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Li M, Liang H, Yang H, Ding Q, Xia R, Chen J, Zhou W, Yang Y, Zhang Z, Yao Y, Ran C, Zhou Z. Deciphering the gut microbiome of grass carp through multi-omics approach. Microbiome 2024; 12:2. [PMID: 38167330 PMCID: PMC10763231 DOI: 10.1186/s40168-023-01715-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 11/03/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Aquaculture plays an important role in global protein supplies and food security. The ban on antibiotics as feed additive proposes urgent need to develop alternatives. Gut microbiota plays important roles in the metabolism and immunity of fish and has the potential to give rise to novel solutions for challenges confronted by fish culture. However, our understanding of fish gut microbiome is still lacking. RESULTS We identified 575,856 non-redundant genes by metagenomic sequencing of the intestinal content samples of grass carp. Taxonomic and functional annotation of the gene catalogue revealed specificity of the gut microbiome of grass carp compared with mammals. Co-occurrence analysis indicated exclusive relations between the genera belonging to Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes, suggesting two independent ecological groups of the microbiota. The association pattern of Proteobacteria with the gene expression modules of fish gut and the liver was consistently opposite to that of Fusobacteria, Firmicutes, and Bacteroidetes, implying differential functionality of Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes. Therefore, the two ecological groups were considered as two functional groups, i.e., Functional Group 1: Proteobacteria and Functional Group 2: Fusobacteria/Firmicutes/Bacteroidetes. Further analysis revealed that the two functional groups differ in genetic capacity for carbohydrate utilization, virulence factors, and antibiotic resistance. Finally, we proposed that the ratio of "Functional Group 2/Functional Group 1" can be used as a biomarker that efficiently reflects the structural and functional characteristics of the microbiota of grass carp. CONCLUSIONS The gene catalogue is an important resource for investigating the gut microbiome of grass carp. Multi-omics analysis provides insights into functional implications of the main phyla that comprise the fish microbiota and shed lights on targets for microbiota regulation. Video Abstract.
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Affiliation(s)
- Ming Li
- China-Norway Joint Lab On Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hui Liang
- China-Norway Joint Lab On Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongwei Yang
- China-Norway Joint Lab On Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qianwen Ding
- Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Rui Xia
- China-Norway Joint Lab On Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jie Chen
- China-Norway Joint Lab On Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenhao Zhou
- China-Norway Joint Lab On Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yalin Yang
- Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhen Zhang
- Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuanyuan Yao
- Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chao Ran
- Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Zhigang Zhou
- China-Norway Joint Lab On Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Yadav S, Koenen M, Bale N, Sinninghe Damsté JS, Villanueva L. The physiology and metabolic properties of a novel, low-abundance Psychrilyobacter species isolated from the anoxic Black Sea shed light on its ecological role. Environ Microbiol Rep 2021; 13:899-910. [PMID: 34668338 DOI: 10.1111/1758-2229.13012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/26/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Members of the Psychrilyobacter spp. of the phylum Fusobacteria have been recently suggested to be amongst the most significant primary degraders of the detrital organic matter in sulfidic marine habitats, despite representing only a small proportion (<0.1%) of the microbial community. In this study, we have isolated a previously uncultured Psychrilyobacter species (strains SD5T and BL5; Psychrilyobacter piezotolerans sp. nov.) from the sulfidic waters (i.e., 2000 m depth) of the Black Sea and investigated its physiology and genomic capability in order to better understand potential ecological adaptation strategies. P. piezotolerans utilized a broad range of organic substituents (carbohydrates and proteins) and, remarkably, grew at sulfide concentrations up to 32 mM. These flexible physiological properties were supported by the presence of the respective metabolic pathways in the genomes of both strains. Growth at varying hydrostatic pressure (0.1-50 MPa) was sustained by modifying its membrane lipid composition. Thus, we have isolated a novel member of the 'rare biosphere', which endures the extreme conditions and may play a significant role in the degradation of detrital organic matter sinking into the sulfidic waters of the Black Sea.
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Affiliation(s)
- Subhash Yadav
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
| | - Michel Koenen
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
| | - Nicole Bale
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands
| | - Laura Villanueva
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands
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Toro‐Valdivieso C, Toro F, Stubbs S, Castro‐Nallar E, Blacklaws B. Patterns of the fecal microbiota in the Juan Fernández fur seal (Arctocephalus philippii). Microbiologyopen 2021; 10:e1215. [PMID: 34459554 PMCID: PMC8302013 DOI: 10.1002/mbo3.1215] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/26/2021] [Accepted: 06/03/2021] [Indexed: 12/13/2022] Open
Abstract
As apex predators, pinnipeds are considered to be useful bioindicators of marine and coastal environments. Endemic to a small archipelago in the South Pacific, the Juan Fernandez fur seal (JFFS) is one of the less-studied members of the pinniped family Otariidae. This study aimed to characterize the fecal microbiome of the JFFS for the first time, to establish a baseline for future studies of host-microbial-environment interactions and monitoring programs. During two consecutive reproductive seasons, 57 fecal samples were collected from seven different JFFS colonies within the Juan Fernandez Archipelago, Chile. Bacterial composition and abundance were characterized by sequencing the V4 region of the 16S rRNA gene. The overall microbiome composition was dominated by five phyla: Firmicutes (40% ±24), Fusobacteria (30% ±17), Bacteroidetes (22% ±10), Proteobacteria (6% ±4), and Actinobacteria (2% ±3). Alpha diversity was higher in Tierras Blancas. However, location was not found to be a dominant driver of microbial composition. Interestingly, the strongest signal in the data was a negative association between the genera Peptoclostridium and Fusobacterium, which explained 29.7% of the total microbial composition variability between samples. The genus Peptoclostridium has not been reported in other pinniped studies, and its role here is unclear, with interpretation challenging due to a lack of information regarding microbiome functionality in marine mammals. As a first insight into the JFFS fecal microbiome, these results contribute towards our understanding of the natural microbial diversity and composition in free-ranging pinnipeds.
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Affiliation(s)
| | - Frederick Toro
- Facultad de Ciencias de la VidaUniversidad Andres BelloSantiagoChile
- Escuela de Medicina VeterinariaFacultad de Recursos Naturales y Medicina VeterinariaUniversidad Santo TomásViña del MarChile
- ONG PanthalassaRed de Estudios de Vertebrados Marinos en ChileSantiagoChile
- Ph.D. Program in Conservation MedicineFacultad de Ecología y Recursos NaturalesUniversidad Andrés BelloSantiagoChile
| | - Samuel Stubbs
- Department of Infectious Disease EpidemiologyLondon School of Hygiene and Tropical MedicineLondonUK
| | - Eduardo Castro‐Nallar
- Center for Bioinformatics and Integrative BiologyUniversidad Andres BelloSantiagoChile
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Abstract
A critical challenge in microbiome data analysis is the existence of many non-biological zeros, which distort taxon abundance distributions, complicate data analysis, and jeopardize the reliability of scientific discoveries. To address this issue, we propose the first imputation method for microbiome data-mbImpute-to identify and recover likely non-biological zeros by borrowing information jointly from similar samples, similar taxa, and optional metadata including sample covariates and taxon phylogeny. We demonstrate that mbImpute improves the power of identifying disease-related taxa from microbiome data of type 2 diabetes and colorectal cancer, and mbImpute preserves non-zero distributions of taxa abundances.
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Affiliation(s)
- Ruochen Jiang
- Department of Statistics, University of California, Los Angeles, 90095-1554, CA, USA
| | - Wei Vivian Li
- Department of Statistics, University of California, Los Angeles, 90095-1554, CA, USA
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, 08854, NJ, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, 90095-1554, CA, USA.
- Department of Human Genetics, University of California, Los Angeles, 90095-7088, CA, USA.
- Department of Computational Medicine, University of California, Los Angeles, 90095-1766, CA, USA.
- Department of Biostatistics, University of California, Los Angeles, 90095-1772, CA, USA.
