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Rojas CA, Entrolezo Z, Jarett JK, Jospin G, Martin A, Ganz HH. Microbiome Responses to Oral Fecal Microbiota Transplantation in a Cohort of Domestic Dogs. Vet Sci 2024; 11:42. [PMID: 38275924 PMCID: PMC10821121 DOI: 10.3390/vetsci11010042] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 01/27/2024] Open
Abstract
Fecal microbiota transplants (FMTs) have been successful at treating digestive and skin conditions in dogs. The degree to which the microbiome is impacted by FMT in a cohort of dogs has not been thoroughly investigated. Using 16S rRNA gene sequencing, we document the changes in the microbiome of fifty-four dogs that took capsules of lyophilized fecal material for their chronic diarrhea, vomiting, or constipation. We found that the relative abundances of five bacterial genera (Butyricicoccus, Faecalibacterium, Fusobacterium, Megamonas, and Sutterella) were higher after FMT than before FMT. Fecal microbiome alpha- and beta-diversity were correlated with kibble and raw food consumption, and prior antibiotic use. On average, 18% of the stool donor's bacterial amplicon sequence variants (ASVs) engrafted in the FMT recipient, with certain bacterial taxa like Bacteroides spp., Fusobacterium spp., and Lachnoclostridium spp. engrafting more frequently than others. Lastly, analyses indicated that the degree of overlap between the donor bacteria and the community of microbes already established in the FMT recipient likely impacts engraftment. Collectively, our work provides further insight into the microbiome and engraftment dynamics of dogs before and after taking oral FMTs.
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Affiliation(s)
| | | | | | | | | | - Holly H. Ganz
- AnimalBiome, Oakland, CA 94609, USA; (C.A.R.); (Z.E.); (J.K.J.); (G.J.); (A.M.)
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2
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Anderson JG, Rojas CA, Scarsella E, Entrolezo Z, Jospin G, Hoffman SL, Force J, MacLellan RH, Peak M, Shope BH, Tsugawa AJ, Ganz HH. The Oral Microbiome across Oral Sites in Cats with Chronic Gingivostomatitis, Periodontal Disease, and Tooth Resorption Compared with Healthy Cats. Animals (Basel) 2023; 13:3544. [PMID: 38003162 PMCID: PMC10668797 DOI: 10.3390/ani13223544] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Feline chronic gingivostomatitis (FCGS) is a chronic mucosal and gingival inflammatory disease in which pathogenesis remains unclear. Interactions between the host inflammatory process, the host immune response, and the oral microbiome are implicated in this pathogenesis. To begin to understand this disease and the impact of the microbiome to host inflammatory disease states, we collected sterile noninvasive plaque biofilm samples from ten distinct sites within the oral cavity in cats with stomatitis (n = 12), healthy cats (n = 9), and cats with tooth resorption or periodontitis (n = 11). Analysis of full-length 16S rRNA gene sequences indicated that the microbiomes of cats with FCGS presented marked dysbiosis at multiple oral sites. Additionally, microbiome beta diversity varied with oral condition, indicating that stomatitis, periodontitis, and/or tooth resorption influence the microbiome differently. Lastly, we found that the microbiomes of swabs taken from the oral cavity were comparable to those taken from plaque using endodontic paper points, validating this as another sampling method. Collectively, our work furthers our understanding of the dysbiosis and composition of bacteria in the oral microbiome in FCGS, with hopes of contributing to the prevention, diagnosis, and treatment of this challenging condition in felines.
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Affiliation(s)
- Jamie G. Anderson
- Department of Oral Medicine, Penn Dental Medicine, Philadelphia, PA 19104, USA
| | - Connie A. Rojas
- AnimalBiome, Oakland, CA 94609, USA; (C.A.R.); (E.S.); (Z.E.); (G.J.); (H.H.G.)
| | - Elisa Scarsella
- AnimalBiome, Oakland, CA 94609, USA; (C.A.R.); (E.S.); (Z.E.); (G.J.); (H.H.G.)
| | - Zhandra Entrolezo
- AnimalBiome, Oakland, CA 94609, USA; (C.A.R.); (E.S.); (Z.E.); (G.J.); (H.H.G.)
| | - Guillaume Jospin
- AnimalBiome, Oakland, CA 94609, USA; (C.A.R.); (E.S.); (Z.E.); (G.J.); (H.H.G.)
| | | | - Judy Force
- Dentistry for Animals, Aptos, CA 95003, USA
| | - Roxane H. MacLellan
- VCA Highlands Ranch Animal Specialty and Emergency Center, Highlands Ranch, CO 80126, USA;
| | - Mike Peak
- The Pet Dentist, Inc., Tampa, FL 33544, USA;
| | | | | | - Holly H. Ganz
- AnimalBiome, Oakland, CA 94609, USA; (C.A.R.); (E.S.); (Z.E.); (G.J.); (H.H.G.)
