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Dungan AM, Thomas JL. Fecal bacterial communities of the platypus (Ornithorhynchus anatinus) reflect captivity status-Implications for conservation and management. Integr Zool 2024. [PMID: 39075976 DOI: 10.1111/1749-4877.12865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
The duck-billed platypus (Ornithorhynchus anatinus) is currently listed as near-threatened. A key part of the conservation strategy for this species is its captive maintenance; however, captive animals often have dysbiotic gut bacterial microbiomes. Here, for the first time, we characterize the gut microbiome of wild platypus via fecal samples using high-throughput sequencing of the bacterial 16S rRNA gene and identify microbial biomarkers of captivity in this species. At the phylum level, Firmicutes (50.4%) predominated among all platypuses, followed by Proteobacteria (28.7%), Fusobacteria (13.4%), and Bacteroidota (6.9%), with 21 "core" bacteria identified. Captive individuals did not differ in their microbial α-diversity compared to wild platypus but had significantly different community composition (β-diversity) and exhibited higher abundances of Enterococcus, which are potential pathogenic bacteria. Four taxa were identified as biomarkers of wild platypus, including Rickettsiella, Epulopiscium, Clostridium, and Cetobacterium. This contrast in gut microbiome composition between wild and captive platypus is an essential insight for guiding conservation management, as the rewilding of captive animal microbiomes is a new and emerging tool to improve captive animal health, maximize captive breeding efforts, and give reintroduced or translocated animals the best chance of survival.
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Affiliation(s)
- Ashley M Dungan
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
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2
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Paar J, Willis JR, Sette L, Wood SA, Bogomolni A, Dulac M, Sivaganesan M, Shanks OC. Occurrence of recreational water quality monitoring general fecal indicator bacteria and fecal source identification genetic markers in gray seal scat. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 934:173220. [PMID: 38761521 DOI: 10.1016/j.scitotenv.2024.173220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 05/11/2024] [Accepted: 05/11/2024] [Indexed: 05/20/2024]
Abstract
The number of gray seals (Halichoerus grypus) observed along the United States Northwest Atlantic region has been increasing for decades. These colonial animals often haul-out on beaches seasonally in numbers ranging from a few individuals to several thousands. While these larger aggregations are an important part of gray seal behavior, there is public concern that haul-outs could lead to large amounts of fecal waste in recreational areas, potentially resulting in beach closures. Yet, data to confirm whether these animals contribute to beach closures is lacking and minimal information is available on the occurrence of key water quality monitoring genetic markers in gray seal scat. This study evaluates the concentration of E. coli (EC23S857), enterococci (Entero1a), and fecal Bacteroidetes (GenBac3) as well as six fecal source identification genetic markers (HF183/BacR287, HumM2, CPQ_056, Rum2Bac, DG3, and GFD) measured by qPCR in 48 wild gray seal scat samples collected from two haul-out areas in Cape Cod (Massachusetts, U.S.A.). Findings indicate that FIB genetic markers are shed in gray seal scat at significantly different concentrations with the Entero1a genetic marker exhibiting the lowest average concentration (-0.73 log10 estimated mean copies per nanogram of DNA). In addition, systematic testing of scat samples demonstrated that qPCR assays targeting host-associated genetic markers indicative of human, ruminant, and canine fecal pollution sources remain highly specific in waters frequented by gray seals (>97 % specificity).
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Affiliation(s)
- Jack Paar
- U.S. Environmental Protection Agency, New England Regional Laboratory, North Chelmsford, MA 01863, USA
| | - Jessica R Willis
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Cincinnati, OH 45268, USA
| | - Lisa Sette
- Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Stephanie A Wood
- University of Massachusetts, Boston, Biology Department, 100 Morrissey Blvd., Boston, MA 02125, USA
| | - Andrea Bogomolni
- Massachusetts Maritime Academy, Marine Science, Safety and Environmental Protection, 101 Academy Drive, Buzzards Bay, MA 02532, USA
| | - Monique Dulac
- U.S. Environmental Protection Agency, New England Regional Laboratory, North Chelmsford, MA 01863, USA
| | - Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Cincinnati, OH 45268, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Cincinnati, OH 45268, USA.
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3
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Kalvaitienė G, Picazo Espinosa R, Vaičiūtė D, Kataržytė M. Diverse sources of fecal contamination in macroalgae wrack-affected environment adjacent to river outflow along the Baltic Sea coast. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 357:124429. [PMID: 38925212 DOI: 10.1016/j.envpol.2024.124429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 06/21/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024]
Abstract
We investigated the dynamics of feces-associated microorganisms in areas with wrack accumulation in the southeastern part of the Baltic Sea. Our study covered single-day (2021 ) and multi-day (2022) observations during the recreational season. We collected water, sand, and wrack samples and assessed the abundance of fecal indicator bacteria (FIB), as well metagenomic analysis was conducted to monitor changes in microbial composition. Based on metagenomic data we identified taxa associated with feces, sewage, and ruminant sources. Human-related fecal pollution based on genetic markers correlated with the presence of Lachnospiraceae, Prevotellaceae and Rickenellacea abundance. Higher abundance and diversity of feces-associated and ruminant-associated taxa and the presence of enteric pathogens were observed when wrack accumulated near the river outflow in 2021, suggesting a potential link with fecal pollution from the river. As a preventive measure, it is recommended to remove the wrack to reduce the risk of exposure to potential enteric pathogens if it is accumulated next to the river outflow.