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Romero PE, Calla-Quispe E, Castillo-Vilcahuaman C, Yokoo M, Fuentes-Rivera HL, Ramirez JL, Ampuero A, Ibáñez AJ, Wong P. From the Andes to the desert: 16S rRNA metabarcoding characterization of aquatic bacterial communities in the Rimac river, the main source of water for Lima, Peru. PLoS One 2021; 16:e0250401. [PMID: 33886647 PMCID: PMC8061919 DOI: 10.1371/journal.pone.0250401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 04/06/2021] [Indexed: 01/04/2023] Open
Abstract
The Rimac river is the main source of water for Lima, Peru's capital megacity. The river is constantly affected by different types of contamination including mine tailings in the Andes and urban sewage in the metropolitan area. In this work, we aim to produce the first characterization of aquatic bacterial communities in the Rimac river using a 16S rRNA metabarcoding approach which would be useful to identify bacterial diversity and potential understudied pathogens. We report a lower diversity in bacterial communities from the Lower Rimac (Metropolitan zone) in comparison to other sub-basins. Samples were generally grouped according to their geographical location. Bacterial classes Alphaproteobacteria, Bacteroidia, Campylobacteria, Fusobacteriia, and Gammaproteobacteria were the most frequent along the river. Arcobacter cryaerophilus (Campylobacteria) was the most frequent species in the Lower Rimac while Flavobacterium succinicans (Bacteroidia) and Hypnocyclicus (Fusobacteriia) were the most predominant in the Upper Rimac. Predicted metabolic functions in the microbiota include bacterial motility and quorum sensing. Additional metabolomic analyses showed the presence of some insecticides and herbicides in the Parac-Upper Rimac and Santa Eulalia-Parac sub-basins. The dominance in the Metropolitan area of Arcobacter cryaerophilus, an emergent pathogen associated with fecal contamination and antibiotic multiresistance, that is not usually reported in traditional microbiological quality assessments, highlights the necessity to apply next-generation sequencing tools to improve pathogen surveillance. We believe that our study will encourage the integration of omics sciences in Peru and its application on current environmental and public health issues.
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Affiliation(s)
- Pedro E Romero
- Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Erika Calla-Quispe
- Instituto de Ciencias Ómicas y Biotecnología Aplicada (ICOBA), Pontificia Universidad Católica del Peru, Lima, Peru
| | - Camila Castillo-Vilcahuaman
- Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mateo Yokoo
- Departamento de Ciencias de la Medicina, Facultad de Medicina Humana, Universidad de Piura, Lima, Peru
| | - Hammerly Lino Fuentes-Rivera
- Instituto de Ciencias Ómicas y Biotecnología Aplicada (ICOBA), Pontificia Universidad Católica del Peru, Lima, Peru
| | - Jorge L Ramirez
- Departamento de Biología Celular y Genética, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - André Ampuero
- Departamento de Malacología y Carcinología, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Alfredo J Ibáñez
- Instituto de Ciencias Ómicas y Biotecnología Aplicada (ICOBA), Pontificia Universidad Católica del Peru, Lima, Peru
| | - Paolo Wong
- Departamento de Ciencias de la Medicina, Facultad de Medicina Humana, Universidad de Piura, Lima, Peru
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Gal A, Barko PC, Biggs PJ, Gedye KR, Midwinter AC, Williams DA, Burchell RK, Pazzi P. One dog's waste is another dog's wealth: A pilot study of fecal microbiota transplantation in dogs with acute hemorrhagic diarrhea syndrome. PLoS One 2021; 16:e0250344. [PMID: 33872339 PMCID: PMC8055013 DOI: 10.1371/journal.pone.0250344] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 04/05/2021] [Indexed: 01/04/2023] Open
Abstract
Canine acute hemorrhagic diarrhea syndrome (AHDS) has been associated in some studies with Clostridioides perfringens overgrowth and toxin-mediated necrosis of the intestinal mucosa. We aimed to determine the effect of a single fecal microbiota transplantation (FMT) on clinical scores and fecal microbiomes of 1 and 7 dogs with AHDS from New Zealand and South Africa. We hypothesized that FMT would improve AHDS clinical scores and increase microbiota alpha-diversity and short-chain fatty acid (SCFA)-producing microbial communities’ abundances in dogs with AHDS after FMT. We sequenced the V3-V4 region of the 16S-rRNA gene in the feces of AHDS FMT-recipients and sham-treated control dogs, and their healthy donors at admission, discharge, and 30 days post-discharge. There were no significant differences in median AHDS clinical scores between FMT-recipients and sham-treated controls at admission or discharge (P = 0.22, P = 0.41). At admission, the Shannon diversity index (SDI) was lower in AHDS dogs than healthy donors (P = 0.002). The SDI did not change from admission to 30 days in sham-treated dogs yet increased in FMT-recipients from admission to discharge (P = 0.04) to levels not different than donors (P = 0.33) but significantly higher than sham-treated controls (P = 0.002). At 30 days, the SDI did not differ between FMT recipients, sham-treated controls, and donors (P = 0.88). Principal coordinate analysis of the Bray-Curtis index separated post-FMT and donor dogs from pre-FMT and sham-treated dogs (P = 0.009) because of increased SCFA-producing genera’s abundances after FMT. A single co-abundance subnetwork contained many of the same OTUs found to be differentially abundant in FMT-recipients, and the abundance of this module was increased in FMT-recipients at discharge and 30 days, compared to sham-treated controls. We conclude in this small pilot study FMT did not have any clinical benefit. A single FMT procedure has the potential to increase bacterial communities of SCFA-producing genera important for intestinal health up to 30 days post-FMT.
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Affiliation(s)
- Arnon Gal
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
| | - Patrick C. Barko
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Patrick J. Biggs
- Molecular Epidemiology & Public Health Laboratory, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- Bioinformatics and Statistics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Kristene R. Gedye
- Molecular Epidemiology & Public Health Laboratory, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Anne C. Midwinter
- Molecular Epidemiology & Public Health Laboratory, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - David A. Williams
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Richard K. Burchell
- North Coast Veterinary and Referral Centre, Sunshine Coast, Queensland, Australia
| | - Paolo Pazzi
- Department of Companion Animal Clinical Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
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Ravegnini G, Fosso B, Saverio VD, Sammarini G, Zanotti F, Rossi G, Ricci M, D’Amico F, Valori G, Ioli A, Turroni S, Brigidi P, Hrelia P, Angelini S. Gastric Adenocarcinomas and Signet-Ring Cell Carcinoma: Unraveling Gastric Cancer Complexity through Microbiome Analysis-Deepening Heterogeneity for a Personalized Therapy. Int J Mol Sci 2020; 21:E9735. [PMID: 33419357 PMCID: PMC7766162 DOI: 10.3390/ijms21249735] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 02/07/2023] Open
Abstract
Gastric cancer (GC) is the fifth most prevalent cancer worldwide and the third leading cause of global cancer mortality. With the advances of the omic studies, a heterogeneous GC landscape has been revealed, with significant molecular diversity. Given the multifaceted nature of GC, identification of different patient subsets with prognostic and/or predictive outcomes is a key aspect to allow tailoring of specific treatments. Recently, the involvement of the microbiota in gastric carcinogenesis has been described. To deepen this aspect, we compared microbiota composition in signet-ring cell carcinoma (SRCC) and adenocarcinoma (ADC), two distinct GC subtypes. To this purpose, 10 ADC and 10 SRCC and their paired non-tumor (PNT) counterparts were evaluated for microbiota composition through 16S rRNA analysis. Weighted and unweighted UniFrac and Bray-Curtis dissimilarity showed significant community-level separation between ADC and SRCC. Through the LEfSe (linear discriminant analysis coupled with effect size) tool, we identified potential microbial biomarkers associated with GC subtypes. In particular, SRCCs were significantly enriched in the phyla Fusobacteria, Bacteroidetes, Patescibacteria, whereas in the ADC type, Proteobacteria and Acidobacteria phyla were found. Overall, our data add new insights into GC heterogeneity and may contribute to deepening the GC classification.
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Affiliation(s)
- Gloria Ravegnini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (G.R.); (G.S.); (F.Z.); (F.D.); (G.V.); (S.T.); (P.H.)
| | - Bruno Fosso
- National Research Council, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), 70126 Bari, Italy;
| | - Viola Di Saverio
- Anatomy and Pathological Histology Unit, Infermi Hospital, 47923 Rimini, Italy; (V.D.S.); (G.R.); (M.R.); (A.I.)
| | - Giulia Sammarini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (G.R.); (G.S.); (F.Z.); (F.D.); (G.V.); (S.T.); (P.H.)
| | - Federica Zanotti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (G.R.); (G.S.); (F.Z.); (F.D.); (G.V.); (S.T.); (P.H.)
| | - Giulio Rossi
- Anatomy and Pathological Histology Unit, Infermi Hospital, 47923 Rimini, Italy; (V.D.S.); (G.R.); (M.R.); (A.I.)
| | - Monica Ricci
- Anatomy and Pathological Histology Unit, Infermi Hospital, 47923 Rimini, Italy; (V.D.S.); (G.R.); (M.R.); (A.I.)
| | - Federica D’Amico
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (G.R.); (G.S.); (F.Z.); (F.D.); (G.V.); (S.T.); (P.H.)
| | - Giorgia Valori
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (G.R.); (G.S.); (F.Z.); (F.D.); (G.V.); (S.T.); (P.H.)
| | - Antonella Ioli
- Anatomy and Pathological Histology Unit, Infermi Hospital, 47923 Rimini, Italy; (V.D.S.); (G.R.); (M.R.); (A.I.)
