51
|
Ahasan MS, Waltzek TB, Huerlimann R, Ariel E. Comparative analysis of gut bacterial communities of green turtles (Chelonia mydas) pre-hospitalization and post-rehabilitation by high-throughput sequencing of bacterial 16S rRNA gene. Microbiol Res 2017; 207:91-99. [PMID: 29458874 DOI: 10.1016/j.micres.2017.11.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/30/2017] [Accepted: 11/18/2017] [Indexed: 02/06/2023]
Abstract
Stranded green turtles (Chelonia mydas) are often cared for in rehabilitation centers until they recover. Although the specific causal agents of diseases in stranded turtles are difficult to diagnose, we know that gut microbiota of green turtles play a vital role in health as well as a wide range of diseases. The objective of this study was to characterize and compare the gut bacterial communities between pre-hospitalization (PH) and post-rehabilitation (PR) stranded green turtles using high-throughput sequencing analysis targeting V1-V3 regions of the bacterial 16S rRNA gene. A total of eight cloacal swab samples were collected from four green turtles undergoing rehabilitation. Proteobacteria dominating in both PH and PR samples without any significant difference. Firmicutes was the second and Bacteroidetes was the third most abundant phylum in PH samples, while Bacteroidetes prevailed in PR samples, followed by Firmicutes. The predominance of the genus Bacteroides in both PH and PR samples indicates the importance of this genus in turtle gut health. At a class level, Epsilonproteobacteria was significantly (P<0.05) associated with PH samples and Deltaproteobacteria predominated (P<0.05) in PR samples. The significant abundance of Campylobacter fetus, Escherichia coli, Clostridium botulinum and Vibrio parahaemolyticus in PH samples indicate pathogenic associations with stranded green turtles with zoonotic potential. The presence of Salmonella enterica in only PR samples suggest possible acquisition of this bacteria during rehabilitation. In this study, all post-rehabilitation green turtles exhibited similar bacterial communities, irrespective of their microbial compositions at pre-hospitalization. The marked differences in the gut bacterial communities of PH and PR turtles indicate the outcome of dietary, management and environmental shift during rehabilitation. Therefore, it is important to address the process of restoring normal gut microbiota of recovered turtles prior to release back to their natural habitat.
Collapse
Affiliation(s)
- Md Shamim Ahasan
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, 4811, Qld, Australia.
| | - Thomas B Waltzek
- College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Roger Huerlimann
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, 4811, Qld, Australia
| | - Ellen Ariel
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, 4811, Qld, Australia
| |
Collapse
|
52
|
Analysis of the Microbial Diversity in the Fecal Material of Giraffes. Curr Microbiol 2017; 75:323-327. [PMID: 29085995 DOI: 10.1007/s00284-017-1383-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/24/2017] [Indexed: 10/18/2022]
Abstract
Using bacterial and fungal tag-encoded FLX-Titanium amplicon pyrosequencing, the microbiota of the fecal material of seven giraffes living in captivity at the Jacksonville Zoo and Gardens, Jacksonville, FL was investigated. In all samples, the most predominant bacterial phylum was the Firmicutes followed by Bacteroidetes. The most predominant fungi were members of the phylum Ascomycota followed by Neocallimastigomycota in five of seven samples. The reverse was true in the other two samples.
Collapse
|
53
|
O’ Donnell MM, Harris HMB, Ross RP, O'Toole PW. Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals. Microbiologyopen 2017; 6:e00509. [PMID: 28834331 PMCID: PMC5635170 DOI: 10.1002/mbo3.509] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/22/2017] [Accepted: 05/25/2017] [Indexed: 12/21/2022] Open
Abstract
In this pilot study, we determined the core fecal microbiota composition and overall microbiota diversity of domesticated herbivorous animals of three digestion types: hindgut fermenters, ruminants, and monogastrics. The 42 animals representing 10 animal species were housed on a single farm in Ireland and all the large herbivores consumed similar feed, harmonizing two of the environmental factors that influence the microbiota. Similar to other mammals, the fecal microbiota of all these animals was dominated by the Firmicutes and Bacteroidetes phyla. The fecal microbiota spanning all digestion types comprised 42% of the genera identified. Host phylogeny and, to a lesser extent, digestion type determined the microbiota diversity in these domesticated herbivores. This pilot study forms a platform for future studies into the microbiota of nonbovine and nonequine domesticated herbivorous animals.