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Rojas CA, Marks SL, Borras E, Lesea H, McCartney MM, Coil DA, Davis CE, Eisen JA. Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics. Sci Rep 2023; 13:19382. [PMID: 37938241 PMCID: PMC10632438 DOI: 10.1038/s41598-023-45997-1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Many mammals rely on volatile organic chemical compounds (VOCs) produced by bacteria for their communication and behavior, though little is known about the exact molecular mechanisms or bacterial species that are responsible. We used metagenomic sequencing, mass-spectrometry based metabolomics, and culturing to profile the microbial and volatile chemical constituents of anal gland secretions in twenty-three domestic cats (Felis catus), in attempts to identify organisms potentially involved in host odor production. We found that the anal gland microbiome was dominated by bacteria in the genera Corynebacterium, Bacteroides, Proteus, Lactobacillus, and Streptococcus, and showed striking variation among individual cats. Microbiome profiles also varied with host age and obesity. Metabolites such as fatty-acids, ketones, aldehydes and alcohols were detected in glandular secretions. Overall, microbiome and metabolome profiles were modestly correlated (r = 0.17), indicating that a relationship exists between the bacteria in the gland and the metabolites produced in the gland. Functional analyses revealed the presence of genes predicted to code for enzymes involved in VOC metabolism such as dehydrogenases, reductases, and decarboxylases. From metagenomic data, we generated 85 high-quality metagenome assembled genomes (MAGs). Of importance were four MAGs classified as Corynebacterium frankenforstense, Proteus mirabilis, Lactobacillus johnsonii, and Bacteroides fragilis. They represent strong candidates for further investigation of the mechanisms of volatile synthesis and scent production in the mammalian anal gland.
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Affiliation(s)
- Connie A Rojas
- Genome Center, University of California-Davis, Davis, CA, USA.
- Department of Evolution and Ecology, University of California-Davis, Davis, CA, USA.
| | - Stanley L Marks
- Department of Medicine and Epidemiology, University of California-Davis, School of Veterinary Medicine, Davis, CA, USA
| | - Eva Borras
- Department of Mechanical and Aerospace Engineering, University of California-Davis, Davis, CA, USA
- UC Davis Lung Center, University of California-Davis, Davis, CA, USA
| | - Hira Lesea
- Department of Microbiology and Molecular Genetics, University of California-Davis, Davis, CA, USA
| | - Mitchell M McCartney
- Department of Mechanical and Aerospace Engineering, University of California-Davis, Davis, CA, USA
- UC Davis Lung Center, University of California-Davis, Davis, CA, USA
- VA Northern California Health Care System, Mather, CA, USA
| | - David A Coil
- Genome Center, University of California-Davis, Davis, CA, USA
| | - Cristina E Davis
- Department of Mechanical and Aerospace Engineering, University of California-Davis, Davis, CA, USA
- UC Davis Lung Center, University of California-Davis, Davis, CA, USA
- VA Northern California Health Care System, Mather, CA, USA
| | - Jonathan A Eisen
- Genome Center, University of California-Davis, Davis, CA, USA
- Department of Evolution and Ecology, University of California-Davis, Davis, CA, USA
- Department of Medical Microbiology and Immunology, University of California-Davis, Davis, CA, USA
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Rojas CA, Gardy J, Eisen JA, Ganz HH. Recovery of 52 bacterial genomes from the fecal microbiome of the domestic cat ( Felis catus) using Hi-C proximity ligation and shotgun metagenomics. Microbiol Resour Announc 2023; 12:e0060123. [PMID: 37695121 PMCID: PMC10586161 DOI: 10.1128/mra.00601-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/08/2023] [Indexed: 09/12/2023] Open
Abstract
We used Hi-C proximity ligation with shotgun sequencing to retrieve metagenome-assembled genomes (MAGs) from the fecal microbiomes of two domestic cats (Felis catus). The genomes were assessed for completeness and contamination, classified taxonomically, and annotated for putative antimicrobial resistance (AMR) genes.