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (G.R.); (G.S.); (F.Z.); (F.D.); (G.V.); (S.T.); (P.H.)
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences, University of Bologna, 40126 Bologna, Italy;
| | - Patrizia Hrelia
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (G.R.); (G.S.); (F.Z.); (F.D.); (G.V.); (S.T.); (P.H.)
| | - Sabrina Angelini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (G.R.); (G.S.); (F.Z.); (F.D.); (G.V.); (S.T.); (P.H.)
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Saito Y, Sato T, Nomoto K, Tsuji H. Identification of phenol- and p-cresol-producing intestinal bacteria by using media supplemented with tyrosine and its metabolites. FEMS Microbiol Ecol 2019; 94:5042942. [PMID: 29982420 PMCID: PMC6424909 DOI: 10.1093/femsec/fiy125] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/21/2018] [Indexed: 12/12/2022] Open
Abstract
To identify intestinal bacteria that produce phenols (phenol and p-cresol), we screened 153 strains within 152 species in 44 genera by culture-based assay using broth media supplemented with 200 µM each of tyrosine and its predicted microbial metabolic intermediates (4-hydroxyphenylpyruvate, DL-4-hydroxyphenyllactate, 3-(p-hydroxyphenyl)propionate, 4-hydroxyphenylacetate and 4-hydroxybenzoate). Phenol-producing activity was found in 36 strains and p-cresol-producing activity in 55 strains. Fourteen strains had both types of activity. Phylogenetic analysis based on the 16S rRNA gene sequences of strains that produced 100 µM or more of phenols revealed that 16 phenol producers belonged to the Coriobacteriaceae, Enterobacteriaceae, Fusobacteriaceae and Clostridium clusters I and XIVa; four p-cresol-producing bacteria belonged to the Coriobacteriaceae and Clostridium clusters XI and XIVa; and one strain producing both belonged to the Coriobacteriaceae. A genomic search for protein homologs of enzymes involved in the metabolism of tyrosine to phenols in 10 phenol producers and four p-cresol producers, the draft genomes of which were available in public databases, predicted that phenol producers harbored tyrosine phenol-lyase or hydroxyarylic acid decarboxylase, or both, and p-cresol producers harbored p-hydroxyphenylacetate decarboxylase or tyrosine lyase, or both. These results provide important information about the bacterial strains that contribute to production of phenols in the intestine.
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Affiliation(s)
- Yuki Saito
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
- Corresponding author: Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan. Tel: +81-42-577-8960; Fax: +81-42-577-3020; E-mail:
| | - Tadashi Sato
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Koji Nomoto
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
- Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Hirokazu Tsuji
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
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Wang T, Yu L, Xu C, Pan K, Mo M, Duan M, Zhang Y, Xiong H. Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function. PLoS One 2018; 13:e0203503. [PMID: 30204780 PMCID: PMC6133361 DOI: 10.1371/journal.pone.0203503] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 08/21/2018] [Indexed: 12/18/2022] Open
Abstract
Host–microbe interactions have been implicated in the pathogenesis of chronic fatigue syndrome (CFS), but whether the oral microbiome is altered in CFS patients is unknown. We explored alterations of the oral microbiome in Chinese Han CFS patients using 16S rRNA gene sequencing and alterations in the functional potential of the oral microbiome using PICRUSt. We found that Shannon and Simpson diversity indices were not different in CFS patients compared to healthy controls, but the overall oral microbiome composition was different (MANOVA, p < 0.01). CFS patients had a higher relative abundance of Fusobacteria compared with healthy controls. Further, the genera Leptotrichia, Prevotella, and Fusobacterium were enriched and Haemophilus, Veillonella, and Porphyromonas were depleted in CFS patients compared to healthy controls. Functional analysis from inferred metagenomes showed that bacterial genera altered in CFS patients were primarily associated with amino acid and energy metabolism. Our findings demonstrate that the oral microbiome in CFS patients is different from healthy controls, and these differences lead to shifts in functional pathways with implications for CFS pathogenesis. These findings increase our understanding of the relationship between the oral microbiota and CFS, which will advance our understanding of CFS pathogenesis and may contribute to future improvements in treatment and diagnosis.
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Affiliation(s)
- Taiwu Wang
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People’s Republic of China
- Research Institute for Medicine of Nanjing Command, Nanjing, P. R. China, Nanjing, China
| | - Lei Yu
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People’s Republic of China
| | - Cong Xu
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People’s Republic of China
| | - Keli Pan
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People’s Republic of China
| | - Minglu Mo
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People’s Republic of China
| | - Mingxiang Duan
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People’s Republic of China
| | - Yao Zhang
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People’s Republic of China
- * E-mail: (YZ); (HX)
| | - Hongyan Xiong
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People’s Republic of China
- * E-mail: (YZ); (HX)
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10
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Zhang Z, Li D. Thermal processing of food reduces gut microbiota diversity of the host and triggers adaptation of the microbiota: evidence from two vertebrates. Microbiome 2018; 6:99. [PMID: 29855351 PMCID: PMC5984331 DOI: 10.1186/s40168-018-0471-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 04/19/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Adoption of thermal processing of the diet drives human evolution and gut microbiota diversity changes in a dietary habit-dependent manner. However, whether thermal processing of food triggers gut microbial variation remains unknown. Herein, we compared the microbiota of non-thermally processed and thermally processed food (NF and TF) and investigated gut microbiota associated with NF and TF in catfish Silurus meridionalis and C57BL/6 mice to assess effects of thermal processing of food on gut microbiota and to further identify the differences in host responses. RESULTS We found no differences in overall microbial composition and structure in the pairwise NF and TF, but identified differential microbial communities between food and gut. Both fish and mice fed TF had significantly lower gut microbial diversity than those fed NF. Moreover, thermal processing of food triggered the changes in their microbial communities. Comparative host studies further indicated host species determined gut microbial assemblies, even if fed with the same food. Fusobacteria was the most abundant phylum in the fish, and Bacteroidetes and Firmicutes dominated in the mice. Besides the consistent reduction of Bacteroidetes and the balanced Protebacteria, the response of other dominated gut microbiota in the fish and mice to TF was taxonomically opposite at the phylum level, and those further found at the genus level. CONCLUSIONS Our results reveal that thermal processing of food strongly contributes to the reduction of gut microbial diversity and differentially drives microbial alterations in a host-dependent manner, suggesting specific adaptations of host-gut microbiota in vertebrates responding to thermal processing of food. These findings open a window of opportunity to understand the decline in gut microbial diversity and the community variation in human evolution and provide new insights into the host-specific microbial assemblages associated with the use of processing techniques in food preparation in humans and domesticated animals.
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Affiliation(s)
- Zhimin Zhang
- Department of Fishery Resources and Environment, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, People’s Republic of China
| | - Dapeng Li
- Department of Fishery Resources and Environment, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, People’s Republic of China
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11
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Liu J, Abdelfattah A, Norelli J, Burchard E, Schena L, Droby S, Wisniewski M. Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence. Microbiome 2018; 6:18. [PMID: 29374490 PMCID: PMC5787276 DOI: 10.1186/s40168-018-0403-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 01/18/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND High-throughput amplicon sequencing spanning conserved portions of microbial genomes (16s rRNA and ITS) was used in the present study to describe the endophytic microbiota associated with three apple varieties, "Royal Gala," "Golden Delicious," and "Honey Crisp," and two rootstocks, M.9 and M.M.111. The objectives were to (1) determine if the microbiota differs in different rootstocks and apple varieties and (2) determine if specific rootstock-scion combinations influence the microbiota composition of either component. RESULTS Results indicated that Ascomycota (47.8%), Zygomycota (31.1%), and Basidiomycota (11.6%) were the dominant fungal phyla across all samples. The majority of bacterial sequences were assigned to Proteobacteria (58.4%), Firmicutes (23.8%), Actinobacteria (7.7%), Bacteroidetes (2%), and Fusobacteria (0.4%). Rootstocks appeared to influence the microbiota of associated grafted scion, but the effect was not statistically significant. Pedigree also had an impact on the composition of the endophytic microbiota, where closely-related cultivars had a microbial community that was more similar to each other than it was to a scion cultivar that was more distantly-related by pedigree. The more vigorous rootstock (M.M.111) was observed to possess a greater number of growth-promoting bacterial taxa, relative to the dwarfing rootstock (M.9). CONCLUSIONS The mechanism by which an apple genotype, either rootstock or scion, has a determinant effect on the composition of a microbial community is not known. The similarity of the microbiota in samples with a similar pedigree suggests the possibility of some level of co-evolution or selection as proposed by the "holobiont" concept in which metaorganisms have co-evolved. Clearly, however, the present information is only suggestive, and a more comprehensive analysis is needed.
