene. We show that early in the fasting the whale blow samples had a higher diversity and richness combined with a larger number of core taxa and a different bacterial composition than later in the fasting. This study provides some evidence that the rich blow microbiota at the beginning of their fasting might reflect the whales’ uncompromised physiology and that changes in the microbiota occur during the whales’ migration.
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28
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Vendl C, Slavich E, Nelson T, Acevedo-Whitehouse K, Montgomery K, Ferrari B, Thomas T, Rogers T. Does sociality drive diversity and composition of airway microbiota in cetaceans? ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:324-333. [PMID: 32162479 DOI: 10.1111/1758-2229.12835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 02/25/2020] [Accepted: 03/09/2020] [Indexed: 05/23/2023]
Abstract
The number of social contacts of mammals is positively correlated with the diversity of their gut microbes. There is some evidence that sociality also affects microbes in the respiratory tract. We tested whether the airway microbiota of cetacean species differ depending on the whales' level of sociality. We sampled the blow of blue (Balaenoptera musculus), grey (Eschrichtius robustus), humpback (Megaptera novaeangliae) and long-finned pilot whales (PWs) (Globicephala melas) and analysed the blow microbiota by barcode tag sequencing targeting the V4 region of the bacterial 16S rRNA gene. Humpback whales (HWs) show higher levels of sociality than blue (BW) and grey (GW), while PWs are the most gregarious among the four species. The blow samples of the HWs showed the highest richness and diversity. HWs were also the only species with a species-specific clustering of their microbial community composition and a relatively large number of core taxa. Therefore, we conclude that it cannot be sociality alone shaping the diversity and composition of airway microbiota. We suggest the whale species' lung volume and size of the plume of exhaled air as an additional factor impacting the transmission potential of blow microbiota from one individual whale to another.
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Affiliation(s)
- Catharina Vendl
- Evolution & Ecology Research Centre, School of Biological, Environmental and Earth Science, UNSW Sydney, NSW, 2052, Australia
| | - Eve Slavich
- Evolution & Ecology Research Centre, School of Biological, Environmental and Earth Science, UNSW Sydney, NSW, 2052, Australia
- Stats Central, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, UNSW, 2052, Australia
| | - Tiffanie Nelson
- Queensland Facility for Advanced Bioinformatics, School of Medicine, Menzies Health Institute Queensland, Building G40, Level 9, Gold Coast Campus, Griffith University, Southport, QLD, 4215, Australia
| | - Karina Acevedo-Whitehouse
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Queretaro, 76230, Mexico
| | - Kate Montgomery
- The School of Biotechnology and Biomolecular Sciences, UNSW Sydney, NSW, 2052, Australia
| | - Belinda Ferrari
- The School of Biotechnology and Biomolecular Sciences, UNSW Sydney, NSW, 2052, Australia
| | - Torsten Thomas
- Centre of Marine Bio-Innovation (CMB), School of Biological, Environmental and Earth Science, UNSW Sydney, NSW, 2052, Australia
| | - Tracey Rogers
- Evolution & Ecology Research Centre, School of Biological, Environmental and Earth Science, UNSW Sydney, NSW, 2052, Australia
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29
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Lee EA, Johnson LR, Johnson EG, Vernau W. Clinical features and radiographic findings in cats with eosinophilic, neutrophilic, and mixed airway inflammation (2011-2018). J Vet Intern Med 2020; 34:1291-1299. [PMID: 32338397 PMCID: PMC7255660 DOI: 10.1111/jvim.15772] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 03/16/2020] [Indexed: 01/01/2023] Open
Abstract