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Affiliation(s)
| | - Jennifer Gardy
- Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - Jonathan A. Eisen
- Evolution and Ecology, University of California, Davis, California, USA
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Rojas CA, Entrolezo Z, Jarett JK, Jospin G, Kingsbury DD, Martin A, Eisen JA, Ganz HH. Microbiome Responses to Fecal Microbiota Transplantation in Cats with Chronic Digestive Issues. Vet Sci 2023; 10:561. [PMID: 37756083 PMCID: PMC10537086 DOI: 10.3390/vetsci10090561] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/25/2023] [Accepted: 09/02/2023] [Indexed: 09/28/2023] Open
Abstract
There is growing interest in the application of fecal microbiota transplants (FMTs) in small animal medicine, but there are few published studies that have tested their effects in the domestic cat (Felis catus). Here we use 16S rRNA gene sequencing to examine fecal microbiome changes in 46 domestic cats with chronic digestive issues that received FMTs using lyophilized stool that was delivered in oral capsules. Fecal samples were collected from FMT recipients before and two weeks after the end of the full course of 50 capsules, as well as from their stool donors (N = 10), and other healthy cats (N = 113). The fecal microbiomes of FMT recipients varied with host clinical signs and dry kibble consumption, and shifts in the relative abundances of Clostridium, Collinsella, Megamonas, Desulfovibrio and Escherichia were observed after FMT. Overall, donors shared 13% of their bacterial amplicon sequence variants (ASVs) with FMT recipients and the most commonly shared ASVs were classified as Prevotella 9, Peptoclostridium, Bacteroides, and Collinsella. Lastly, the fecal microbiomes of cats with diarrhea became more similar to the microbiomes of age-matched and diet-matched healthy cats compared to cats with constipation. Overall, our results suggest that microbiome responses to FMT may be modulated by the FMT recipient's initial presenting clinical signs, diet, and their donor's microbiome.
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Affiliation(s)
- Connie A. Rojas
- Genome Center, University of California, Davis, CA 95616, USA; (C.A.R.); (J.A.E.)
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Zhandra Entrolezo
- AnimalBiome, Oakland, CA 94609, USA; (Z.E.); (J.K.J.); (G.J.); (A.M.)
| | - Jessica K. Jarett
- AnimalBiome, Oakland, CA 94609, USA; (Z.E.); (J.K.J.); (G.J.); (A.M.)
| | - Guillaume Jospin
- AnimalBiome, Oakland, CA 94609, USA; (Z.E.); (J.K.J.); (G.J.); (A.M.)
| | - Dawn D. Kingsbury
- AnimalBiome, Oakland, CA 94609, USA; (Z.E.); (J.K.J.); (G.J.); (A.M.)
| | - Alex Martin
- AnimalBiome, Oakland, CA 94609, USA; (Z.E.); (J.K.J.); (G.J.); (A.M.)
| | - Jonathan A. Eisen
- Genome Center, University of California, Davis, CA 95616, USA; (C.A.R.); (J.A.E.)
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Holly H. Ganz
- AnimalBiome, Oakland, CA 94609, USA; (Z.E.); (J.K.J.); (G.J.); (A.M.)
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6
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Rojas CA, Marks SL, Borras E, Lesea H, McCartney MM, Coil D, Davis CE, Eisen JA. Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics. Res Sq 2023:rs.3.rs-2883555. [PMID: 37214811 PMCID: PMC10197813 DOI: 10.21203/rs.3.rs-2883555/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Animals rely on volatile chemical compounds for their communication and behavior. Many of these compounds are sequestered in endocrine and exocrine glands and are synthesized by anaerobic microbes. While the volatile organic compound (VOC) or microbiome composition of glandular secretions has been investigated in several mammalian species, few have linked specific bacterial taxa to the production of volatiles or to specific microbial gene pathways. Here, we use metagenomic sequencing, mass-spectrometry based metabolomics, and culturing to profile the microbial and volatile chemical constituents of anal gland secretions in twenty-three domestic cats (Felis catus), in attempts to identify organisms potentially involved in host odor production. We found that the anal gland microbiome was dominated by bacteria in the genera Corynebacterium, Bacteroides, Proteus, Lactobacillus, and Streptococcus, and showed striking variation among individual cats. Microbiome profiles also varied with host age and obesity. Metabolites such as fatty-acids, ketones, aldehydes and alcohols were detected in glandular secretions. Overall, microbiome and metabolome profiles were modestly correlated (r=0.17), indicating that a relationship exists between the bacteria in the gland and the metabolites produced in the gland. Functional analyses revealed the presence of genes predicted to code for enzymes involved in VOC metabolism such as dehydrogenases, reductases, and decarboxylases. From metagenomic data, we generated 85 high-quality metagenome assembled genomes (MAGs). Of these, four were inferred to have high relative abundance in metagenome profiles and had close relatives that were recovered as cultured isolates. These four MAGs were classified as Corynebacterium frankenforstense, Proteus mirabilis, Lactobacillus johnsonii, and Bacteroides fragilis. They represent strong candidates for further investigation of the mechanisms of volatile synthesis and scent production in the mammalian anal gland.