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Affiliation(s)
- Jia Liu
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Institute of Special Plants/College of Forestry and Life Science, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, 402160 China
| | - Ahmed Abdelfattah
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, 89122 Reggio Calabria, Italy
| | - John Norelli
- US Department of Agriculture, Agricultural Research Service (USDA-ARS), Kearneysville, WV 25430 USA
| | - Erik Burchard
- US Department of Agriculture, Agricultural Research Service (USDA-ARS), Kearneysville, WV 25430 USA
| | - Leonardo Schena
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, 89122 Reggio Calabria, Italy
| | - Samir Droby
- Agricultural Research Organization (ARO), the Volcani Center, 50250 Bet Dagan, Israel
| | - Michael Wisniewski
- US Department of Agriculture, Agricultural Research Service (USDA-ARS), Kearneysville, WV 25430 USA
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12
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Guard BC, Mila H, Steiner JM, Mariani C, Suchodolski JS, Chastant-Maillard S. Characterization of the fecal microbiome during neonatal and early pediatric development in puppies. PLoS One 2017; 12:e0175718. [PMID: 28448583 PMCID: PMC5407640 DOI: 10.1371/journal.pone.0175718] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/30/2017] [Indexed: 01/24/2023] Open
Abstract
Limited information is available describing the development of the neonatal fecal microbiome in dogs. Feces from puppies were collected at 2, 21, 42, and 56 days after birth. Feces were also collected from the puppies’ mothers at a single time point within 24 hours after parturition. DNA was extracted from fecal samples and 454-pyrosequencing was used to profile 16S rRNA genes. Species richness continued to increase significantly from 2 days of age until 42 days of age in puppies. Furthermore, microbial communities clustered separately from each other at 2, 21, and 42 days of age. The microbial communities belonging to dams clustered separately from that of puppies at any given time point. Major phylogenetic changes were noted at all taxonomic levels with the most profound changes being a shift from primarily Firmicutes in puppies at 2 days of age to a co-dominance of Bacteroidetes, Fusobacteria, and Firmicutes by 21 days of age. Further studies are needed to elucidate the relationship between puppy microbiota development, physiological growth, neonatal survival, and morbidity.
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Affiliation(s)
- Blake C. Guard
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Hanna Mila
- NeoCare, IHAP, Reproduction, Université de Toulouse, Toulouse, France
| | - Jörg M. Steiner
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, Texas, United States of America
| | | | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, Texas, United States of America
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13
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Adams SE, Arnold D, Murphy B, Carroll P, Green AK, Smith AM, Marsh PD, Chen T, Marriott RE, Brading MG. A randomised clinical study to determine the effect of a toothpaste containing enzymes and proteins on plaque oral microbiome ecology. Sci Rep 2017; 7:43344. [PMID: 28240240 PMCID: PMC5327414 DOI: 10.1038/srep43344] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/20/2017] [Indexed: 12/13/2022] Open
Abstract
The numerous species that make up the oral microbiome are now understood to play a key role in establishment and maintenance of oral health. The ability to taxonomically identify community members at the species level is important to elucidating its diversity and association to health and disease. We report the overall ecological effects of using a toothpaste containing enzymes and proteins compared to a control toothpaste on the plaque microbiome. The results reported here demonstrate that a toothpaste containing enzymes and proteins can augment natural salivary defences to promote an overall community shift resulting in an increase in bacteria associated with gum health and a concomitant decrease in those associated with periodontal disease. Statistical analysis shows significant increases in 12 taxa associated with gum health including Neisseria spp. and a significant decrease in 10 taxa associated with periodontal disease including Treponema spp. The results demonstrate that a toothpaste containing enzymes and proteins can significantly shift the ecology of the oral microbiome (at species level) resulting in a community with a stronger association to health.
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Affiliation(s)
- S. E. Adams
- Unilever R&D Port Sunlight, Bebington, Wirral, CH63 3JW, UK
| | - D. Arnold
- Unilever R&D Port Sunlight, Bebington, Wirral, CH63 3JW, UK
| | - B. Murphy
- Unilever R&D Port Sunlight, Bebington, Wirral, CH63 3JW, UK
| | - P. Carroll
- Unilever R&D Port Sunlight, Bebington, Wirral, CH63 3JW, UK
| | - A. K. Green
- Unilever R&D Port Sunlight, Bebington, Wirral, CH63 3JW, UK
| | - A. M. Smith
- Unilever R&D Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - P. D. Marsh
- School of Dentistry, University of Leeds, LS2 9LU, UK
| | - T. Chen
- Forsyth Dental Institute, 245 First Street, Cambridge, MA 02142, USA
| | - R. E. Marriott
- Unilever R&D Port Sunlight, Bebington, Wirral, CH63 3JW, UK
| | - M. G. Brading
- Unilever R&D Port Sunlight, Bebington, Wirral, CH63 3JW, UK
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14
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Bledsoe JW, Peterson BC, Swanson KS, Small BC. Ontogenetic Characterization of the Intestinal Microbiota of Channel Catfish through 16S rRNA Gene Sequencing Reveals Insights on Temporal Shifts and the Influence of Environmental Microbes. PLoS One 2016; 11:e0166379. [PMID: 27846300 PMCID: PMC5113000 DOI: 10.1371/journal.pone.0166379] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/27/2016] [Indexed: 01/08/2023] Open
Abstract
Aquaculture recently overtook capture fisheries as the largest producer of food fish, but to continue increasing fish production the industry is in search of better methods of improving fish health and growth. Pre- and probiotic supplementation has gained attention as a means of solving these issues, however, for such approaches to be successful, we must first gain a more holistic understanding of the factors influencing the microbial communities present in the intestines of fish. In this study, we characterize the bacterial communities associated with the digestive tract of a highly valuable U.S. aquaculture species, channel catfish Ictalurus punctatus, over the first 193 days of life to evaluate temporal changes that may occur throughout ontogenetic development of the host. Intestinal microbiota were surveyed with high-throughput DNA sequencing of 16S rRNA V4 gene amplicons derived from fish at 3, 65, 125, and 193 days post hatch (dph), while also characterizing the environmental microbes derived from the water supply and the administered diets. Microbial communities inhabiting the intestines of catfish early in life were dynamic, with significant shifts occurring up to 125 dph when the microbiota somewhat stabilized, as shifts were less apparent between 125 to 193 dph. Bacterial phyla present in the gut of catfish throughout ontogeny include Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria; with the species Cetobacterium somerae and Plesiomonas shigelloides showing the highest abundance in the catfish microbiota after 3 dph. Comparisons of the gut microbiota to the environmental microbes reveals that the fish gut is maintained as a niche habitat, separate from the overall microbial communities present in diets and water-supply. Although, there is also evidence that the environmental microbiota serves as an inoculum to the fish gut. Our results have implications for future research related to channel catfish biology and culture, and increase our understanding of ontogenetic effects on the microbiota of teleost fish.
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Affiliation(s)
- Jacob W. Bledsoe
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Department of Animal Science, Southern Illinois University, Carbondale, IL, United States of America
| | - Brian C. Peterson
- Warmwater Aquaculture Research Unit, USDA-ARS, Stoneville, MS, 38776, United States of America
| | - Kelly S. Swanson
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois-Urbana Champaign, Urbana, IL, United States of America
| | - Brian C. Small
- Aquaculture Research Institute, Department of Fish and Wildlife Sciences, University of Idaho, Hagerman, ID, United States of America
- * E-mail:
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15
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Liu Y, Yao Y, Li H, Qiao F, Wu J, Du ZY, Zhang M. Influence of Endogenous and Exogenous Estrogenic Endocrine on Intestinal Microbiota in Zebrafish. PLoS One 2016; 11:e0163895. [PMID: 27701432 PMCID: PMC5049800 DOI: 10.1371/journal.pone.0163895] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/18/2016] [Indexed: 02/04/2023] Open
Abstract
Gender is one of the factors influencing the intestinal microbial composition in mammals, but whether fish also have gender-specific intestinal microbial patterns remains unknown. In this decade, endocrine disrupting chemicals in surface and ground water of many areas and increasing observation of freshwater male fish displaying female sexual characteristics have been reported. Here we identified the difference in intestinal microbiota between male and female zebrafish, and revealed the influence of endocrine disrupting chemicals on zebrafish intestinal microbiota by using high-throughput sequencing. The results indicated that Fusobacteria, Bacteroidetes and Proteobacteria were dominant in the gut of zebrafish and there were no obvious gender-specific intestinal microbial patterns. Two endocrine disrupting chemicals, Estradiol (E2) and Bisphenol A (BPA), were selected to treat male zebrafish for 5 weeks. E2 and BPA increased vitellogenin expression in the liver of male zebrafish and altered the intestinal microbial composition with the abundance of the phylum CKC4 increased significantly. Our results suggested that because of the developmental character and living environment, gender did not influence the assembly of intestinal microbiota in zebrafish as it does in mammals, but exposure extra to endocrine disrupting chemicals disturbed the intestinal microbial composition, which may be related to changes in host physiological metabolism.