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Affiliation(s)
- Greta Kalvaitienė
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
| | - Rafael Picazo Espinosa
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
| | - Diana Vaičiūtė
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
| | - Marija Kataržytė
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
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4
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Kalvaitienė G, Bučas M, Vaičiūtė D, Balčiūnas A, Gyraitė G, Kataržytė M. Impact of beach wrack on microorganisms associated with faecal pollution at the Baltic Sea Sandy beaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170442. [PMID: 38278231 DOI: 10.1016/j.scitotenv.2024.170442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/21/2023] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
We investigated whether higher quantities of faecal indicator bacteria (FIB) are in the areas with red algae-dominated wrack compared to areas without it and if the birds are the primary source of faecal pollution on sandy beaches of the Baltic Sea. Water, sand and wrack samples were collected during the recreational season, and abundances of FIB, HF183 (human faecal pollution) and GFD (bird faecal pollution) markers, as well as the presence of Salmonella and Campylobacter, were assessed. Significantly higher levels of Enterococcus spp. were found in the wrack accumulation areas in water and sand than in the areas without wrack when there was a faecal pollution event, which could be explained by entrapment and changed physico-chemical water conditions. Both faecal pollution markers were identified, however, with no apparent pattern. Campylobacter bacteria were identified in the wrack-affected water, sand, and beach wrack. While this research provides valuable insights into beach wrack serving as a reservoir for FIB, further investigations, including multi-day samplings, are necessary to gain a deeper understanding of the long-term dynamics of microbiota within red algae-dominated wrack.
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Affiliation(s)
- Greta Kalvaitienė
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
| | - Martynas Bučas
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
| | - Diana Vaičiūtė
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
| | - Arūnas Balčiūnas
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
| | - Greta Gyraitė
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
| | - Marija Kataržytė
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
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5
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Vanderzalm J, Currie S, Smith W, Metcalfe S, Taylor N, Ahmed W. Microbial source tracking of fecal pollution to coral reef lagoons of Norfolk Island, Australia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168906. [PMID: 38016554 DOI: 10.1016/j.scitotenv.2023.168906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 11/30/2023]
Abstract
Fecal pollution contributes to global degradation of water quality and requires identification of the source(s) for predicting human health risk, tracking disease, and developing management strategies. While fecal indicator bacteria are commonly used to detect fecal pollution, they cannot identify sources. Novel approaches, such as microbial source tracking (MST), can be applied to evaluate the origin of fecal pollution. This study examined fecal pollution in the coral reef lagoons of Norfolk Island, Australia where reef health decline has been related to nutrient input. The primary objective of this study was to evaluate the host sensitivity and specificity of two human wastewater-associated marker genes (Bacteroides HF183 (HF183) and cross-assembly phage (crAssphage)) and four animal feces associated marker genes targeting avian, ruminant, dog, and pig (Helicobacter-associated GFD (GFD), Bacteroides BacR (BacR), Bacteroides DogBact (DogBact), and Bacteroides Pig-2-Bac (Pig-2-Bac)) in wastewater and animal fecal samples collected from Norfolk Island. The prevalence and concentrations of these marker genes along with enterococci genetic marker (ENT 23S rRNA) of general fecal pollution and human adenovirus (HAdV), which is considered predominantly a pathogen but also a human-wastewater associated marker gene, were determined in surface, ground, and marine water resources. A secondary objective of this study was to assess the sources and pathways of fecal pollution to a sensitive marine environment under rainfall events. HF183, crAssphage, HAdV, and BacR demonstrated absolute host sensitivity values of 1.00, while GFD and Pig-2-Bac had host sensitivity values of 0.60, and 0.20, respectively. Host specificity values were > 0.94 for all marker genes. Human and animal (avian, ruminant, dog) fecal sources were present in the coral reef lagoons and surface water whereas groundwater was polluted by human wastewater markers. This study provides understanding of fecal pollution in water resources on Norfolk Island, Australia after precipitation events. The results may aid in effective water quality management, mitigating potential adverse effects on both human and environmental health.