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7
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Mejia MP, Rojas CA, Curd E, Renshaw MA, Edalati K, Shih B, Vincent N, Lin M, Nguyen PH, Wayne R, Jessup K, Parker SS. Soil Microbial Community Composition and Tolerance to Contaminants in an Urban Brownfield Site. Microb Ecol 2023; 85:998-1012. [PMID: 35802172 PMCID: PMC10156844 DOI: 10.1007/s00248-022-02061-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/21/2022] [Indexed: 05/04/2023]
Abstract
Brownfields are unused sites that contain hazardous substances due to previous commercial or industrial use. The sites are inhospitable for many organisms, but some fungi and microbes can tolerate and thrive in the nutrient-depleted and contaminated soils. However, few studies have characterized the impacts of long-term contamination on soil microbiome composition and diversity at brownfields. This study focuses on an urban brownfield-a former rail yard in Los Angeles that is contaminated with heavy metals, volatile organic compounds, and petroleum-derived pollutants. We anticipate that heavy metals and organic pollutants will shape soil microbiome diversity and that several candidate fungi and bacteria will be tolerant to the contaminants. We sequence three gene markers (16S ribosomal RNA, 18S ribosomal RNA, and the fungal internal transcribed spacer (FITS)) in 55 soil samples collected at five depths to (1) profile the composition of the soil microbiome across depths; (2) determine the extent to which hazardous chemicals predict microbiome variation; and (3) identify microbial taxonomic groups that may metabolize these contaminants. Detected contaminants in the samples included heavy metals, petroleum hydrocarbons, polycyclic aromatic hydrocarbons, and volatile organic compounds. Bacterial, eukaryotic, and fungal communities all varied with depth and with concentrations of arsenic, chromium, cobalt, and lead. 18S rRNA microbiome richness and fungal richness were positively correlated with lead and cobalt levels, respectively. Furthermore, bacterial Paenibacillus and Iamia, eukaryotic Actinochloris, and fungal Alternaria were enriched in contaminated soils compared to uncontaminated soils and represent taxa of interest for future bioremediation research. Based on our results, we recommend incorporating DNA-based multi-marker microbial community profiling at multiple sites and depths in brownfield site assessment standard methods and restoration.
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Affiliation(s)
- Maura Palacios Mejia
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Connie A Rojas
- Ecology, Evolution, and Behavior Program, Michigan State University, Lansing, MI, USA
| | - Emily Curd
- Natural Science, Landmark College, Putney, VT, USA
| | - Mark A Renshaw
- Cherokee Federal, USGS Wetland and Aquatic Research Center, Gainesville, FL, USA
| | - Kiumars Edalati
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Beverly Shih
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nitin Vincent
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Meixi Lin
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peggy H Nguyen
- Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
| | - Robert Wayne
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
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Rojas CA, De Santiago Torio A, Park S, Bosak T, Klepac-Ceraj V. Organic Electron Donors and Terminal Electron Acceptors Structure Anaerobic Microbial Communities and Interactions in a Permanently Stratified Sulfidic Lake. Front Microbiol 2021; 12:620424. [PMID: 33967973 PMCID: PMC8103211 DOI: 10.3389/fmicb.2021.620424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/23/2021] [Indexed: 01/04/2023] Open
Abstract
The extent to which nutrients structure microbial communities in permanently stratified lakes is not well understood. This study characterized microbial communities from the anoxic layers of the meromictic and sulfidic Fayetteville Green Lake (FGL), NY, United States, and investigated the roles of organic electron donors and terminal electron acceptors in shaping microbial community structure and interactions. Bacterial communities from the permanently stratified layer below the chemocline (monimolimnion) and from enrichment cultures inoculated by lake sediments were analyzed using 16S rRNA gene sequencing. Results showed that anoxygenic phototrophs dominated microbial communities in the upper monimolimnion (21 m), which harbored little diversity, whereas the most diverse communities resided at the bottom of the lake (∼52 m). Organic electron donors explained 54% of the variation in the microbial community structure in aphotic cultures enriched on an array of organic electron donors and different inorganic electron acceptors. Electron acceptors only explained 10% of the variation, but were stronger drivers of community assembly in enrichment cultures supplemented with acetate or butyrate compared to the cultures amended by chitin, lignin or cellulose. We identified a range of habitat generalists and habitat specialists in both the water column and enrichment samples using Levin’s index. Network analyses of interactions among microbial groups revealed Chlorobi and sulfate reducers as central to microbial interactions in the upper monimolimnion, while Syntrophaceae and other fermenting organisms were more important in the lower monimolimnion. The presence of photosynthetic microbes and communities that degrade chitin and cellulose far below the chemocline supported the downward transport of microbes, organic matter and oxidants from the surface and the chemocline. Collectively, our data suggest niche partitioning of bacterial communities via interactions that depend on the availability of different organic electron donors and terminal electron acceptors. Thus, light, as well as the diversity and availability of chemical resources drive community structure and function in FGL, and likely in other stratified, meromictic lakes.