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Affiliation(s)
- Yukun Liu
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yayun Yao
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Huan Li
- Nextomics Biosciences Co. Ltd., Wuhan, 430073, China
| | - Fang Qiao
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Junlin Wu
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Zhen-yu Du
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, 200241, China
- * E-mail: (MZ); (ZD)
| | - Meiling Zhang
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, 200241, China
- * E-mail: (MZ); (ZD)
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16
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Eichmiller JJ, Hamilton MJ, Staley C, Sadowsky MJ, Sorensen PW. Environment shapes the fecal microbiome of invasive carp species. Microbiome 2016; 4:44. [PMID: 27514729 PMCID: PMC4981970 DOI: 10.1186/s40168-016-0190-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 08/02/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Although the common, silver, and bighead carps are native and sparsely distributed in Eurasia, these fish have become abundant and invasive in North America. An understanding of the biology of these species may provide insights into sustainable control methods. The animal-associated microbiome plays an important role in host health. Characterization of the carp microbiome and the factors that affect its composition is an important step toward understanding the biology and interrelationships between these species and their environments. RESULTS We compared the fecal microbiomes of common, silver, and bighead carps from wild and laboratory environments using Illumina sequencing of bacterial 16S ribosomal RNA (rRNA). The fecal bacterial communities of fish were diverse, with Shannon indices ranging from 2.3 to 4.5. The phyla Proteobacteria, Firmicutes, and Fusobacteria dominated carp guts, comprising 76.7 % of total reads. Environment played a large role in shaping fecal microbial community composition, and microbiomes among captive fishes were more similar than among wild fishes. Although differences among wild fishes could be attributed to feeding preferences, diet did not strongly affect microbial community structure in laboratory-housed fishes. Comparison of wild- and lab-invasive carps revealed five shared OTUs that comprised approximately 40 % of the core fecal microbiome. CONCLUSIONS The environment is a dominant factor shaping the fecal bacterial communities of invasive carps. Captivity alters the microbiome community structure relative to wild fish, while species differences are pronounced within habitats. Despite the absence of a true stomach, invasive carp species exhibited a core microbiota that warrants future study.
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Affiliation(s)
- Jessica J. Eichmiller
- Department of Fisheries, Wildlife, and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, Twin Cities, Saint Paul, MN 55108 USA
| | - Matthew J. Hamilton
- Department of Soil, Water and Climate, Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108 USA
| | - Christopher Staley
- Department of Soil, Water and Climate, Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108 USA
| | - Michael J. Sadowsky
- Department of Fisheries, Wildlife, and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, Twin Cities, Saint Paul, MN 55108 USA
- Department of Soil, Water and Climate, Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108 USA
| | - Peter W. Sorensen
- Department of Fisheries, Wildlife, and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, Twin Cities, Saint Paul, MN 55108 USA
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17
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Morris A, Paulson JN, Talukder H, Tipton L, Kling H, Cui L, Fitch A, Pop M, Norris KA, Ghedin E. Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection. Microbiome 2016; 4:38. [PMID: 27391224 PMCID: PMC4939015 DOI: 10.1186/s40168-016-0183-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/27/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND Longitudinal studies of the lung microbiome are challenging due to the invasive nature of sample collection. In addition, studies of the lung microbiome in human disease are usually performed after disease onset, limiting the ability to determine early events in the lung. We used a non-human primate model to assess lung microbiome alterations over time in response to an HIV-like immunosuppression and determined impact of the lung microbiome on development of obstructive lung disease. Cynomolgous macaques were infected with the SIV-HIV chimeric virus SHIV89.6P. Bronchoalveolar lavage fluid samples were collected pre-infection and every 4 weeks for 53 weeks post-infection. The microbiota was characterized at each time point by 16S ribosomal RNA (rRNA) sequencing. RESULTS We observed individual variation in the composition of the lung microbiota with a proportion of the macaques having Tropheryma whipplei as the dominant organism in their lungs. Bacterial communities varied over time both within and between animals, but there did not appear to be a systematic alteration due to SHIV infection. Development of obstructive lung disease in the SHIV-infected animals was characterized by a relative increase in abundance of oral anaerobes. Network analysis further identified a difference in community composition that accompanied the development of obstructive disease with negative correlations between members of the obstructed and non-obstructed groups. This emphasizes how species shifts can impact multiple other species, potentially resulting in disease. CONCLUSIONS This study is the first to investigate the dynamics of the lung microbiota over time and in response to immunosuppression in a non-human primate model. The persistence of oral bacteria in the lung and their association with obstruction suggest a potential role in pathogenesis. The lung microbiome in the non-human primate is a valuable tool for examining the impact of the lung microbiome in human health and disease.
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Affiliation(s)
- Alison Morris
- />Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
- />Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Joseph N. Paulson
- />Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD USA
- />Present address: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- />Present address: Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Hisham Talukder
- />Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD USA
| | - Laura Tipton
- />Department of Biology, Center for Genomics & Systems Biology and College of Global Public Health, New York University, 12 Waverly Place, New York, NY 10003 USA
- />Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Heather Kling
- />Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Lijia Cui
- />Tsinghua University School of Medicine, Beijing, China
| | - Adam Fitch
- />Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Mihai Pop
- />Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD USA
| | - Karen A. Norris
- />Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Elodie Ghedin
- />Department of Biology, Center for Genomics & Systems Biology and College of Global Public Health, New York University, 12 Waverly Place, New York, NY 10003 USA
- />Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
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18
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Eisenberg T, Kämpfer P, Ewers C, Semmler T, Glaeser SP, Collins E, Ruttledge M, Palmer R. Oceanivirga salmonicida gen. nov., sp. nov., a member of the Leptotrichiaceae isolated from Atlantic salmon (Salmo salar). Int J Syst Evol Microbiol 2016; 66:2429-2437. [PMID: 27031261 DOI: 10.1099/ijsem.0.001050] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A pleomorphic, Gram-negative, rod-shaped, indole-, oxidase- and catalase- negative, non-spore-forming, non-motile bacterium was originally isolated in 1992 from moribund, seawater farmed Atlantic salmon with multifocal tissue necrosis. Strain AVG 2115T displayed considerable similarities with Streptobacillus moniliformis, one of the two etiological agents of rat bite fever, and has been stored as Streptobacillus sp. NCIMB 703044T. On the basis of 16S rRNA gene sequence analyses, this strain displayed >99 % sequence similarities with uncultured bacterial clones from the digestive tracts of marine mammals, followed by Sneathia sanguinegens CCUG 41628T (92.7 %), 'Sneathia amnii' Sn35 (92.5 %), Caviibacter abscessus CCUG 39713T (92.2 %), Streptobacillus ratti OGS16T (91.3 %), Streptobacillus notomytis AHL 370-1T (91.2 %), S. moniliformis DSM 12112T (91.0 %), Streptobacillus felis 131000547T (90.9 %) and Streptobacillus hongkongensis DSM 26322T (89.7 %). Sequence similarities to all other taxa were below 89 %. Phylogenetic analysis for strain NCIMB 703044T revealed highly similar results for gyrB, groEL and recA nucleotide and deduced amino acid sequence analyses independent of the employed treeing method. Average nucleotide identities (ANI) for complete genomes ranged from 66.00 % to 72.08 % between strain NCIMB 703044T and the type strains of Sebaldella termitidis, Leptotrichiabuccalis, Streptobacillus moniliformis, Sneathia sanguinegens and Caviibacter abscessus. Chemotaxonomic and physiological data of strain NCIMB 703044t were in congruence with closely related members of the family Leptotrichiaceae, represented by highly similar enzyme profiles and fatty acid patterns. MALDI-TOF MS analysis was capable to clearly discriminate strain NCIMB 703044T from all currently described taxa of the family Leptotrichiaceae. On the basis of these data we propose the novel taxon Oceanivirga salmonicida gen. nov. sp. nov. with the type strain AVG 2115T (=NCIMB 703044T) (=DSM 101867T). The G+C content is 25.4 %, genome size is 1.77 Mbp.