Background Idiopathic inflammatory airway disease (IAD) in cats often is described as asthmatic (eosinophilic) or bronchitic (neutrophilic), but this designation requires collection of airway fluid and it fails to consider cats with mixed airway inflammation. Objective To identify clinical features that would differentiate inflammatory disease types. Animals Forty‐nine cats with nonspecific airway inflammation identified by bronchoscopic bronchoalveolar lavage (BAL) between 2011 and 2018 were evaluated. Methods This is a retrospective study. Cats were categorized by BAL differential cytology as having eosinophilic (eosinophils >20% with neutrophils <14%, or eosinophils >50%), mixed (eosinophils 20%‐50% and neutrophils >14% or discordant inflammation from 2 BAL sites), or neutrophilic (neutrophils >14% and eosinophils <20%) inflammation. Type and duration of presenting complaints, signalment, body condition score, respiratory rate, CBC results, bronchoscopy, BAL results (% recovery, total nucleated cell count, differential cell count), and radiographic findings were compared among groups. Results Idiopathic IAD was diagnosed in 49 cats, with BAL eosinophilic inflammation in 23, mixed inflammation in 14, and neutrophilic inflammation in 12. Cough was the predominant presenting complaint with no difference in duration of signs among groups (median, 5.5 months). Respiratory rate and effort also did not differ. Cats with eosinophilic inflammation were significantly younger (4.4 ± 3.3 years) than those with neutrophilic (8.0 ±5.6 years) or mixed inflammation (7.5 ± 4.0 years; P = .03). Results of CBC and interpretation of radiographic findings did not differ among groups. Conclusions and Clinical Importance Substantial overlap exists in clinical and radiographic findings in cats with various forms of idiopathic airway inflammation.
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Affiliation(s)
- Elizabeth A Lee
- William R. Pritchard Veterinary Medical Teaching Hospital, University of California School of Veterinary Medicine, Davis, California, USA
| | - Lynelle R Johnson
- Department of Medicine and Epidemiology, University of California School of Veterinary Medicine, Davis, California, USA
| | - Eric G Johnson
- Department of Surgical and Radiological Sciences, University of California School of Veterinary Medicine, Davis, California, USA
| | - William Vernau
- Department of Pathology, Microbiology and Immunology, University of California School of Veterinary Medicine, Davis, California, USA
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30
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Garcia-Mazcorro JF, Minamoto Y, Kawas JR, Suchodolski JS, de Vos WM. Akkermansia and Microbial Degradation of Mucus in Cats and Dogs: Implications to the Growing Worldwide Epidemic of Pet Obesity. Vet Sci 2020; 7:vetsci7020044. [PMID: 32326394 PMCID: PMC7355976 DOI: 10.3390/vetsci7020044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 02/07/2023] Open
Abstract
Akkermansia muciniphila is a mucin-degrading bacterium that has shown the potential to provide anti-inflammatory and anti-obesity effects in mouse and man. We here focus on companion animals, specifically cats and dogs, and evaluate the microbial degradation of mucus and its health impact in the context of the worldwide epidemic of pet obesity. A literature survey revealed that the two presently known Akkermansia spp., A. muciniphila and A. glycaniphila, as well as other members of the phylum of Verrucomicrobia seem to be neither very prevalent nor abundant in the digestive tract of cats and dog. While this may be due to methodological aspects, it suggests that bacteria related to Akkermansia are not the major mucus degraders in these pets and hence other mucus-utilizing taxa may deserve attention. Hence, we will discuss the potential of these endogenous mucus utilizers and dietary interventions to boost these as well as the use of Akkermansia spp. related bacteria or their components as strategies to target feline and canine obesity.