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Affiliation(s)
- Joanne Vanderzalm
- CSIRO Environment, Waite Campus, Waite Rd, Urrbrae, SA 5064, Australia.
| | - Sharon Currie
- CSIRO Environment, Waite Campus, Waite Rd, Urrbrae, SA 5064, Australia
| | - Wendy Smith
- CSIRO Environment, Ecosciences Precint, 41 Boggo Road, Dutton Park, QLD 4202, Australia
| | - Suzanne Metcalfe
- CSIRO Environment, Ecosciences Precint, 41 Boggo Road, Dutton Park, QLD 4202, Australia
| | - Nathan Taylor
- Norfolk Island Water Resource Assessment Team, Kingston, Norfolk Island
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precint, 41 Boggo Road, Dutton Park, QLD 4202, Australia
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Gao M, Tan F, Shen Y, Peng Y. Rapid detection method of bacterial pathogens in surface waters and a new risk indicator for water pathogenic pollution. Sci Rep 2024; 14:1614. [PMID: 38238351 PMCID: PMC10796392 DOI: 10.1038/s41598-023-49774-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 12/12/2023] [Indexed: 01/22/2024] Open
Abstract
In this study, a accurate, rapid quantitative PCR method for the simultaneous detection of 4 kinds of pathogenic bacteria in water was established, and the distribution of pathogenic bacteria in surface waters with different levels of pollution (Yulin region, China) was detected. The results showed that the detection accuracy was 94%; the detection limit was 2.7 in bacterial cells. Salmonella enterica subsp. enterica serovar typhimurium and Salmonella dysenteria were always present in water when the universal primer for pathogenic bacteria abundance detection was greater than 104 copies 100 mL-1. When the detection value is lower than 104 copy 100 mL-1, the bacteria in the water are rarely pathogenic bacteria, so the detection value of 104 copy 100 mL-1 can be used as a new indicator of waterborne pathogen pollution.
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Affiliation(s)
- Min Gao
- College of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Xi'an Polytechnic University, Xi'an, 710000, People's Republic of China.
| | - Feiyang Tan
- College of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Xi'an Polytechnic University, Xi'an, 710000, People's Republic of China
| | - Yuan Shen
- College of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Xi'an Polytechnic University, Xi'an, 710000, People's Republic of China
| | - Yao Peng
- College of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Xi'an Polytechnic University, Xi'an, 710000, People's Republic of China
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Ramírez AS, Poveda JB, Dijkman R, Poveda C, Suárez-Pérez A, Rosales RS, Feberwee A, Szostak MP, Ressel L, Viver T, Calabuig P, Catania S, Gobbo F, Timofte D, Spergser J. Mycoplasma bradburyae sp. nov. isolated from the trachea of sea birds. Syst Appl Microbiol 2023; 46:126472. [PMID: 37839385 DOI: 10.1016/j.syapm.2023.126472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 10/17/2023]
Abstract
In the search for mollicutes in wild birds, six Mycoplasma strains were isolated from tracheal swabs taken from four different species of seabirds. Four strains originated from three Yellow-legged gulls (Larus michahellis) and a Cory's shearwater (Calonectris borealis) from Spain, one from a South African Kelp gull (Larus dominicanus), and one from an Italian Black-headed gull (Chroicocephalus ridibundus). These Mycoplasma strains presented 99 % 16S rRNA gene sequence similarity values with Mycoplasma (M.) gallisepticum. Phylogenetic analyses of marker genes (16S rRNA gene and rpoB) confirmed the close relationship of the strains to M. gallisepticum and M. tullyi. The seabirds' strains grew well in modified Hayflick medium, and colonies showed typical fried egg morphology. They produced acid from glucose and mannose but did not hydrolyze arginine or urea. Transmission electron microscopy revealed a cell morphology characteristic of mycoplasmas, presenting spherical to flask-shaped cells with an attachment organelle. Gliding motility was also observed. Furthermore, serological tests, MALDI-ToF mass spectrometry and genomic studies demonstrated that the strains were different to any known Mycoplasma species, for which the name Mycoplasma bradburyae sp. nov. is proposed; the type strain is T158T (DSM 110708 = NCTC 14398).
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Affiliation(s)
- Ana S Ramírez
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - José B Poveda
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain.
| | - Remco Dijkman
- GD Animal Health, Arnsbergstraat 7, 7418 EZ, Deventer, the Netherlands
| | - Carlos Poveda
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Alejandro Suárez-Pérez
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Rubén S Rosales
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Anneke Feberwee
- GD Animal Health, Arnsbergstraat 7, 7418 EZ, Deventer, the Netherlands
| | - Michael P Szostak
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Lorenzo Ressel
- University of Liverpool, Institute of Veterinary Science, Leahurst Campus, Neston CH64 7TE, UK
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), 07190, Esporles, Spain
| | - Pascual Calabuig
- Centro de Recuperación de Fauna Silvestre, Cabildo de Gran Canaria, Spain
| | - Salvatore Catania
- Mycoplasma Unit - SCT1-Verona, WOAH Reference Laboratory for Avian Mycoplasmosis, Istituto Zooprofilattico Sperimentale delle Venezie, 37060 Buttapietra (VR), Italy
| | - Federica Gobbo
- Mycoplasma Unit - SCT1-Verona, WOAH Reference Laboratory for Avian Mycoplasmosis, Istituto Zooprofilattico Sperimentale delle Venezie, 37060 Buttapietra (VR), Italy
| | - Dorina Timofte
- University of Liverpool, Institute of Veterinary Science, Leahurst Campus, Neston CH64 7TE, UK
| | - Joachim Spergser
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
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8
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Tournayre O, Wolfe R, McCurdy-Adams H, Chabot AA, Lougheed SC. A species-specific digital PCR assay for the endangered blue racer ( Coluber constrictor foxii) in Canada. Genome 2023; 66:251-260. [PMID: 37270848 DOI: 10.1139/gen-2023-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The only population of the endangered blue racer (Coluber constrictor foxii) in Canada occurs on Pelee Island, Ontario. The species is threatened by multiple factors, including habitat degradation and loss, road mortality, persecution, and potentially predation. We designed and evaluated the performance of an environmental DNA droplet digital PCR assay that can be used for multiple facets of conservation of this species. We tested the assay in silico and in vitro using DNA of blue racers and co-occurring snake species and estimated the LOD and LOQ using synthetic DNA. As wild turkey predation has been suggested to negatively affect racers, we tested the assay on eight wild turkey faecal samples. Our assay is specific, can detect the target species at very low levels of concentration (0.002 copies/µL), and can accurately quantify copy numbers ≥ 0.26 copies/µL. We detected no racer DNA in any wild turkey faecal sample. More faecal samples collected at strategic locations during snake peak activity on Pelee Island would enable a more thorough assessment of the possibility of turkey predation. Our assay should be effective for other environmental samples and can be used for investigating other factors negatively affecting blue racers, for example, helping to quantify blue racer habitat suitability and site occupancy.