Collapse
Affiliation(s)
- Michelle M. O’ Donnell
- Food Biosciences DepartmentTeagasc Food Research CentreCorkIreland
- Department of MicrobiologyUniversity College CorkCorkIreland
| | | | - R. Paul Ross
- Food Biosciences DepartmentTeagasc Food Research CentreCorkIreland
- Department of MicrobiologyUniversity College CorkCorkIreland
| | - Paul W. O'Toole
- Department of MicrobiologyUniversity College CorkCorkIreland
| |
Collapse
|
54
|
Erwin PM, Rhodes RG, Kiser KB, Keenan-Bateman TF, McLellan WA, Pabst DA. High diversity and unique composition of gut microbiomes in pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales. Sci Rep 2017; 7:7205. [PMID: 28775301 PMCID: PMC5543158 DOI: 10.1038/s41598-017-07425-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/28/2017] [Indexed: 02/07/2023] Open
Abstract
Mammals host diverse bacterial and archaeal symbiont communities (i.e. microbiomes) that play important roles in digestive and immune system functioning, yet cetacean microbiomes remain largely unexplored, in part due to sample collection difficulties. Here, fecal samples from stranded pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales were used to characterize the gut microbiomes of two closely-related species with similar diets. 16S rRNA gene sequencing revealed diverse microbial communities in kogiid whales dominated by Firmicutes and Bacteroidetes. Core symbiont taxa were affiliated with phylogenetic lineages capable of fermentative metabolism and sulfate respiration, indicating potential symbiont contributions to energy acquisition during prey digestion. The diversity and phylum-level composition of kogiid microbiomes differed from those previously reported in toothed whales, which exhibited low diversity communities dominated by Proteobacteria and Actinobacteria. Community structure analyses revealed distinct gut microbiomes in K. breviceps and K. sima, driven by differential relative abundances of shared taxa, and unique microbiomes in kogiid hosts compared to other toothed and baleen whales, driven by differences in symbiont membership. These results provide insight into the diversity, composition and structure of kogiid gut microbiomes and indicate that host identity plays an important role in structuring cetacean microbiomes, even at fine-scale taxonomic levels.
Collapse
Affiliation(s)
- Patrick M Erwin
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, 28409, USA.
| | - Ryan G Rhodes
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - Kevin B Kiser
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - Tiffany F Keenan-Bateman
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - William A McLellan
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - D Ann Pabst
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| |
Collapse
|
55
|
Amphibian gut microbiota shifts differentially in community structure but converges on habitat-specific predicted functions. Nat Commun 2016; 7:13699. [PMID: 27976718 PMCID: PMC5171763 DOI: 10.1038/ncomms13699] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/26/2016] [Indexed: 02/06/2023] Open
Abstract
Complex microbial communities inhabit vertebrate digestive systems but thorough understanding of the ecological dynamics and functions of host-associated microbiota within natural habitats is limited. We investigate the role of environmental conditions in shaping gut and skin microbiota under natural conditions by performing a field survey and reciprocal transfer experiments with salamander larvae inhabiting two distinct habitats (ponds and streams). We show that gut and skin microbiota are habitat-specific, demonstrating environmental factors mediate community structure. Reciprocal transfer reveals that gut microbiota, but not skin microbiota, responds differentially to environmental change. Stream-to-pond larvae shift their gut microbiota to that of pond-to-pond larvae, whereas pond-to-stream larvae change to a community structure distinct from both habitat controls. Predicted functions, however, match that of larvae from the destination habitats in both cases. Thus, microbial function can be matched without taxonomic coherence and gut microbiota appears to exhibit metagenomic plasticity.
Host-associated microbial communities can shift in structure or function when hosts change locations. Bletz et al. reciprocally transfer salamander larvae between pond and stream habitats to show that gut microbiomes shift in function, but not necessarily taxonomic identities, when hosts encounter a new environment.
Collapse
|
56
|
Tucker MA, Ord TJ, Rogers TL. Revisiting the cost of carnivory in mammals. J Evol Biol 2016; 29:2181-2190. [PMID: 27396857 DOI: 10.1111/jeb.12936] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/28/2016] [Indexed: 11/29/2022]
Abstract
Predator-prey relationships play a key role in the evolution and ecology of carnivores. An understanding of predator-prey relationships and how this differs across species and environments provides information on how carnivorous strategies have evolved and how they may change in response to environmental change. We aim to determine how mammals overcame the challenges of living within the marine environment; specifically, how this altered predator-prey body mass relationships relative to terrestrial mammals. Using predator and prey mass data collected from the literature, we applied phylogenetic piecewise regressions to investigate the relationship between predator and prey size across carnivorous mammals (51 terrestrial and 56 marine mammals). We demonstrate that carnivorous mammals have four broad dietary groups: small marine carnivores (< 11 000 kg) and small terrestrial carnivores (< 11 kg) feed on prey less than 5 kg and 2 kg, respectively. On average, large marine carnivores (> 11 000 kg) feed on prey equal to 0.01% of the carnivore's body size, compared to 45% or greater in large terrestrial carnivores (> 11 kg). We propose that differences in prey availability, and the relative ease of processing large prey in the terrestrial environment and small prey in marine environment, have led to the evolution of these novel foraging behaviours. Our results provide important insights into the selection pressures that may have been faced by early marine mammals and ultimately led to the evolution of a range of feeding strategies and predatory behaviours.