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Affiliation(s)
- Jose F. Garcia-Mazcorro
- Research and Development, MNA de Mexico, San Nicolas de los Garza, Nuevo Leon 66477, Mexico
- Correspondence: ; Tel.: +52-81-8850-5204
| | | | - Jorge R. Kawas
- Faculty of Agronomy, Universidad Autonoma de Nuevo Leon, General Escobedo, Nuevo Leon 66050, Mexico;
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4474, USA;
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, The Netherlands;
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, P.O. Box 63, 00014 Helsinki, Finland
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31
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Piersigilli F, Van Grambezen B, Hocq C, Danhaive O. Nutrients and Microbiota in Lung Diseases of Prematurity: The Placenta-Gut-Lung Triangle. Nutrients 2020; 12:E469. [PMID: 32069822 PMCID: PMC7071142 DOI: 10.3390/nu12020469] [Citation(s) in RCA: 28] [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: 01/26/2020] [Accepted: 02/05/2020] [Indexed: 02/07/2023] Open
Abstract
Cardiorespiratory function is not only the foremost determinant of life after premature birth, but also a major factor of long-term outcomes. However, the path from placental disconnection to nutritional autonomy is enduring and challenging for the preterm infant and, at each step, will have profound influences on respiratory physiology and disease. Fluid and energy intake, specific nutrients such as amino-acids, lipids and vitamins, and their ways of administration -parenteral or enteral-have direct implications on lung tissue composition and cellular functions, thus affect lung development and homeostasis and contributing to acute and chronic respiratory disorders. In addition, metabolomic signatures have recently emerged as biomarkers of bronchopulmonary dysplasia and other neonatal diseases, suggesting a profound implication of specific metabolites such as amino-acids, acylcarnitine and fatty acids in lung injury and repair, inflammation and immune modulation. Recent advances have highlighted the profound influence of the microbiome on many short- and long-term outcomes in the preterm infant. Lung and intestinal microbiomes are deeply intricated, and nutrition plays a prominent role in their establishment and regulation. There is an emerging evidence that human milk prevents bronchopulmonary dysplasia in premature infants, potentially through microbiome composition and/or inflammation modulation. Restoring antibiotic therapy-mediated microbiome disruption is another potentially beneficial action of human milk, which can be in part emulated by pre- and probiotics and supplements. This review will explore the many facets of the gut-lung axis and its pathophysiology in acute and chronic respiratory disorders of the prematurely born infant, and explore established and innovative nutritional approaches for prevention and treatment.
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Affiliation(s)
- Fiammetta Piersigilli
- Division of Neonatology, St-Luc University Hospital, Catholic University of Louvain, Brussels 1200, Belgium; (F.P.); (B.V.G.); (C.H.)
| | - Bénédicte Van Grambezen
- Division of Neonatology, St-Luc University Hospital, Catholic University of Louvain, Brussels 1200, Belgium; (F.P.); (B.V.G.); (C.H.)
| | - Catheline Hocq
- Division of Neonatology, St-Luc University Hospital, Catholic University of Louvain, Brussels 1200, Belgium; (F.P.); (B.V.G.); (C.H.)
| | - Olivier Danhaive
- Division of Neonatology, St-Luc University Hospital, Catholic University of Louvain, Brussels 1200, Belgium; (F.P.); (B.V.G.); (C.H.)
- Department of Pediatrics, Benioff Children’s Hospital, University of California San Francisco, San Francisco, CA 94158, USA
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Ericsson AC, Personett AR, Rindt H, Grobman ME, Reinero CR. Respiratory dysbiosis and population-wide temporal dynamics in canine chronic bronchitis and non-inflammatory respiratory disease. PLoS One 2020; 15:e0228085. [PMID: 31990924 PMCID: PMC6986754 DOI: 10.1371/journal.pone.0228085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 01/07/2020] [Indexed: 01/12/2023] Open
Abstract
The lungs of people and companion animals are now recognized to harbor diverse, low biomass bacterial communities. While these communities are difficult to characterize using culture-based approaches, targeted molecular methods such as 16S rRNA amplicon sequencing can do so using DNA extracted from samples such as bronchoalveolar lavage fluid (BALF). Previous studies identified a surprisingly uniform composition of the microbiota in the lungs of healthy research dogs living in a controlled environment, however there are no reports of the lung microbiota of client-owned dogs. Moreover, compositional changes in the lung microbiota depending on disease status have been reported in people, suggesting that similar events may occur in dogs, a species subject to several respiratory disease mechanisms analogous to those seen in people. To address these knowledge gaps, BALF samples from client-owned dogs presenting to the University of Missouri Veterinary Health Center for respiratory signs between 2014 and 2017 were processed for and subjected to 16S rRNA sequencing. Based on specific diagnostic criteria, dogs were categorized as Chronic Bronchitis (CB, n = 53) or non-CB (n = 11). Community structure was compared between groups, as well as to historical data from healthy research dogs (n = 16) of a uniform breed and environment. The lung microbiota detected in all client-owned dogs was markedly different in composition from that previously detected in research dogs and contained increased relative abundance of multiple canine fecal and environmental bacteria, likely due to aspiration associated with their clinical signs. While inter-sample diversity differed significantly between samples from CB and non-CB dogs, the variability within both groups made it difficult to discern reproducible bacterial classifiers of disease. During subsequent analyses to identify other sources of variability within the data however, population-wide temporal dynamics in community structure were observed, with substantial changes occurring in late 2015 and again in early 2017. A review of regional climate data indicated that the first change occurred during a historically warm and wet period, suggesting that changes in environmental conditions may be associated with changes in the respiratory microbiota in the context of respiratory disease. As the lung microbiota in humans and other animals is believed to result from repetitive micro-aspirations during health and in certain disease states associated with dyspnea and laryngeal dysfunction, these data support the increased colonization of the lower airways during compromised airway function, and the potential for temporal effects due to putative factors such as climate.