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Affiliation(s)
- Orianne Tournayre
- Biology Department, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Ryan Wolfe
- Natural Resource Solutions Inc., Waterloo, ON N2L 3X2, Canada
| | | | - Amy A Chabot
- African Lion Safari, Cambridge, ON N1R 5S2, Canada
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Ferrari ED, Oliveira BCM, Creasey HN, Romualdo da Silva DR, Nakamura AA, Bresciani KDS, Widmer G. The Impact of Physical Effort on the Gut Microbiota of Long-Distance Fliers. Microorganisms 2023; 11:1766. [PMID: 37512938 PMCID: PMC10386721 DOI: 10.3390/microorganisms11071766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/24/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
Flying pigeons (Columbia livia) are extensively studied for their physical endurance and superior sense of orientation. The extreme physical endurance of which these birds are capable creates a unique opportunity to investigate the possible impact of long-distance flying on the taxonomy and metabolic function of the gut microbiota. This project was enabled by access to two groups of pigeons raised by the same breeder in the same conditions, except that one group was trained in long-distance flying and participated in multiple races covering a total distance of over 2600 km over a 9-week period. In contrast, the second group did not fly. The fecal microbiota was analyzed using 16S amplicon sequencing, and the taxonomy and metabolic function were inferred from this sequence data. Based on phylogenetic distance and metabolic function, flying and non-flying pigeons were found to harbor distinct bacterial microbiota. The microbiota taxonomy varied extensively between the birds, whereas the inferred metabolic potential was relatively stable. Age was not a significant determinant of the fecal microbiota profile. In flying birds, the metabolic pathways annotated with biosynthesis were enriched, representing 60% of the 20 metabolic pathways that were most closely associated with flying.
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Affiliation(s)
- Elís Domingos Ferrari
- União das Facultades dos Grandes Lagos (UNILAGO), São José do Rio Preto 15030-070, São Paulo, Brazil
| | | | - Hannah N Creasey
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA
| | - Débora R Romualdo da Silva
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA
- School of Veterinary Medicine, São Paulo State University (UNESP), Araçatuba 16050-680, São Paulo, Brazil
| | - Alex Akira Nakamura
- School of Veterinary Medicine, São Paulo State University (UNESP), Araçatuba 16050-680, São Paulo, Brazil
| | - Katia D Saraiva Bresciani
- School of Veterinary Medicine, São Paulo State University (UNESP), Araçatuba 16050-680, São Paulo, Brazil
| | - Giovanni Widmer
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA
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Tang K, Tao L, Wang Y, Wang Q, Fu C, Chen B, Zhang Z, Fu Y. Temporal Variations in the Gut Microbiota of the Globally Endangered Sichuan Partridge (Arborophila rufipectus): Implications for Adaptation to Seasonal Dietary Change and Conservation. Appl Environ Microbiol 2023; 89:e0074723. [PMID: 37272815 PMCID: PMC10305732 DOI: 10.1128/aem.00747-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/06/2023] Open
Abstract
Host-associated microbiotas are known to influence host health by aiding digestion, metabolism, nutrition, physiology, immune function, and pathogen resistance. Although an increasing number of studies have investigated the avian microbiome, there is a lack of research on the gut microbiotas of wild birds, especially endangered pheasants. Owing to the difficulty of characterizing the dynamics of dietary composition, especially in omnivores, how the gut microbiotas of birds respond to seasonal dietary changes remains poorly understood. The Sichuan partridge (Arborophila rufipectus) is an endangered pheasant species with a small population endemic to the mountains of southwest China. Here, 16S rRNA sequencing and Tax4Fun were used to characterize and compare community structure and functions of the gut microbiota in the Sichuan partridges across three critical periods of their annual life cycle (breeding, postbreeding wandering, and overwintering). We found that the microbial communities were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Cyanobacteria throughout the year. Diversity of the gut microbiotas was highest during postbreeding wandering and lowest during the overwintering periods. Seasonal dietary changes and reassembly of the gut microbial community occurred consistently. Composition, diversity, and functions of the gut microbiota exhibited diet-associated variations, which might facilitate host adaptation to diverse diets in response to environmental shifts. Moreover, 28 potential pathogenic genera were detected, and their composition differed significantly between the three periods. Investigation of the wild bird gut microbiota dynamics has enhanced our understanding of diet-microbiota associations over the annual life cycle of birds, aiding in the integrative conservation of this endangered bird. IMPORTANCE Characterizing the gut microbiotas of wild birds across seasons will shed light on their annual life cycle. Due to sampling difficulties and the lack of detailed dietary information, studies on how the gut microbiota adapts to seasonal dietary changes of wild birds are scarce. Based on more detailed dietary composition, we found a seasonal reshaping pattern of the gut microbiota of Sichuan partridges corresponding to their seasonal dietary changes. The variation in diet and gut microbiota potentially facilitated the diversity of dietary niches of this endangered pheasant, revealing a seasonal diet-microbiota association across the three periods of the annual cycle. In addition, identifying a variety of potentially pathogenic bacterial genera aids in managing the health and improving survival of Sichuan partridges. Incorporation of microbiome research in the conservation of endangered species contributes to our comprehensive understanding the diet-host-microbiota relationship in wild birds and refinement of conservation practices.