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Affiliation(s)
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Christa Ewers
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | | | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Evelyn Collins
- Marine Institute, Rinville, Oranmore, Co. Galway, Ireland
| | | | - Roy Palmer
- Maribio Consultants, Moycullen, Co. Galway, Ireland
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Harris S, Croft J, O’Flynn C, Deusch O, Colyer A, Allsopp J, Milella L, Davis IJ. A Pyrosequencing Investigation of Differences in the Feline Subgingival Microbiota in Health, Gingivitis and Mild Periodontitis. PLoS One 2015; 10:e0136986. [PMID: 26605793 PMCID: PMC4659563 DOI: 10.1371/journal.pone.0136986] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/11/2015] [Indexed: 12/02/2022] Open
Abstract
Periodontitis is the most frequently diagnosed health problem in cats yet little is known about the bacterial species important for the disease. The objective of this study was to identify bacterial species associated with health, gingivitis or mild periodontitis (<25% attachment loss) in feline plaque. Knowledge of these species is a first step in understanding the potential for improving oral health of cats via dietary interventions that alter the proportions of influential species. Subgingival plaque samples were collected from 92 cats with healthy gingiva, gingivitis or mild periodontitis. Pyrosequencing of the V1-V3 region of the 16S rDNA from these plaque samples generated more than one million reads and identified a total of 267 operational taxonomic units after bioinformatic and statistical analysis. Porphyromonas was the most abundant genus in all gingival health categories, particularly in health along with Moraxella and Fusobacteria. The Peptostreptococcaceae were the most abundant family in gingivitis and mild periodontitis. Logistic regression analysis identified species from various genera that were significantly associated with health, gingivitis or mild periodontitis. The species identified were very similar to those observed in canine plaque in the corresponding health and disease states. Such similarities were not observed between cat and human at the bacterial species level but with disease progression similarities did emerge at the phylum level. This suggests that interventions targeted at human pathogenic species will not be effective for use in cats but there is more potential for commonalities in interventions for cats and dogs.
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Affiliation(s)
- Stephen Harris
- The WALTHAM Centre for Pet Nutrition, Mars Petcare UK, Leicestershire, United Kingdom
| | - Julie Croft
- The WALTHAM Centre for Pet Nutrition, Mars Petcare UK, Leicestershire, United Kingdom
| | - Ciaran O’Flynn
- The WALTHAM Centre for Pet Nutrition, Mars Petcare UK, Leicestershire, United Kingdom
| | - Oliver Deusch
- The WALTHAM Centre for Pet Nutrition, Mars Petcare UK, Leicestershire, United Kingdom
| | - Alison Colyer
- The WALTHAM Centre for Pet Nutrition, Mars Petcare UK, Leicestershire, United Kingdom
| | - Judi Allsopp
- The WALTHAM Centre for Pet Nutrition, Mars Petcare UK, Leicestershire, United Kingdom
| | - Lisa Milella
- The Veterinary Dental Surgery, Surrey, United Kingdom
| | - Ian J. Davis
- The WALTHAM Centre for Pet Nutrition, Mars Petcare UK, Leicestershire, United Kingdom
- * E-mail:
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Oh C, Lee K, Cheong Y, Lee SW, Park SY, Song CS, Choi IS, Lee JB. Comparison of the Oral Microbiomes of Canines and Their Owners Using Next-Generation Sequencing. PLoS One 2015; 10:e0131468. [PMID: 26134411 PMCID: PMC4489859 DOI: 10.1371/journal.pone.0131468] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 06/02/2015] [Indexed: 11/21/2022] Open
Abstract
The oral microbiome, which is closely associated with many diseases, and the resident pathogenic oral bacteria, which can be transferred by close physical contact, are important public health considerations. Although the dog is the most common companion animal, the composition of the canine oral microbiome, which may include human pathogenic bacteria, and its relationship with that of their owners are unclear. In this study, 16S rDNA pyrosequencing was used to compare the oral microbiomes of 10 dogs and their owners and to identify zoonotic pathogens. Pyrosequencing revealed 246 operational taxonomic units in the 10 samples, representing 57 genera from eight bacterial phyla. Firmicutes (57.6%), Proteobacteria (21.6%), Bacteroidetes (9.8%), Actinobacteria (7.1%), and Fusobacteria (3.9%) were the predominant phyla in the human oral samples, whereas Proteobacteria (25.7%), Actinobacteria (21%), Bacteroidetes (19.7%), Firmicutes (19.3%), and Fusobacteria (12.3%) were predominant in the canine oral samples. The predominant genera in the human samples were Streptococcus (43.9%), Neisseria (10.3%), Haemophilus (9.6%), Prevotella (8.4%), and Veillonella (8.1%), whereas the predominant genera in the canine samples were Actinomyces (17.2%), Unknown (16.8), Porphyromonas (14.8), Fusobacterium (11.8), and Neisseria (7.2%). The oral microbiomes of dogs and their owners were appreciably different, and similarity in the microbiomes of canines and their owners was not correlated with residing in the same household. Oral-to-oral transfer of Neisseria shayeganii, Porphyromonas canigingivalis, Tannerella forsythia, and Streptococcus minor from dogs to humans was suspected. The finding of potentially zoonotic and periodontopathic bacteria in the canine oral microbiome may be a public health concern.
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Affiliation(s)
- Changin Oh
- Laboratory of Infectious Diseases, College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Kunkyu Lee
- Laboratory of Infectious Diseases, College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Yeotaek Cheong
- Laboratory of Infectious Diseases, College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Sang-Won Lee
- Laboratory of Infectious Diseases, College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Seung-Yong Park
- Laboratory of Infectious Diseases, College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Chang-Seon Song
- Laboratory of Infectious Diseases, College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 143-701, Republic of Korea
| | - In-Soo Choi
- Laboratory of Infectious Diseases, College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Joong-Bok Lee
- Laboratory of Infectious Diseases, College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 143-701, Republic of Korea
- * E-mail:
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Gerzova L, Videnska P, Faldynova M, Sedlar K, Provaznik I, Cizek A, Rychlik I. Characterization of microbiota composition and presence of selected antibiotic resistance genes in carriage water of ornamental fish. PLoS One 2014; 9:e103865. [PMID: 25084116 PMCID: PMC4118911 DOI: 10.1371/journal.pone.0103865] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 07/03/2014] [Indexed: 12/20/2022] Open
Abstract
International trade with ornamental fish is gradually recognized as an important source of a wide range of different antibiotic resistant bacteria. In this study we therefore characterized the prevalence of selected antibiotic resistance genes in the microbiota found in the carriage water of ornamental fish originating from 3 different continents. Real-time PCR quantification showed that the sul1 gene was present in 11 out of 100 bacteria. tet(A) was present in 6 out of 100 bacteria and strA, tet(G), sul2 and aadA were present in 1-2 copies per 100 bacteria. Class I integrons were quite common in carriage water microbiota, however, pyrosequencing showed that only 12 different antibiotic gene cassettes were present in class I integrons. The microbiota characterized by pyrosequencing of the V3/V4 variable region of 16S rRNA genes consisted of Proteobacteria (48%), Bacteroidetes (29.5%), Firmicutes (17.8%), Actinobacteria (2.1%) and Fusobacteria (1.6%). Correlation analysis between antibiotic resistance gene prevalence and microbiota composition verified by bacterial culture showed that major reservoirs of sul1 sul2, tet(A), tet(B) tet(G), cat, cml, bla, strA, aacA, aph and aadA could be found among Alpha-, Beta- and Gammaproteobacteria with representatives of Enterobacteriaceae, Pseudomonadaceae, Rhizobiaceae and Comamonadaceae being those most positively associated with the tested antibiotic resistance genes.