Collapse
Affiliation(s)
- M A Tucker
- Evolution and Ecology Research Centre, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia.
| | - T J Ord
- Evolution and Ecology Research Centre, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - T L Rogers
- Evolution and Ecology Research Centre, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
57
|
Kelley JL, Brown AP, Therkildsen NO, Foote AD. The life aquatic: advances in marine vertebrate genomics. Nat Rev Genet 2016; 17:523-34. [DOI: 10.1038/nrg.2016.66] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
58
|
Abstract
The microbiome refers to the thousands of microbial species that inhabit a specific host or environment. Extensive microbiome surveys have been conducted for soils, the built environment, and our oceans. In addition, extensive studies of the human microbiome have revealed significant microbial diversity across all body sites and have hinted at new opportunities for diagnostic and therapeutic approaches to addressing human health and disease. Mammals in general are known to hold a complicated mix of species within their gastrointestinal tracts, including virus, archaea, bacteria, and fungi. These microbial species present beneficial aspects to the host species through the production of vitamins, metabolism of plant structural compounds and sugars, and education of the immune system. In addition to a vast number of studies on humans, studies of the mammalian microbiome have been performed, with several publications on a variety of animal species currently available. These have included studies on the microbiome of companion animals, animals used for research, and animals used for agricultural and food purposes, and various human/animal models.
Collapse
Affiliation(s)
- Karen E Nelson
- Karen E. Nelson is President at the J. Craig Venter Institute (JCVI) in Rockville, Maryland
| |
Collapse
|
59
|
Delport TC, Power ML, Harcourt RG, Webster KN, Tetu SG. Colony Location and Captivity Influence the Gut Microbial Community Composition of the Australian Sea Lion (Neophoca cinerea). Appl Environ Microbiol 2016; 82:3440-3449. [PMID: 27037116 PMCID: PMC4959163 DOI: 10.1128/aem.00192-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/19/2016] [Indexed: 02/01/2023] Open
Abstract
UNLABELLED Gut microbiota play an important role in maintenance of mammalian metabolism and immune system regulation, and disturbances to this community can have adverse impacts on animal health. To better understand the composition of gut microbiota in marine mammals, fecal bacterial communities of the Australian sea lion (Neophoca cinerea), an endangered pinniped with localized distribution, were examined. A comparison of samples from individuals across 11 wild colonies in South and Western Australia and three Australian captive populations showed five dominant bacterial phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria The phylum Firmicutes was dominant in both wild (76.4% ± 4.73%) and captive animals (61.4% ± 10.8%), while Proteobacteria contributed more to captive (29.3% ± 11.5%) than to wild (10.6% ± 3.43%) fecal communities. Qualitative differences were observed between fecal communities from wild and captive animals based on principal-coordinate analysis. SIMPER (similarity percentage procedure) analyses indicated that operational taxonomic units (OTU) from the bacterial families Clostridiaceae and Ruminococcaceae were more abundant in wild than in captive animals and contributed most to the average dissimilarity between groups (SIMPER contributions of 19.1% and 10.9%, respectively). Differences in the biological environment, the foraging site fidelity, and anthropogenic impacts may provide various opportunities for unique microbial establishment in Australian sea lions. As anthropogenic disturbances to marine mammals are likely to increase, understanding the potential for such disturbances to impact microbial community compositions and subsequently affect animal health will be beneficial for management of these vulnerable species. IMPORTANCE The Australian sea lion is an endangered species for which there is currently little information regarding disease and microbial ecology. In this work, we present an in-depth study of the fecal microbiota of a large number of Australian sea lions from geographically diverse wild and captive populations. Colony location and captivity were found to influence the gut microbial community compositions of these animals. Our findings significantly extend the baseline knowledge of marine mammal gut microbiome composition and variability.