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Affiliation(s)
- Keyi Tang
- Ministry of Education Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Ling Tao
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yufeng Wang
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Qiong Wang
- Ministry of Education Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Changkun Fu
- Ministry of Education Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Benping Chen
- Laojunshan National Nature Reserve Administration, Pingshan, Sichuan, China
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yiqiang Fu
- Ministry of Education Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
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11
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Herder EA, Skeen HR, Lutz HL, Hird SM. Body Size Poorly Predicts Host-Associated Microbial Diversity in Wild Birds. Microbiol Spectr 2023; 11:e0374922. [PMID: 37039681 PMCID: PMC10269867 DOI: 10.1128/spectrum.03749-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/12/2023] [Indexed: 04/12/2023] Open
Abstract
The composition and diversity of avian microbiota are shaped by many factors, including host ecologies and environmental variables. In this study, we examine microbial diversity across 214 bird species sampled in Malawi at five major body sites: blood, buccal cavity, gizzard, intestinal tract, and cloaca. Microbial community dissimilarity differed significantly across body sites. Ecological theory predicts that as area increases, so does diversity. We tested the hypothesis that avian microbiota diversity is correlated with body size, used as a proxy for area, using comparative phylogenetic methods. Using Pagel's lambda, we found that few microbial diversity metrics had significant phylogenetic signals. Phylogenetic generalized least squares identified a significant but weak negative correlation between host size and microbial diversity of the blood and a similarly significant but weakly positive correlation between the cloacal microbiota and host size among birds within the order Passeriformes. Phylosymbiosis, or a congruent branching pattern between host phylogeny and their associated microbiota similarity, was tested and found to be weak or not significant in four of the body sites with sufficient sample size (blood, buccal, cloaca, and intestines). Taken together, these results suggest that the avian microbiome is highly variable, with microbiota diversity demonstrating few clear associations with bird size. Finally, the blood microbiota have a unique relationship with host size. IMPORTANCE All animals coexist and interact with microorganisms, including bacteria, archaea, microscopic eukaryotes, and viruses. These microorganisms can have an enormous influence on the biology and health of macro-organisms. However, the general rules that govern these host-associated microbial communities are poorly described, especially in wild animals. In this paper, we investigate the microbial communities of over 200 species of birds from Malawi and characterize five body site bacterial microbiota in depth. Because the evolutionary relationships of the host underlie the relationship between any host-associated microbiota relationships, we use phylogenetic comparative methods to account for this relationship. We find that the size of a host (the bird) and the diversity and composition of the microbiota are largely uncorrelated. We also find that the general pattern of similarity between host phylogeny and microbiota similarity is weak. Together, we see that bird microbiota are not strongly tied to host size or evolutionary history.