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Affiliation(s)
| | | | | | - Karel Sedlar
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Ivo Provaznik
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Alois Cizek
- University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Ivan Rychlik
- Veterinary Research Institute, Brno, Czech Republic
- * E-mail:
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Piombino P, Genovese A, Esposito S, Moio L, Cutolo PP, Chambery A, Severino V, Moneta E, Smith DP, Owens SM, Gilbert JA, Ercolini D. Saliva from obese individuals suppresses the release of aroma compounds from wine. PLoS One 2014; 9:e85611. [PMID: 24465618 PMCID: PMC3899019 DOI: 10.1371/journal.pone.0085611] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 12/04/2013] [Indexed: 01/07/2023] Open
Abstract
Background Recent evidence suggests that a lower extent of the retronasal aroma release correspond to a higher amount of ad libitum food intake. This has been regarded as one of the bases of behavioral choices towards food consumption in obese people. In this pilot study we investigated the hypothesis that saliva from obese individuals could be responsible for an alteration of the retro-nasal aroma release. We tested this hypothesis in vitro, by comparing the release of volatiles from a liquid food matrix (wine) after its interaction with saliva from 28 obese (O) and 28 normal-weight (N) individuals. Methods and Findings Amplicon sequencing of the 16S rRNA V4 region indicated that Firmicutes and Actinobacteria were more abundant in O, while Proteobacteria and Fusobacteria dominated in N. Streptococcaceae were significantly more abundant in the O subjects and constituted 34% and 19% on average of the saliva microbiota of O and N subjects, respectively. The Total Antioxidant Capacity was higher in O vs N saliva samples. A model mouth system was used to test whether the in-mouth wine aroma release differs after the interaction with O or N saliva. In O samples, a 18% to 60% significant decrease in the mean concentration of wine volatiles was detected as a result of interaction with saliva, compared with N. This suppression was linked to biochemical differences in O and N saliva composition, which include protein content. Conclusion Microbiological and biochemical differences were found in O vs N saliva samples. An impaired retronasal aroma release from white wine was detected in vitro and linked to compositional differences between saliva from obese and normal-weight subjects. Additional in vivo investigations on diverse food matrices could contribute to understanding whether a lower olfactory stimulation due to saliva composition can be a co-factor in the development/maintenance of obesity.
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Affiliation(s)
- Paola Piombino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- * E-mail:
| | - Alessandro Genovese
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Silvia Esposito
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Luigi Moio
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Pier Paolo Cutolo
- General and Laparoscopic Surgery Unit, S., Giovanni Bosco Hospital, Naples, Italy
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Caserta, Italy
- IRCCS, Multimedica, Milano, Italy
| | - Valeria Severino
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Caserta, Italy
| | - Elisabetta Moneta
- Research Center on Food and Nutrition, Agricultural Research Council, Rome, Italy
| | - Daniel P. Smith
- Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Sarah M. Owens
- Argonne National Laboratory, Argonne, Illinois, United States of America
- Computation Institute, University of Chicago, Chicago, Illinois, United States of America
| | - Jack A. Gilbert
- Argonne National Laboratory, Argonne, Illinois, United States of America
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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Vandecandelaere I, Matthijs N, Van Nieuwerburgh F, Deforce D, Vosters P, De Bus L, Nelis HJ, Depuydt P, Coenye T. Assessment of microbial diversity in biofilms recovered from endotracheal tubes using culture dependent and independent approaches. PLoS One 2012; 7:e38401. [PMID: 22693635 PMCID: PMC3367921 DOI: 10.1371/journal.pone.0038401] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 05/04/2012] [Indexed: 12/27/2022] Open
Abstract
Ventilator-associated pneumonia (VAP) is a common nosocomial infection in mechanically ventilated patients. Biofilm formation is one of the mechanisms through which the endotracheal tube (ET) facilitates bacterial contamination of the lower airways. In the present study, we analyzed the composition of the ET biofilm flora by means of culture dependent and culture independent (16 S rRNA gene clone libraries and pyrosequencing) approaches. Overall, the microbial diversity was high and members of different phylogenetic lineages were detected (Actinobacteria, beta-Proteobacteria, Candida spp., Clostridia, epsilon-Proteobacteria, Firmicutes, Fusobacteria and gamma-Proteobacteria). Culture dependent analysis, based on the use of selective growth media and conventional microbiological tests, resulted in the identification of typical aerobic nosocomial pathogens which are known to play a role in the development of VAP, e.g. Staphylococcus aureus and Pseudomonas aeruginosa. Other opportunistic pathogens were also identified, including Staphylococcus epidermidis and Kocuria varians. In general, there was little correlation between the results obtained by sequencing 16 S rRNA gene clone libraries and by cultivation. Pyrosequencing of PCR amplified 16 S rRNA genes of four selected samples resulted in the identification of a much wider variety of bacteria. The results from the pyrosequencing analysis suggest that these four samples were dominated by members of the normal oral flora such as Prevotella spp., Peptostreptococcus spp. and lactic acid bacteria. A combination of methods is recommended to obtain a complete picture of the microbial diversity of the ET biofilm.
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Chugal N, Wang JK, Wang R, He X, Kang M, Li J, Zhou X, Shi W, Lux R. Molecular characterization of the microbial flora residing at the apical portion of infected root canals of human teeth. J Endod 2011; 37:1359-64. [PMID: 21924182 DOI: 10.1016/j.joen.2011.06.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 06/07/2011] [Accepted: 06/23/2011] [Indexed: 11/18/2022]
Abstract
INTRODUCTION This study investigated the bacterial communities residing in the apical portion of human teeth with apical periodontitis in primary and secondary infections by using a culture-independent molecular biology approach. METHODS Root canal samples from the apical root segments of extracted teeth were collected from 18 teeth with necrotic pulp and 8 teeth with previous endodontic treatment. Samples were processed for amplification via polymerase chain reaction and separated with denaturing gradient gel electrophoresis. Selected bands were excised from the gel and sequenced for identification. RESULTS Comparable to previous studies of entire root canals, the apical bacterial communities in primary infections were significantly more diverse than in secondary infections (P = .0003). Interpatient and intrapatient comparisons exhibited similar variations in profiles. Different roots of the same teeth with secondary infections displayed low similarity in bacterial composition, whereas an equivalent sample collected from primary infection contained almost identical populations. Sequencing revealed a high prevalence of Fusobacteria, Actinomyces species, and oral Anaeroglobus geminatus in both types of infection. Many secondary infections contained Burkholderiales or Pseudomonas species, both of which represent opportunistic environmental pathogens. CONCLUSIONS Certain microorganisms exhibit similar prevalence in primary and secondary infection, indicating that they are likely not eradicated during endodontic treatment. The presence of Burkholderiales and Pseudomonas species underscores the problem of environmental contamination. Treatment appears to affect the various root canals of multirooted teeth differently, resulting in local changes of the microbiota.
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Affiliation(s)
- Nadia Chugal
- Section of Endodontics, UCLA School of Dentistry, UCLA School of Medicine, Los Angeles, California 90095-1668, USA
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Hattori K, Matsui H. Diversity of fumarate reducing bacteria in the bovine rumen revealed by culture dependent and independent approaches. Anaerobe 2007; 14:87-93. [PMID: 18276172 DOI: 10.1016/j.anaerobe.2007.12.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Revised: 10/23/2007] [Accepted: 12/20/2007] [Indexed: 11/19/2022]
Abstract
Diversity of fumarate reducing (dissimilating) bacteria in the bovine rumen was analyzed by both culture dependent and independent methodologies. A total of 39 strains were isolated by using three different media and belonged to three different phyla (Proteobacteria, Fusobacteria, and Firmicutes). A primer set that amplified the fumarate reductase gene (frdA) from Proteobacteria was developed and two frdA clone libraries were constructed. Identities of deduced amino acid sequences of cloned frdA amplicons against known sequences ranged from 58% to 85% suggesting the presence of unknown fumarate reducing bacteria. This is the first report on the diversity of fumarate reducing bacteria in the rumen.
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Affiliation(s)
- Kimihiro Hattori
- Graduate School of Bioresources, Mie University, Tsu, Mie, Japan
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26
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Abstract
The F1F0 ATP synthase utilizes energy stored in an electrochemical gradient of protons (or Na+ ions) across the membrane to synthesize ATP from ADP and phosphate. Current models predict that the protonation/deprotonation of specific acidic c ring residues is at the core of the proton translocation mechanism by this enzyme. To probe the mode of proton binding, we measured the covalent modification of the acidic c ring residues with the inhibitor dicyclohexylcarbodiimide (DCCD) over the pH range from 5 to 11. With the H+-translocating ATP synthase from the archaeum Halobacterium salinarium or the Na+-translocating ATP synthase from Ilyobacter tartaricus, the pH profile of DCCD labeling followed a titration curve with a pKa around neutral, reflecting protonation of the acidic c ring residues. However, with the ATP synthases from Escherichia coli, mitochondria, or chloroplasts, a clearly different, bell-shaped pH profile for DCCD labeling was observed which is not compatible with carboxylate protonation but might be explained by the coordination of a hydronium ion as proposed earlier [Boyer, P. D. (1988) Trends Biochem. Sci. 13, 5-7]. Upon site-directed mutagenesis of single binding site residues of the structurally resolved c ring, the sigmoidal pH profile for DCCD labeling could be converted to a more bell-shaped one, demonstrating that the different ion binding modes are based on subtle changes in the amino acid sequence of the protein. The concept of two different binding sites in the ATP synthase family is supported by the ATP hydrolysis pH profiles of the investigated enzymes.