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Affiliation(s)
- Aaron C. Ericsson
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- University of Missouri Metagenomics Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- * E-mail: (ACE); (CRR)
| | - Alexa R. Personett
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
| | - Hansjorg Rindt
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- Comparative Internal Medicine Laboratory, University of Missouri, Columbia, Missouri, United States of America
| | - Megan E. Grobman
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- Comparative Internal Medicine Laboratory, University of Missouri, Columbia, Missouri, United States of America
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
| | - Carol R. Reinero
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- Comparative Internal Medicine Laboratory, University of Missouri, Columbia, Missouri, United States of America
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- * E-mail: (ACE); (CRR)
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33
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Vientós-Plotts AI, Ericsson AC, Rindt H, Reinero CR. Respiratory Dysbiosis in Canine Bacterial Pneumonia: Standard Culture vs. Microbiome Sequencing. Front Vet Sci 2019; 6:354. [PMID: 31681810 PMCID: PMC6798064 DOI: 10.3389/fvets.2019.00354] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 09/26/2019] [Indexed: 12/31/2022] Open
Abstract
It is unknown how the respiratory microbiome influences and is influenced by bacterial pneumonia in dogs, as culture of lung samples and not microbial sequencing guides clinical practice. While accurate identification of pathogens are essential for treatment, not all bacteria are cultivable and the impact of respiratory dysbiosis on development of pneumonia is unclear. The study purposes were to (1) characterize the lung microbiome in canine bacterial pneumonia and compare deviations in dominant microbial populations with historical healthy controls, (2) compare bacteria identified by culture vs. 16S rDNA sequencing from bronchoalveolar lavage fluid (BALF) culture-, and (3) evaluate similarities in lung and oropharyngeal (OP) microbial communities in community-acquired and secondary bacterial pneumonia. Twenty BALF samples from 15 client-owned dogs diagnosed with bacterial pneumonia were enrolled. From a subset of dogs, OP swabs were collected. Extracted DNA underwent PCR of the 16S rRNA gene. Relative abundance of operational taxonomic units (OTUs) were determined. The relative abundance of bacterial community members found in health was decreased in dogs with pneumonia. Taxa identified via culture were not always the dominant phylotype identified with sequencing. Dogs with community-acquired pneumonia were more likely to have overgrowth of a single organism suggesting loss of dominant species associated with health. Dogs with secondary bacterial pneumonia had a greater regional continuity between the upper and lower airways. Collectively, these data suggest that dysbiosis occurs in canine bacterial pneumonia, and culture-independent techniques may provide greater depth of understanding of the changes in bacterial community composition that occur in disease.