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Affiliation(s)
- Elizabeth A. Herder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Heather R. Skeen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Holly L. Lutz
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
- Department of Pediatrics, UC San Diego School of Medicine, La Jolla, California, USA
| | - Sarah M. Hird
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
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12
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Devane ML, Taylor W, Dupont PY, Armstrong B, Weaver L, Gilpin BJ. Exploring the Bacterial Community in Aged Fecal Sources from Dairy Cows: Impacts on Fecal Source Tracking. Microorganisms 2023; 11:1161. [PMID: 37317135 DOI: 10.3390/microorganisms11051161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 06/16/2023] Open
Abstract
(1) Background: This paper discusses the impact of agricultural activities on stream health, particularly in relation to dairy cow fecal pollution. The study explores the fecal microbiome of cattle and the potential ecological implications of aging fecal pollution on waterways. (2) Methods: The study examines changes in the bacterial community available for mobilization from in-situ decomposing cowpats and the effects of simulated rainfall. The microbiome of individual cowpats was monitored over 5.5 months. We used 16S rRNA metagenomics and machine learning software, FEAST (Fast Expectation-mAximization for microbial Source Tracking), for bacterial and fecal source assignments. (3) Results: The phyla Bacillota and Bacteroidota are dominant in the fecal microbiota of fresh cow feces but shift to Pseudomonodota, Actinomycetota, and environmental Bacteroidota in aged cowpats. Potential impacts of these bacterial community shifts on inputs to local agricultural streams are discussed in relation to water quality monitoring and aging sources of fecal contamination. We identified taxon orders that are potential indicators of fresh cattle sources (Oscillospirales and Bacteroidales) and aged sources (Peptostreptococcales-Tissierellales) in water bodies. (4) The paper highlights that bacterial metagenomic profiling can inform our understanding of the ecology of microbial communities in aquatic environments and the potential impacts of agricultural activities on ecosystem health.
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Affiliation(s)
- Megan L Devane
- Health and Environment Group, Institute of Environmental Science and Research, Christchurch 8041, New Zealand
| | - William Taylor
- Health and Environment Group, Institute of Environmental Science and Research, Christchurch 8041, New Zealand
| | - Pierre-Yves Dupont
- Health and Environment Group, Institute of Environmental Science and Research, Christchurch 8041, New Zealand
| | - Bridget Armstrong
- Health and Environment Group, Institute of Environmental Science and Research, Christchurch 8041, New Zealand
| | - Louise Weaver
- Health and Environment Group, Institute of Environmental Science and Research, Christchurch 8041, New Zealand
| | - Brent J Gilpin
- Health and Environment Group, Institute of Environmental Science and Research, Christchurch 8041, New Zealand
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Ríos-Castro R, Cabo A, Teira E, Cameselle C, Gouveia S, Payo P, Novoa B, Figueras A. High-throughput sequencing as a tool for monitoring prokaryote communities in a wastewater treatment plant. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 861:160531. [PMID: 36470389 DOI: 10.1016/j.scitotenv.2022.160531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
In this study, the DNA metabarcoding technique was used to explore the prokaryote diversity and community structure in wastewater collected in spring and winter 2020-2021 as well as the efficiency of the treatment in a wastewater treatment plant (WWTP) in Ría de Vigo (NW Spain). The samplings included raw wastewater from the inlet stream (M1), the discharge water after the disinfection treatment (M3) and mussels used as bioindicators of possible contamination of the marine environment. Significant differences were discovered in the microbiome of each type of sample (M1, M3 and mussels), with 92 %, 45 % and 44 % of exclusive OTUs found in mussel, M3 and M1 samples respectively. Seasonal differences were also detected in wastewater samples, with which abiotic parameters (temperature, pH) could be strongly involved. Bacteria present in raw wastewater (M1) were associated with the human gut microbiome, and therefore, potential pathogens that could be circulating in the population in specific periods were detected (e.g., Arcobacter sp. and Clostridium sp.). A considerable decrease in putative pathogenic organisms from the M1 to M3 wastewater fractions and the scarce presence in mussels (<0.5 % total reads) confirmed the effectiveness of pathogen removal in the wastewater treatment plant. Our results showed the potential of the DNA metabarcoding technique for monitoring studies and confirmed its application in wastewater-based epidemiology (WBE) and environmental contamination studies. Although this technique cannot determine if the infective pathogens are present, it can characterize the microbial communities and the putative pathogens that are circulating through the population (microbiome of M1) and also confirm the efficacy of depuration treatment, which can directly affect the aquaculture sector and even human and veterinary health.
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Affiliation(s)
- Raquel Ríos-Castro
- Marine Research Institute IIM-CSIC, Spanish National Research Council, Eduardo Cabello 6, 36208 Vigo, Spain.
| | - Adrián Cabo
- University of Vigo, BiotecnIA Group, Department of Chemical Engineering, 36310 Vigo, Spain.
| | - Eva Teira
- University of Vigo, Departamento de Ecología y Biología Animal, Centro de Investigación Marina (CIM), Universidad de Vigo, Facultad de Ciencias do Mar, 36310 Vigo, Spain.
| | - Claudio Cameselle
- University of Vigo, BiotecnIA Group, Department of Chemical Engineering, 36310 Vigo, Spain
| | - Susana Gouveia
- University of Vigo, BiotecnIA Group, Department of Chemical Engineering, 36310 Vigo, Spain
| | - Pedro Payo
- GESECO Aguas S.A., Teixugueiras 13, 36212 Vigo, Spain.
| | - Beatriz Novoa
- Marine Research Institute IIM-CSIC, Spanish National Research Council, Eduardo Cabello 6, 36208 Vigo, Spain.
| | - Antonio Figueras
- Marine Research Institute IIM-CSIC, Spanish National Research Council, Eduardo Cabello 6, 36208 Vigo, Spain.