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Affiliation(s)
- Connie A Rojas
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States.,Ecology, Evolution, and Behavior, Michigan State University, East Lansing, MI, United States
| | - Ana De Santiago Torio
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Serry Park
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Tanja Bosak
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
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Rojas CA, Ramírez-Barahona S, Holekamp KE, Theis KR. Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales. Anim Microbiome 2021; 3:33. [PMID: 33892813 PMCID: PMC8063394 DOI: 10.1186/s42523-021-00094-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 04/04/2021] [Indexed: 12/13/2022] Open
Abstract
The gut microbiota is critical for host function. Among mammals, host phylogenetic relatedness and diet are strong drivers of gut microbiota structure, but one factor may be more influential than the other. Here, we used 16S rRNA gene sequencing to determine the relative contributions of host phylogeny and host diet in structuring the gut microbiotas of 11 herbivore species from 5 families living sympatrically in southwest Kenya. Herbivore species were classified as grazers, browsers, or mixed-feeders and dietary data (% C4 grasses in diet) were compiled from previously published sources. We found that herbivore gut microbiotas were highly species-specific, and that host taxonomy accounted for more variation in the gut microbiota (30%) than did host dietary guild (10%) or sample month (8%). Overall, similarity in the gut microbiota increased with host phylogenetic relatedness (r = 0.74) across the 11 species of herbivores, but among 7 closely related Bovid species, dietary %C4 grass values more strongly predicted gut microbiota structure (r = 0.64). Additionally, within bovids, host dietary guild explained more of the variation in the gut microbiota (17%) than did host species (12%). Lastly, while we found that the gut microbiotas of herbivores residing in southwest Kenya converge with those of distinct populations of conspecifics from central Kenya, fine-scale differences in the abundances of bacterial amplicon sequence variants (ASVs) between individuals from the two regions were also observed. Overall, our findings suggest that host phylogeny and taxonomy strongly structure the gut microbiota across broad host taxonomic scales, but these gut microbiotas can be further modified by host ecology (i.e., diet, geography), especially among closely related host species.
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Affiliation(s)
- Connie A. Rojas
- Department of Integrative Biology, Michigan State University, East Lansing, MI USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI USA
| | - Santiago Ramírez-Barahona
- Departament of Botany, Institute of Biology, Universidad Nacional Autónoma de México, Mexico City, MX Mexico
| | - Kay E. Holekamp
- Department of Integrative Biology, Michigan State University, East Lansing, MI USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI USA
| | - Kevin R. Theis
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI USA
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI USA
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Rojas CA, Holekamp KE, Winters AD, Theis KR. Body site-specific microbiota reflect sex and age-class among wild spotted hyenas. FEMS Microbiol Ecol 2020; 96:5700710. [PMID: 31926016 DOI: 10.1093/femsec/fiaa007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/10/2020] [Indexed: 02/06/2023] Open
Abstract
Host-associated microbial communities, henceforth 'microbiota', can affect the physiology and behavior of their hosts. In mammals, host ecological, social and environmental variables are associated with variation in microbial communities. Within individuals in a given mammalian species, the microbiota also partitions by body site. Here, we build on this work and sequence the bacterial 16S rRNA gene to profile the microbiota at six distinct body sites (ear, nasal and oral cavities, prepuce, rectum and anal scent gland) in a population of wild spotted hyenas (Crocuta crocuta), which are highly social, large African carnivores. We inquired whether microbiota at these body sites vary with host sex or social rank among juvenile hyenas, and whether they differ between juvenile females and adult females. We found that the scent gland microbiota differed between juvenile males and juvenile females, whereas the prepuce and rectal microbiota differed between adult females and juvenile females. Social rank, however, was not a significant predictor of microbiota profiles. Additionally, the microbiota varied considerably among the six sampled body sites and exhibited strong specificity among individual hyenas. Thus, our findings suggest that site-specific niche selection is a primary driver of microbiota structure in mammals, but endogenous host factors may also be influential.