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Affiliation(s)
- Christoph von Ballmoos
- Institut für Mikrobiologie, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
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27
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De Hertogh G, Aerssens J, de Hoogt R, Peeters P, Verhasselt P, Van Eyken P, Ectors N, Vermeire S, Rutgeerts P, Coulie B, Geboes K. Validation of 16S rDNA sequencing in microdissected bowel biopsies from Crohn's disease patients to assess bacterial flora diversity. J Pathol 2006; 209:532-9. [PMID: 16739113 DOI: 10.1002/path.2006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The bowel flora is implicated in Crohn's disease (CD) pathogenesis but its precise role is still unclear. Several non-mutually exclusive hypotheses have been proposed: an unidentified persistent pathogen; excessive bacterial translocation; an immune system abnormality in response to normal bacteria; or a breakdown in the balance between protective and harmful bacteria. These hypotheses can be tested by identifying bacteria in specific microscopic bowel structures or lesions. The present paper describes a novel technique to assess bacterial flora diversity in bowel biopsies, by combining laser capture microdissection with broad-range 16S rDNA sequencing. Fifty-four samples comprising histologically normal and pathological mucosa, MALT, ulcers, submucosal lymphangiectasias, epithelioid granulomas, and lymph nodes were microdissected out of 30 bowel biopsies from five CD patients. Bacterial 16S rDNA was successfully amplified by PCR in all samples, and PCR products from 15 samples were selected for cloning and sequence analysis. A total of 729 bacterial DNA sequences were analysed, which could be attributed to six different phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria, and Planctomycetes). DNA from typical bowel bacteria (Enterobacteriaceae, Clostridiales, Bacteroidetes, Fusobacteria) was detected in all microdissected areas. It was thus convincingly demonstrated that 16S rDNA sequencing can be combined with microdissection to study the bowel flora. However, no specific persistent pathogen causal for CD was identified. The results suggest that Enterobacteriaceae may initiate or colonize ulcers in CD. Translocation of bacteria through established mucosal lesions or as a result of increased permeability may be involved in the evolution towards chronic inflammation and in the establishment of persistent lesions. Further study is needed to confirm these preliminary findings.
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Affiliation(s)
- G De Hertogh
- Department of Morphology and Molecular Pathology, University Hospitals KULeuven, Belgium.
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Gmür R, Munson MA, Wade WG. Genotypic and phenotypic characterization of fusobacteria from Chinese and European patients with inflammatory periodontal diseases. Syst Appl Microbiol 2006; 29:120-30. [PMID: 16464693 DOI: 10.1016/j.syapm.2005.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2005] [Indexed: 10/25/2022]
Abstract
Phylogenetic and antigenic studies were performed on 48 human oral Fusobacterium strains from Chinese patients with either necrotizing ulcerative gingivitis (NUG) or gingivitis and on 23 Fusobacterium nucleatum or Fusobacterium periodonticum strains from European periodontitis patients. Alignment of partial 16S rRNA gene sequences resulted in a phylogenetic tree that corresponded well with the current classification of oral fusobacteria into F. periodonticum and several subspecies of F. nucleatum, in spite of much minor genetic variability. F. periodonticum, F. nucleatum subsp. animalis and a previously undescribed phylogenetic cluster (C4), that may represent an additional F. nucleatum subspecies, constituted discrete clusters distinct from the remainder of F. nucleatum with high bootstrap values. Chinese and European strains differed markedly with regard to their respective classification patterns, suggesting a predominance of F. peridonticum and F. nucleatum susp. animalis over F. nucleatum subsp. nucleatum and F. nucleatum subsp. fusiforme/vincentii in samples from China. Antigenic typing enabled the association of many previously described serovars with distinct phylogenetic clusters and when applied directly to uncultured clinical samples confirmed the differential distribution of oral Fusobacterium taxa in Chinese and European samples. Bacteria from cluster C4 and F. nucleatum subsp. animalis were significantly more prevalent and accounted for higher cell numbers in NUG than in gingivitis samples, suggesting a possible association of these rarely observed taxa with NUG in Chinese patients.
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Affiliation(s)
- Rudolf Gmür
- Institute for Oral Biology, Center for Dental-, Oral Medicine and Maxillofacial Surgery, University of Zürich, Plattenstrasse 11, CH-8032 Zürich, Switzerland.
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Abstract
The Na+-dependent F-ATP synthases of Ilyobacter tartaricus and Propionigenium modestum contain membrane-embedded ring-shaped c subunit assemblies with a stoichiometry of 11. Subunit c from either organism was overexpressed in Escherichia coli using a plasmid containing the corresponding gene, extracted from the membrane using detergent and then purified. Subsequent analyses by SDS/PAGE revealed that only a minor portion of the c subunits had assembled into stable rings, while the majority migrated as monomers. The population of rings consisted mainly of c11, but more slowly migrating assemblies were also found, which might reflect other c ring stoichiometries. We show that they consisted of higher aggregates of homogeneous c11 rings and/or assemblies of c11 rings and single c monomers. Atomic force microscopy topographs of c rings reconstituted into lipid bilayers showed that the c ring assemblies had identical diameters and that stoichiometries throughout all rings resolved at high resolution. This finding did not depend on whether the rings were assembled into crystalline or densely packed assemblies. Most of these rings represented completely assembled undecameric complexes. Occasionally, rings lacking a few subunits or hosting additional subunits in their cavity were observed. The latter rings may represent the aggregates between c11 and c1, as observed by SDS/PAGE. Our results are congruent with a stable c11 ring stoichiometry that seems to not be influenced by the expression level of subunit c in the bacteria.
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Affiliation(s)
- Thomas Meier
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule, Zürich, Switzerland.
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Budd A, Blandin S, Levashina EA, Gibson TJ. Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome? Genome Biol 2004; 5:R38. [PMID: 15186489 PMCID: PMC463071 DOI: 10.1186/gb-2004-5-6-r38] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2004] [Revised: 04/02/2004] [Accepted: 04/08/2004] [Indexed: 11/14/2022] Open
Abstract
Homologs of metazoan α2-macroglobulins have been found in bacteria. The distribution of these genes in diverse bacterial clades suggests they have been acquired by multiple horizontal transfers. Background Invasive bacteria are known to have captured and adapted eukaryotic host genes. They also readily acquire colonizing genes from other bacteria by horizontal gene transfer. Closely related species such as Helicobacter pylori and Helicobacter hepaticus, which exploit different host tissues, share almost none of their colonization genes. The protease inhibitor α2-macroglobulin provides a major metazoan defense against invasive bacteria, trapping attacking proteases required by parasites for successful invasion. Results Database searches with metazoan α2-macroglobulin sequences revealed homologous sequences in bacterial proteomes. The bacterial α2-macroglobulin phylogenetic distribution is patchy and violates the vertical descent model. Bacterial α2-macroglobulin genes are found in diverse clades, including purple bacteria (proteobacteria), fusobacteria, spirochetes, bacteroidetes, deinococcids, cyanobacteria, planctomycetes and thermotogae. Most bacterial species with bacterial α2-macroglobulin genes exploit higher eukaryotes (multicellular plants and animals) as hosts. Both pathogenically invasive and saprophytically colonizing species possess bacterial α2-macroglobulins, indicating that bacterial α2-macroglobulin is a colonization rather than a virulence factor. Conclusions Metazoan α2-macroglobulins inhibit proteases of pathogens. The bacterial homologs may function in reverse to block host antimicrobial defenses. α2-macroglobulin was probably acquired one or more times from metazoan hosts and has then spread widely through other colonizing bacterial species by more than 10 independent horizontal gene transfers. yfhM-like bacterial α2-macroglobulin genes are often found tightly linked with pbpC, encoding an atypical peptidoglycan transglycosylase, PBP1C, that does not function in vegetative peptidoglycan synthesis. We suggest that YfhM and PBP1C are coupled together as a periplasmic defense and repair system. Bacterial α2-macroglobulins might provide useful targets for enhancing vaccine efficacy in combating infections.
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Affiliation(s)
- Aidan Budd
- European Molecular Biology Laboratory, 69012 Heidelberg, Germany
| | | | - Elena A Levashina
- UPR 9022 du CNRS, IBMC, rue René Descartes, F-67087 Strasbourg CEDEX, France
| | - Toby J Gibson
- European Molecular Biology Laboratory, 69012 Heidelberg, Germany
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