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García-Amado MA, Rudolf CA, Fuentes-Fuentes MDM, Chorna N, Martínez LM, Godoy-Vitorino F. Bacterial composition along the digestive tract of the Horned Screamer ( Anhima cornuta), a tropical herbivorous bird. PeerJ 2023; 11:e14805. [PMID: 36815987 PMCID: PMC9933741 DOI: 10.7717/peerj.14805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/05/2023] [Indexed: 02/15/2023] Open
Abstract
Background The Horned Screamer (Anhima cornuta) is an herbivorous bird that inhabits wetlands of the South American tropical region. We hypothesize that due to its herbivorous niche, its digestive tract compartments may have bacteria specialized in fermenting complex plant carbohydrates. To test this hypothesis, we compared the bacterial communities along the gastrointestinal tract (GIT) of a Horned Screamer captured in Venezuela. Methods Samples were taken from tissues and content of the proventriculus and the small intestine (considered for this study as upper GIT), and the large intestine and cecum (lower GIT). The bacterial community was characterized by sequencing the V4 region of the 16S rRNA gene. Bioinformatic analysis was performed using QIIME, QIITA and Microbiome Analyst. The association between microbial taxonomy and function was analyzed using their Greengenes OTU IDs and a custom KEGG BRITE hierarchical tree and visualized with BURRITO. Results The Screamer's gastrointestinal microbiota was composed by seven phyla being Firmicutes and Bacteroidetes the most predominant. The dominant taxa in the upper GIT were Helicobacter, Vibrio, Enterobacter, Acinetobacter and Staphylococcus. The dominant taxa in the lower GIT were Oribacterium, Blautia, Roseburia, Ruminococcus, Desulfovibrio, Intestinimonas, Marvinbryantia and Parabacteroides. Complete degradation of cellulose to the end-products acetate, propanoate, butanoate and acetoacetate was found in the upper and lower GIT without significant differences. Conclusion Our study confirmed changes in bacterial community composition throughout the GIT of the Horned Screamer primarily associated with the production of metabolic end-products of carbohydrate digestion essential for the fermentation of the herbivorous diet.
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Affiliation(s)
- María Alexandra García-Amado
- Laboratorio de Fisiología Gastrointestinal, Centro de Biofísica y Bioquímica, Instituto Venezolano de Investigaciones Científicas, Miranda, Venezuela
| | - Carla A. Rudolf
- Laboratorio de Fisiología Gastrointestinal, Centro de Biofísica y Bioquímica, Instituto Venezolano de Investigaciones Científicas, Miranda, Venezuela
| | | | - Nataliya Chorna
- Biochemistry Department, University of Puerto Rico School of Medicine, San Juan, PR, Puerto Rico
| | | | - Filipa Godoy-Vitorino
- Microbiology Department, University of Puerto Rico, School of Medicine, San Juan, Puerto Rico
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Gallet A, Yao EK, Foucault P, Bernard C, Quiblier C, Humbert JF, Coulibaly JK, Troussellier M, Marie B, Duperron S. Fish gut-associated bacterial communities in a tropical lagoon (Aghien lagoon, Ivory Coast). Front Microbiol 2022; 13:963456. [PMID: 36246274 PMCID: PMC9556852 DOI: 10.3389/fmicb.2022.963456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Aghien lagoon (Ivory Coast) is a eutrophic freshwater lagoon that harbors high biomasses of phytoplankton. Despite Increasing interest in fish gut microbiomes diversity and functions, little data is currently available regarding wild species from tropical west African lakes. Here, gut-associated bacterial communities are investigated in four fish species that are consumed by locale populations, namely the Cichlidae Hemichromis fasciatus, Tilapia guineensis and Sarotherodon melanotheron, and the Claroteidae Chrysichthys nigrodigitatus. Species-related differences are identified, that can be attributed to host phylogeny and diet. Important variations throughout the year are observed in T. guineensis and C. nigrodigitatus. This result emphasized the importance of time-series sampling and comparison with environmental variables even in tropical regions, that are not often conducted in wild populations. Effects of environmental factors (anthropogenic or not) on the microbiota and potential outcomes for fish health and populations sustainability need to be further explored. Interestingly, fish appear as major reservoirs of bacterial diversity, suggesting that they could contribute to the overall stability and resilience of bacterial communities present in the Aghien lagoon.