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Affiliation(s)
- Connie A Rojas
- Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Kay E Holekamp
- Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Andrew D Winters
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, 540 E Canfield St, Detroit, MI, 48201, USA
| | - Kevin R Theis
- BEACON Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA.,Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, 540 E Canfield St, Detroit, MI, 48201, USA
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Mullane KM, Morrison VA, Camacho LH, Arvin A, McNeil SA, Durrand J, Campbell B, Su SC, Chan ISF, Parrino J, Kaplan SS, Popmihajlov Z, Annunziato PW, Cerana S, Dictar MO, Bonvehi P, Tregnaghi JP, Fein L, Ashley D, Singh M, Hayes T, Playford G, Morrissey O, Thaler J, Kuehr T, Greil R, Pecherstorfer M, Duck L, Van Eygen K, Aoun M, De Prijck B, Franke FA, Barrios CHE, Mendes AVA, Serrano SV, Garcia RF, Moore F, Camargo JFC, Pires LA, Alves RS, Radinov A, Oreshkov K, Minchev V, Hubenova AI, Koynova T, Ivanov I, Rabotilova B, Minchev V, Petrov PA, Chilingirov P, Karanikolov S, Raynov J, Grimard D, McNeil S, Kumar D, Larratt LM, Weiss K, Delage R, Diaz-Mitoma FJ, Cano PO, Couture F, Carvajal P, Yepes A, Torres Ulloa R, Fardella P, Caglevic C, Rojas C, Orellana E, Gonzalez P, Acevedo A, Galvez KM, Gonzalez ME, Franco S, Restrepo JG, Rojas CA, Bonilla C, Florez LE, Ospina AV, Manneh R, Zorica R, Vrdoljak DV, Samarzija M, Petruzelka L, Vydra J, Mayer J, Cibula D, Prausova J, Paulson G, Ontaneda M, Palk K, Vahlberg A, Rooneem R, Galtier F, Postil D, Lucht F, Laine F, Launay O, Laurichesse H, Duval X, Cornely OA, Camerer B, Panse J, Zaiss M, Derigs HG, Menzel H, Verbeek M, Georgoulias V, Mavroudis D, Anagnostopoulos A, Terpos E, Cortes D, Umanzor J, Bejarano S, Galeano RW, Wong RSM, Hui P, Pedrazzoli P, Ruggeri L, Aversa F, Bosi A, Gentile G, Rambaldi A, Contu A, Marei L, Abbadi A, Hayajneh W, Kattan J, Farhat F, Chahine G, Rutkauskiene J, Marfil Rivera LJ, Lopez Chuken YA, Franco Villarreal H, Lopez Hernandez J, Blacklock H, Lopez RI, Alvarez R, Gomez AM, Quintana TS, Moreno Larrea MDC, Zorrilla SJ, Alarcon E, Samanez FCA, Caguioa PB, Tiangco BJ, Mora EM, Betancourt-Garcia RD, Hallman-Navarro D, Feliciano-Lopez LJ, Velez-Cortes HA, Cabanillas F, Ganea DE, Ciuleanu TE, Ghizdavescu DG, Miron L, Cebotaru CL, Cainap CI, Anghel R, Dvorkin MV, Gladkov OA, Fadeeva NV, Kuzmin AA, Lipatov ON, Zbarskaya II, Akhmetzyanov FS, Litvinov IV, Afanasyev BV, Cherenkova M, Lioznov D, Lisukov IA, Smirnova YA, Kolomietz S, Halawani H, Goh YT, Drgona L, Chudej J, Matejkova M, Reckova M, Rapoport BL, Szpak WM, Malan DR, Jonas N, Jung CW, Lee DG, Yoon SS, Lopez Jimenez J, Duran Martinez I, Rodriguez Moreno JF, Solano Vercet C, de la Camara R, Batlle Massana M, Yeh SP, Chen CY, Chou HH, Tsai CM, Chiu CH, Siritanaratkul N, Norasetthada L, Sriuranpong V, Seetalarom K, Akan H, Dane F, Ozcan MA, Ozsan GH, Kalayoglu Besisik SF, Cagatay A, Yalcin S, Peniket A, Mullan SR, Dakhil KM, Sivarajan K, Suh JJG, Sehgal A, Marquez F, Gomez EG, Mullane MR, Skinner WL, Behrens RJ, Trevarthe DR, Mazurczak MA, Lambiase EA, Vidal CA, Anac SY, Rodrigues GA, Baltz B, Boccia R, Wertheim MS, Holladay CS, Zenk D, Fusselman W, Wade III JL, Jaslowsk AJ, Keegan J, Robinson MO, Go RS, Farnen J, Amin B, Jurgens D, Risi GF, Beatty PG, Naqvi T, Parshad S, Hansen VL, Ahmed M, Steen PD, Badarinath S, Dekker A, Scouros MA, Young DE, Graydon Harker W, Kendall SD, Citron ML, Chedid S, Posada JG, Gupta MK, Rafiyath S, Buechler-Price J, Sreenivasappa S, Chay CH, Burke JM, Young SE, Mahmood A, Kugler JW, Gerstner G, Fuloria J, Belman ND, Geller R, Nieva J, Whittenberger BP, Wong BMY, Cescon TP, Abesada-Terk G, Guarino