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Affiliation(s)
- Aida I Vientós-Plotts
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States.,Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, United States.,Comparative Internal Medicine Laboratory, University of Missouri, Columbia, MO, United States
| | - Aaron C Ericsson
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States.,University of Missouri Metagenomics Center, University of Missouri, Columbia, MO, United States.,Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Hansjorg Rindt
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States.,Comparative Internal Medicine Laboratory, University of Missouri, Columbia, MO, United States
| | - Carol R Reinero
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States.,Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, United States.,Comparative Internal Medicine Laboratory, University of Missouri, Columbia, MO, United States
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Abstract
In recent years, tremendous advances have been made in our ability to characterize complex microbial communities such as the gut microbiota, and numerous surveys of the human gut microbiota have identified countless associations between different compositional attributes of the gut microbiota and adverse health conditions. However, most of these findings in humans are purely correlative and animal models are required for prospective evaluation of such changes as causative factors in disease initiation or progression. As in most fields of biomedical research, microbiota-focused studies are predominantly performed in mouse or rat models. Depending on the field of research and experimental question or objective, non-rodent models may be preferable due to better translatability or an inability to use rodents for various reasons. The following review describes the utility and limitations of several non-rodent model species for research on the microbiota and its influence on host physiology and disease. In an effort to balance the breadth of potential model species with the amount of detail provided, four model species are discussed: zebrafish, dogs, pigs, and rabbits.
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Affiliation(s)
- Aaron C Ericsson
- Department of Veterinary Pathobiology, University of Missouri, United States of America
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35
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Wu Z, Gatesoupe FJ, Zhang Q, Wang X, Feng Y, Wang S, Feng D, Li A. High-throughput sequencing reveals the gut and lung prokaryotic community profiles of the Chinese giant salamander (Andrias davidianus). Mol Biol Rep 2019; 46:5143-5154. [PMID: 31364018 DOI: 10.1007/s11033-019-04972-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/05/2019] [Indexed: 12/27/2022]
Abstract
Increasing attention has been attracted to host microbiota, due to their vital impact on host health. Little is known about the microbiota of the Chinese giant salamander (Andrias davidianus), in spite of the high economic and scientific value of this endangered species. This study was designed to characterise and compare the gut and lung prokaryotic communities of the Chinese giant salamander by high-throughput sequencing. Our study showed that the giant salamander had a lung prokaryotic community that clustered separately from its intestinal microbiota. Statistical analysis (LEfSe) revealed that the bacterial populations were dominated by Geobacter, Sulfurimonas, and Dechloromonas from Proteobacteria phylum, and Corynebacterium from Actinobacteria phylum in the lung, while Parabacteroides, Bacteroides, and PW3 from Bacteroidetes phylum, and Oscillospira from Firmicutes phylum were predominant in the intestine. A particularly innovative finding was the fairly high abundance of Archaea, especially methanogenic Euryarchaeota. The gut dominant Archaea were Methanocorpusculum and Thermoplasmata vadinCA11, while Methanosaeta and Methanoculleus were the main Archaea in the lung. PICRUSt analysis revealed differentiated functional profiles between the intestinal miacrobiota and the lung microbiota. Specially, some microbial metabolic functions were significantly more active in the intestinal microbiota, while the functional genes involved in infectious diseases were much richer in the lung microbiota. This study characterized the prokaryotic microbial community profiles in the gut and lung of the Chinese giant salamander, providing foundational support for future study seeking to understand microbiota of the giant salamander and the role of its microbiota on infectious diseases.
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Affiliation(s)
- Zhenbing Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - François-Joël Gatesoupe
- INRA, Nutrition Metabolism and Aquaculture, Center de Bretagne, Ifremer, 29280, Plouzané, France
| | - Qianqian Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,Freshwater Aquaculture Collaborative Innovation Centre of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiehao Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yuqing Feng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuyi Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dongyue Feng
- National Fisheries Technical Extension Center, Ministry of Agriculture, Beijing, 100125, China.
| | - Aihua Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. .,Freshwater Aquaculture Collaborative Innovation Centre of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China.