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Affiliation(s)
- Alison Gallet
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Eric Kouamé Yao
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
- Institut Pasteur de Côte d’Ivoire, Abidjan, Côte d’Ivoire
| | - Pierre Foucault
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Cécile Bernard
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Catherine Quiblier
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
- Université Paris Cité, UFR Sciences du Vivant, Paris, France
| | | | | | - Marc Troussellier
- MARBEC, Centre National de la Recherche Scientifique, Université Montpellier, IFREMER, IRD, Montpellier, France
| | - Benjamin Marie
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Sébastien Duperron
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
- *Correspondence: Sébastien Duperron,
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Mahayri TM, Fliegerová KO, Mattiello S, Celozzi S, Mrázek J, Mekadim C, Sechovcová H, Kvasnová S, Atallah E, Moniello G. Host Species Affects Bacterial Evenness, but Not Diversity: Comparison of Fecal Bacteria of Cows and Goats Offered the Same Diet. Animals (Basel) 2022; 12:ani12162011. [PMID: 36009603 PMCID: PMC9404439 DOI: 10.3390/ani12162011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Comparison of bacterial diversity and composition of feces from cows and goats offered the same pasture-based diet revealed that the animal species had no effect on bacterial species richness and diversity, but significantly affected species evenness. Both diet and host species influence the gut microbiome. Abstract The aim of this study was to compare the diversity and composition of fecal bacteria in goats and cows offered the same diet and to evaluate the influence of animal species on the gut microbiome. A total of 17 female goats (Blond Adamellan) and 16 female cows (Brown Swiss) kept on an organic farm were fed pasture and hay. Bacterial structure in feces was examined by high-throughput sequencing using the V4–V5 region of the 16S rRNA gene. The Alpha diversity measurements of the bacterial community showed no statistical differences in species richness and diversity between the two groups of ruminants. However, the Pielou evenness index revealed a significant difference and showed higher species evenness in cows compared to goats. Beta diversity measurements showed statistical dissimilarities and significant clustering of bacterial composition between goats and cows. Firmicutes were the dominant phylum in both goats and cows, followed by Bacteroidetes, Proteobacteria, and Spirochaetes. Linear discriminant analysis with effect size (LEfSe) showed a total of 36 significantly different taxa between goats and cows. Notably, the relative abundance of Ruminococcaceae UCG-005, Christensenellaceae R-7 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-009, Ruminococcaceae UCG-013, Ruminococcaceae UCG-014, Ruminococcus 1, Ruminococcaceae UCG-002, Lachnospiraceae NK4A136 group, Treponema 2, Lachnospiraceae AC2044 group, and Bacillus was higher in goats compared to cows. In contrast, the relative abundance of Turicibacter, Solibacillus, Alloprevotella, Prevotellaceae UCG-001, Negativibacillus, Lachnospiraceae UCG-006, and Eubacterium hallii group was higher in cows compared with goats. Our results suggest that diet shapes the bacterial community in feces, but the host species has a significant impact on community structure, as reflected primarily in the relative abundance of certain taxa.
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Affiliation(s)
- Tiziana Maria Mahayri
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Kateřina Olša Fliegerová
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
- Correspondence: ; Tel.: +420-267-090-504
| | - Silvana Mattiello
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy
| | - Stefania Celozzi
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy
| | - Jakub Mrázek
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
| | - Chahrazed Mekadim
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
| | - Hana Sechovcová
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences in Prague, 16500 Prague, Czech Republic
| | - Simona Kvasnová
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
| | - Elie Atallah
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Giuseppe Moniello
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
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Zengye Decoction Attenuated Severe Acute Pancreatitis Complicated with Acute Kidney Injury by Modulating the Gut Microbiome and Serum Amino Acid Metabolome. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:1588786. [PMID: 35586694 PMCID: PMC9110161 DOI: 10.1155/2022/1588786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/17/2022] [Indexed: 02/05/2023]
Abstract
Objective To explore the effect and underlying mechanism of Zengye decoction (ZYD), a traditional formula from China, on the severe acute pancreatitis (SAP) rat model with acute kidney injury (AKI). Methods The SAP-AKI model was induced by 3.5% sodium taurocholate. Rats were treated with normal saline or ZYD twice and sacrificed at 36 h after modeling. Amylase, lipase, creatinine, blood urea nitrogen, kidney injury molecule 1(KIM-1), and multiple organs' pathological examinations were used to assess the protective effect of ZYD. Gut microbiome detected by 16S rRNA sequencing analysis and serum amino acid metabolome analyzed by liquid chromatography-mass spectrometry explained the underlying mechanism. The Spearman correlation analysis presented the relationship between microflora and metabolites. Results ZYD significantly decreased KIM-1(P < 0.05) and the pathological score of the pancreas (P < 0.05), colon (P < 0.05), and kidney (P < 0.05). Meanwhile, ZYD shifted the overall gut microbial structure (β-diversity, ANOSIM R = 0.14, P=0.025) and altered the microbial compositions. Notably, ZYD reduced the potentially pathogenic bacteria—Bacteroidetes, Clostridiales vadin BB60 group, and uncultured_Clostridiales_bacterium, but promoted the short-chain fatty acid (SCFA) producers—Erysipelotrichaceae, Bifidobacterium, Lactobacillus, and Moryella (all P < 0.05). Moreover, principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA), and hierarchical clustering analysis (HCA) presented a remarkable change in amino acid metabolome after SAP-AKI induction and an apparent regulation by ZYD treatment (R2Y 0.878, P=0.01; Q2 0.531, P=0.01). Spearman's correlation analysis suggested that gut bacteria likely influenced serum metabolites levels (absolute r > 0.4 and FDR P < 0.02). Conclusions ZYD attenuated SAP-AKI by modulating the gut microbiome and serum amino acid metabolome, which may be a promising adjuvant treatment.
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