MJ, Zweibach A, Ibrahim EN, Takahashi G, Garrison MA, Mowat RB, Choi BS, Oliff IA, Singh J, Guter KA, Ayrons K, Rowland KM, Noga SJ, Rao SB, Columbie A, Nualart MT, Cecchi GR, Campos LT, Mohebtash M, Flores MR, Rothstein-Rubin R, O'Connor BM, Soori G, Knapp M, Miranda FG, Goodgame BW, Kassem M, Belani R, Sharma S, Ortiz T, Sonneborn HL, Markowitz AB, Wilbur D, Meiri E, Koo VS, Jhangiani HS, Wong L, Sanani S, Lawrence SJ, Jones CM, Murray C, Papageorgiou C, Gurtler JS, Ascensao JL, Seetalarom K, Venigalla ML, D'Andrea M, De Las Casas C, Haile DJ, Qazi FU, Santander JL, Thomas MR, Rao VP, Craig M, Garg RJ, Robles R, Lyons RM, Stegemoller RK, Goel S, Garg S, Lowry P, Lynch C, Lash B, Repka T, Baker J, Goueli BS, Campbell TC, Van Echo DA, Lee YJ, Reyes EA, Senecal FM, Donnelly G, Byeff P, Weiss R, Reid T, Roeland E, Goel A, Prow DM, Brandt DS, Kaplan HG, Payne JE, Boeckh MG, Rosen PJ, Mena RR, Khan R, Betts RF, Sharp SA, Morrison VA, Fitz-Patrick D, Congdon J, Erickson N, Abbasi R, Henderson S, Mehdi A, Wos EJ, Rehmus E, Beltzer L, Tamayo RA, Mahmood T, Reboli AC, Moore A, Brown JM, Cruz J, Quick DP, Potz JL, Kotz KW, Hutchins M, Chowhan NM, Devabhaktuni YD, Braly P, Berenguer RA, Shambaugh SC, O'Rourke TJ, Conkright WA, Winkler CF, Addo FEK, Duic JP, High KP, Kutner ME, Collins R, Carrizosa DR, Perry DJ, Kailath E, Rosen N, Sotolongo R, Shoham S, Chen T. Safety and efficacy of inactivated varicella zoster virus vaccine in immunocompromised patients with malignancies: a two-arm, randomised, double-blind, phase 3 trial. The Lancet Infectious Diseases 2019; 19:1001-1012. [DOI: 10.1016/s1473-3099(19)30310-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 12/25/2022]
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Kröpil P, Rojas CA, Ghoshhajra B, Lanzman RS, Miese FR, Scherer A, Antoch G, Abbara S. Prospektiv EKG-getriggerter “high pitch Modus“ zur kardialen CT-Angiographie in der klinischen Routine: Initiale Ergebnisse. ROFO-FORTSCHR RONTG 2011. [DOI: 10.1055/s-0031-1279486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Rojas CA, Vermess D, Bertozzi JC, Whitlow J, Guidi C, Martinez CR. Normal thickness and appearance of the prevertebral soft tissues on multidetector CT. AJNR Am J Neuroradiol 2008; 30:136-41. [PMID: 19001541 DOI: 10.3174/ajnr.a1307] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Analysis of the prevertebral soft tissue (PVST) is helpful in detecting osseous and ligamentous injuries of the cervical spine. Because the standard of care has shifted from radiographs to multidetector CT (MDCT), a re-examination of the PVST on MDCT images is needed to establish normal values for thickness appropriate for this imaging technique. MATERIALS AND METHODS Thickness of the PVST was measured in 192 patients undergoing screening cervical spine MDCT with multiplanar reconstructions as part of a trauma protocol. Patients included in the study were not intubated, had an immobilized cervical spine, had normal findings on cervical spine CT, and did not have a diagnosis of osseous or soft-tissue cervical injury. Exclusion criteria included patients with a congenital or acquired (nondegenerative) abnormality of the cervical spine or PVST. RESULTS The upper limits of normal for the thickness of the PVST were 8.5 mm at C1, 6 mm at C2, 7 mm at C3, 18 mm at C6, and 18 mm at C7. The upper limit of normal was not determined for C4 and C5 levels due to variable position of the esophagus and larynx. The smallest variability and calculated SDs were found at C2 and C3. CONCLUSIONS The thickness of the PVST is important in the detection of underlying injuries to the cervical spine. We propose the obtained values as the upper limits of normal for PVST thickness on MDCT images in the adult population.