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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: 168] [Impact Index Per Article: 33.6] [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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37
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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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38
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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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Mathieu E, Escribano-Vazquez U, Descamps D, Cherbuy C, Langella P, Riffault S, Remot A, Thomas M. Paradigms of Lung Microbiota Functions in Health and Disease, Particularly, in Asthma. Front Physiol 2018; 9:1168. [PMID: 30246806 PMCID: PMC6110890 DOI: 10.3389/fphys.2018.01168] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/03/2018] [Indexed: 12/22/2022] Open
Abstract
Improvements in our knowledge of the gut microbiota have broadened our vision of the microbes associated with the intestine. These microbes are essential actors and protectors of digestive and extra-digestive health and, by extension, crucial for human physiology. Similar reconsiderations are currently underway concerning the endogenous microbes of the lungs, with a shift in focus away from their involvement in infections toward a role in physiology. The discovery of the lung microbiota was delayed by the long-held view that the lungs of healthy individuals were sterile and by sampling difficulties. The lung microbiota has a low density, and the maintenance of small numbers of bacteria seems to be a critical determinant of good health. This review aims to highlight how knowledge about the lung microbiota can change our conception of lung physiology and respiratory health. We provide support for this point of view with knowledge acquired about the gut microbiota and intestinal physiology. We describe the main characteristics of the lung microbiota and its functional impact on lung physiology, particularly in healthy individuals, after birth, but also in asthma. We describe some of the physiological features of the respiratory tract potentially favoring the installation of a dysbiotic microbiota. The gut microbiota feeds and matures the intestinal epithelium and is involved in immunity, when the principal role of the lung microbiota seems to be the orientation and balance of aspects of immune and epithelial responsiveness. This implies that the local and remote effects of bacterial communities are likely to be determinant in many respiratory diseases caused by viruses, allergens or genetic deficiency. Finally, we discuss the reciprocal connections between the gut and lungs that render these two compartments inseparable.
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Affiliation(s)
- Elliot Mathieu
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Unai Escribano-Vazquez
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Delphyne Descamps
- Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Claire Cherbuy
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Philippe Langella
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sabine Riffault
- Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Aude Remot
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Muriel Thomas
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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40
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Kell DB, Pretorius E. No effects without causes: the Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases. Biol Rev Camb Philos Soc 2018; 93:1518-1557. [PMID: 29575574 PMCID: PMC6055827 DOI: 10.1111/brv.12407] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/12/2018] [Accepted: 02/15/2018] [Indexed: 12/11/2022]
Abstract
Since the successful conquest of many acute, communicable (infectious) diseases through the use of vaccines and antibiotics, the currently most prevalent diseases are chronic and progressive in nature, and are all accompanied by inflammation. These diseases include neurodegenerative (e.g. Alzheimer's, Parkinson's), vascular (e.g. atherosclerosis, pre-eclampsia, type 2 diabetes) and autoimmune (e.g. rheumatoid arthritis and multiple sclerosis) diseases that may appear to have little in common. In fact they all share significant features, in particular chronic inflammation and its attendant inflammatory cytokines. Such effects do not happen without underlying and initially 'external' causes, and it is of interest to seek these causes. Taking a systems approach, we argue that these causes include (i) stress-induced iron dysregulation, and (ii) its ability to awaken dormant, non-replicating microbes with which the host has become infected. Other external causes may be dietary. Such microbes are capable of shedding small, but functionally significant amounts of highly inflammagenic molecules such as lipopolysaccharide and lipoteichoic acid. Sequelae include significant coagulopathies, not least the recently discovered amyloidogenic clotting of blood, leading to cell death and the release of further inflammagens. The extensive evidence discussed here implies, as was found with ulcers, that almost all chronic, infectious diseases do in fact harbour a microbial component. What differs is simply the microbes and the anatomical location from and at which they exert damage. This analysis offers novel avenues for diagnosis and treatment.
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Affiliation(s)
- Douglas B. Kell
- School of ChemistryThe University of Manchester, 131 Princess StreetManchesterLancsM1 7DNU.K.
- The Manchester Institute of BiotechnologyThe University of Manchester, 131 Princess StreetManchesterLancsM1 7DNU.K.