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Affiliation(s)
- C A Rojas
- Department of Radiology, University of South Florida College of Medicine, Tampa, FL33611, USA.
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Abstract
BACKGROUND AND PURPOSE As the standard of care for the evaluation of the cervical spine shifts from plain radiographs to multidetector row CT (MDCT), a re-examination of the normal anatomic relationships of the occipitovertebral articulations is needed. We aimed to define the normal anatomic relationships of craniocervical articulations on MDCT and address any discrepancies with currently accepted ranges of normal on plain radiographs. MATERIALS AND METHODS A total of 200 patients underwent an MDCT scan of the cervical spine with multiplanar reconstructions (MPR). We measured the basion-axial interval (BAI), basion-dens interval (BDI), Powers ratio, atlantodental interval (ADI), and atlanto-occipital interval (AOI) in each patient. After statistical analysis, we compared these values to previously accepted data on plain radiographs. RESULTS Ninety-five percent of the population was found to have a BDI less than 8.5 mm compared with 12 mm on data from plain radiographs. The Powers ratio demonstrated no significant difference compared with data obtained by plain radiographs. Ninety-five percent of the population was found to have an ADI less than 2 mm, compared with 3 mm previously accepted. The AOI demonstrated 95% of the population ranged between 0.5 mm and 1.4 mm. The BAI was difficult to reproduce on CT images. CONCLUSION Normal values for the craniocervical relationships on MDCT are significantly different from the accepted ranges of normal on plain radiographs. We propose these values as normal for the adult population.
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Affiliation(s)
- C A Rojas
- University of South Florida College of Medicine, Tampa, FL, USA.
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Abstract
A study was conducted during 1996-1997 in 20 villages of Tumaco, Colombia, to evaluate the effectiveness of personal protective measures against cutaneous leishmaniasis (CL). The intervention was effective, but the high costs of the preventive measures and the lack of a more holistic approach hampered the intervention's sustainability. This paper analyzes the results using an ecosystem approach to human health. Using this approach, we found that CL has been present in the study area for a long time and affects farmers and those living closest to the forest. The forest constitutes the habitat for insect vectors (sandflies) and parasite reservoirs (wild mammals). Four spatial scales were identified in this ecosystem: residential, village, regional, and global. From the ecosystem perspective, three interventions are proposed to prevent CL in the 20 villages: improve housing construction, organize village housing in clusters, and make diagnosis and treatment of CL more accessible. The design and implementation of these interventions require active involvement by people with the disease (village inhabitants) and decision-makers (local authorities).
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Affiliation(s)
- C A Rojas
- Centro Internacional de Entrenamiento e Investigaciones Médicas, Cali, Colombia.
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Alexander B, Cadena H, Usma MC, Rojas CA. Laboratory and field evaluations of a repellent soap containing diethyl toluamide (DEET) and permethrin against phlebotomine sand flies (Diptera: Psychodidae) in Valle del Cauca, Colombia. Am J Trop Med Hyg 1995; 52:169-73. [PMID: 7872447 DOI: 10.4269/ajtmh.1995.52.169] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [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] [Indexed: 01/27/2023] Open
Abstract
The repellency and insecticidal efficacy of Nopikex, a soap formulation containing 20% diethyl toluamide and 0.5% permethrin, was evaluated against a laboratory colony of phlebotomine sand flies (Lutzomyia longipalpis). The repellency of Nopikex soap was also compared with that of a placebo soap against another species (Lu. youngi) in a forest near Tulua, Valle del Cauca, Colombia. In laboratory trials of the soap, no reduction in repellency was seen 4 hr after application, but within 8 hr, repellency decreased significantly to 67.0% of the initial value (P < 0.05) based on calculations of the coefficient of protection (CP). Under field conditions, the soap gave up to 100% protection immediately after application, but within 4 hours its CP value had decreased to a median value of only 44.3%. The placebo soap was also found to be somewhat repellent when compared with no treatment, giving a median CP value of 67.7 immediately after application. No significant mortality was seen in sand flies within 24 hr of exposure to the soap in the laboratory, even in those that had fed on protected volunteers.
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Affiliation(s)
- B Alexander
- Fundacion Centro Internacional de Entrenamiento e Investigaciones Medicas, Cali, Colombia
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