- Department of Physiological SciencesStellenbosch University, Stellenbosch Private Bag X1Matieland7602South Africa
| | - Etheresia Pretorius
- Department of Physiological SciencesStellenbosch University, Stellenbosch Private Bag X1Matieland7602South Africa
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41
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Leblois J, Massart S, Li B, Wavreille J, Bindelle J, Everaert N. Modulation of piglets' microbiota: differential effects by a high wheat bran maternal diet during gestation and lactation. Sci Rep 2017; 7:7426. [PMID: 28784986 PMCID: PMC5547061 DOI: 10.1038/s41598-017-07228-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/26/2017] [Indexed: 12/27/2022] Open
Abstract
Reaching a beneficial intestinal microbiota early in life is desirable for piglets, as microbiota will impact their future health. One strategy to achieve this is the addition of prebiotics to sows’ diet, as their microbiota will be transferred. Transmission of microbiota to the offspring occurs at birth and during lactation but a transfer might also occur during gestation. The objectives of this study were to determine whether and when (before and/or after birth) a maternal transfer of the microbiota occurs, and to observe the impact of wheat bran (WB) in sows’ diet on their faecal microbiota, their offspring’s microbiota and fermentation profile. Sequencing was performed on DNA extracted from umbilical cord blood, meconium, sows’ faeces and piglets’ colon content. Short-chain fatty acid production was determined in piglets’ distal gut. Different bacteria (mostly Proteobacteria, followed by Firmicutes) were found in the umbilical cord blood, suggesting a maternal transfer occurring already during gestation. Less butyrate was produced in the caecum of WB piglets and a lower concentration of valerate was observed in all intestinal parts of WB piglets. Maternal wheat bran supplementation affected microbiota of sows and piglets differently.
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Affiliation(s)
- Julie Leblois
- Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, TERRA, Teaching and Research Centre, University of Liège, 5030, Gembloux, Belgium.,Research Foundation for Industry and Agriculture, National Scientific Research Foundation (FRIA-FNRS), Brussels, Belgium
| | - Sébastien Massart
- Laboratory of Urban and Integrated Plant Pathology, Gembloux Agro-Bio Tech, TERRA, Teaching and Research Centre, University of Liège, 5030, Gembloux, Belgium
| | - Bing Li
- Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, TERRA, Teaching and Research Centre, University of Liège, 5030, Gembloux, Belgium
| | - José Wavreille
- Production and Sectors Department, Walloon Agricultural Research Centre, 5030, Gembloux, Belgium
| | - Jérôme Bindelle
- Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, TERRA, Teaching and Research Centre, University of Liège, 5030, Gembloux, Belgium
| | - Nadia Everaert
- Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, TERRA, Teaching and Research Centre, University of Liège, 5030, Gembloux, Belgium.
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Vientós-Plotts AI, Ericsson AC, Rindt H, Reinero CR. Oral Probiotics Alter Healthy Feline Respiratory Microbiota. Front Microbiol 2017; 8:1287. [PMID: 28744273 PMCID: PMC5504723 DOI: 10.3389/fmicb.2017.01287] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 06/27/2017] [Indexed: 12/14/2022] Open
Abstract
Probiotics have been advocated as a novel therapeutic approach to respiratory disease, but knowledge of how oral administration of probiotics influences the respiratory microbiota is needed. Using 16S rRNA amplicon sequencing of bacterial DNA our objective was to determine whether oral probiotics changed the composition of the upper and lower airway, rectal, and blood microbiota. We hypothesized that oral probiotics would modulate the respiratory microbiota in healthy cats, demonstrated by the detection and/or increased relative abundance of the probiotic bacterial species and altered composition of the microbial population in the respiratory tract. Six healthy young research cats had oropharyngeal (OP), bronchoalveolar lavage fluid (BALF), rectal, and blood samples collected at baseline and 4 weeks after receiving oral probiotics. 16S rRNA gene amplicon libraries were sequenced, and coverage, richness, and relative abundance of representative operational taxonomic units (OTUs) were determined. Hierarchical and principal component analyses (PCA) demonstrated relatedness of samples. Mean microbial richness significantly increased only in the upper and lower airways. The number of probiotic OTUs (out of 5 total) that significantly increased in relative abundance vs. baseline was 5 in OP, 3 in BAL and 2 in feces. Using hierarchical clustering, BALF and blood samples grouped together after probiotic administration, and PERMANOVA supported that these two sites underwent significant changes in microbial composition. PERMANOVA revealed that OP and rectal samples had microbial population compositions that did not significantly change. These findings were visualized via PCA, which revealed distinct microbiomes in each site; samples clustered more tightly at baseline and had more variation after probiotic administration. This is the first study describing the effect of oral probiotics on the respiratory microbiota via detection of probiotic species in the airways. Finding bacterial species present in the oral probiotics in the upper and lower airways provides pilot data suggesting that oral probiotics could serve as a tool to target dysbiosis occurring in inflammatory airway diseases such as feline asthma, a disease in which cats serve as an important comparative and translational model for humans.
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Affiliation(s)
- Aida I Vientós-Plotts
- College of Veterinary Medicine, University of MissouriColumbia, MO, United States.,Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of MissouriColumbia, MO, United States.,Comparative Internal Medicine Laboratory, University of MissouriColumbia, MO, United States
| | - Aaron C Ericsson
- College of Veterinary Medicine, University of MissouriColumbia, MO, United States.,University of Missouri Metagenomics Center, University of MissouriColumbia, MO, United States.,Department of Veterinary Pathobiology, College of Veterinary Medicine, University of MissouriColumbia, MO, United States
| | - Hansjorg Rindt
- College of Veterinary Medicine, University of MissouriColumbia, MO, United States.,Comparative Internal Medicine Laboratory, University of MissouriColumbia, MO, United States
| | - Carol R Reinero
- College of Veterinary Medicine, University of MissouriColumbia, MO, United States.,Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of MissouriColumbia, MO, United States.,Comparative Internal Medicine Laboratory, University of MissouriColumbia, MO, United States
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Dorn ES, Tress B, Suchodolski JS, Nisar T, Ravindran P, Weber K, Hartmann K, Schulz BS. Bacterial microbiome in the nose of healthy cats and in cats with nasal disease. PLoS One 2017; 12:e0180299. [PMID: 28662139 PMCID: PMC5491177 DOI: 10.1371/journal.pone.0180299] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 06/13/2017] [Indexed: 12/22/2022] Open
Abstract
Background Traditionally, changes in the microbial population of the nose have been assessed using conventional culture techniques. Sequencing of bacterial 16S rRNA genes demonstrated that the human nose is inhabited by a rich and diverse bacterial microbiome that cannot be detected using culture-based methods. The goal of this study was to describe the nasal microbiome of healthy cats, cats with nasal neoplasia, and cats with feline upper respiratory tract disease (FURTD). Methodology/Principal findings DNA was extracted from nasal swabs of healthy cats (n = 28), cats with nasal neoplasia (n = 16), and cats with FURTD (n = 15), and 16S rRNA genes were sequenced. High species richness was observed in all samples. Rarefaction analysis revealed that healthy cats living indoors had greater species richness (observed species p = 0.042) and Shannon diversity (p = 0.003) compared with healthy cats living outdoors. Higher species richness (observed species p = 0.001) and Shannon diversity (p<0.001) were found in middle-aged cats in comparison to healthy cats in different age groups. Principal coordinate analysis revealed separate clustering based on similarities in bacterial molecular phylogenetic trees of 16S rRNA genes for indoor and outdoor cats. In all groups examined, the most abundant phyla identified were Proteobacteria, Firmicutes, and Bacteroidetes. At the genus level, 375 operational taxonomic units (OTUs) were identified. In healthy cats and cats with FURTD, Moraxella spp. was the most common genus, while it was unclassified Bradyrhizobiaceae in cats with nasal neoplasia. High individual variability was observed. Conclusion This study demonstrates that the nose of cats is inhabited by much more variable and diverse microbial communities than previously shown. Future research in this field might help to develop new diagnostic tools to easily identify nasal microbial changes, relate them to certain disease processes, and help clinicians in the decision process of antibiotic selection for individual patients.
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Affiliation(s)
- Elisabeth S. Dorn
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
| | - Barbara Tress
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Tariq Nisar
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Prajesh Ravindran
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Karin Weber
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
| | - Katrin Hartmann
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
| | - Bianka S. Schulz
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
- * E-mail:
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