Collapse
Affiliation(s)
- Tiffany C Delport
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Michelle L Power
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Robert G Harcourt
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Koa N Webster
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Sasha G Tetu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| |
Collapse
|
60
|
Analysis of the microbial diversity in faecal material of the endangered blue whale, Balaenoptera musculus. Antonie van Leeuwenhoek 2016; 109:1063-9. [DOI: 10.1007/s10482-016-0698-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/15/2016] [Indexed: 10/21/2022]
|
61
|
Soverini M, Quercia S, Biancani B, Furlati S, Turroni S, Biagi E, Consolandi C, Peano C, Severgnini M, Rampelli S, Brigidi P, Candela M. The bottlenose dolphin (Tursiops truncatus) faecal microbiota. FEMS Microbiol Ecol 2016; 92:fiw055. [DOI: 10.1093/femsec/fiw055] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2016] [Indexed: 12/31/2022] Open
|
62
|
Bik EM, Costello EK, Switzer AD, Callahan BJ, Holmes SP, Wells RS, Carlin KP, Jensen ED, Venn-Watson S, Relman DA. Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nat Commun 2016; 7:10516. [PMID: 26839246 PMCID: PMC4742810 DOI: 10.1038/ncomms10516] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/18/2015] [Indexed: 12/15/2022] Open
Abstract
Marine mammals play crucial ecological roles in the oceans, but little is known about their microbiotas. Here we study the bacterial communities in 337 samples from 5 body sites in 48 healthy dolphins and 18 healthy sea lions, as well as those of adjacent seawater and other hosts. The bacterial taxonomic compositions are distinct from those of other mammals, dietary fish and seawater, are highly diverse and vary according to body site and host species. Dolphins harbour 30 bacterial phyla, with 25 of them in the mouth, several abundant but poorly characterized Tenericutes species in gastric fluid and a surprisingly paucity of Bacteroidetes in distal gut. About 70% of near-full length bacterial 16S ribosomal RNA sequences from dolphins are unique. Host habitat, diet and phylogeny all contribute to variation in marine mammal distal gut microbiota composition. Our findings help elucidate the factors structuring marine mammal microbiotas and may enhance monitoring of marine mammal health.
Collapse
Affiliation(s)
- Elisabeth M. Bik
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
| | - Elizabeth K. Costello
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alexandra D. Switzer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Susan P. Holmes
- Department of Statistics, Stanford University, Stanford, California 94305, USA
| | - Randall S. Wells
- Sarasota Dolphin Research Program, Chicago Zoological Society, c/o Mote Marine Laboratory, Sarasota, Florida 34236, USA
| | - Kevin P. Carlin
- Translational Medicine and Research Program, National Marine Mammal Foundation, San Diego, California 92106, USA
| | - Eric D. Jensen
- Space and Naval Warfare Systems Center Pacific, San Diego, California 92152, USA
| | - Stephanie Venn-Watson
- Translational Medicine and Research Program, National Marine Mammal Foundation, San Diego, California 92106, USA
| | - David A. Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University School of Medicine, Stanford, California 94305, USA
| |
Collapse
|
63
|
Miura T, Kita A, Okamura Y, Aki T, Matsumura Y, Tajima T, Kato J, Nakashimada Y. Semi-continuous methane production from undiluted brown algae using a halophilic marine microbial community. BIORESOURCE TECHNOLOGY 2016; 200:616-23. [PMID: 26547811 DOI: 10.1016/j.biortech.2015.10.090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/15/2015] [Accepted: 10/27/2015] [Indexed: 06/05/2023]
Abstract
Acclimated marine sediment-derived culture was used for semi-continuous methane production from materials equivalent to raw brown algae, without dilution of salinity and without nutrient supply, under 3 consecutive conditions of varying organic loading rates (OLRs) and hydraulic retention time (HRT). Methane production was stable at 2.0gVS/kg/day (39-day HRT); however, it became unstable at 2.9gVS/kg/day (28-day HRT) due to acetate and propionate accumulation. OLR subsequently decreased to 1.7gVS/kg/day (46-day HRT), stabilizing methane production beyond steady state. Methane yield was above 300mL/g VS at all OLRs. These results indicated that the acclimated marine sediment culture was able to produce methane semi-continuously from raw brown algae without dilution and nutrient supply under steady state. Microbial community analysis suggested that hydrogenotrophic methanogens predominated among archaea during unstable methane production, implying a partial shift of the methanogenic pathway from acetoclastic methanogenesis to acetate oxidation.
Collapse
Affiliation(s)
- Toyokazu Miura
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan; CREST, JST, Japan
| | - Akihisa Kita
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan; CREST, JST, Japan
| | - Yoshiko Okamura
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan; CREST, JST, Japan
| | - Tsunehiro Aki
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan; CREST, JST, Japan
| | - Yukihiko Matsumura
- Division of Energy and Environmental Engineering, Institute of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima 739-8527, Japan; CREST, JST, Japan
| | - Takahisa Tajima
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan; CREST, JST, Japan
| | - Junichi Kato
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Yutaka Nakashimada
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan; CREST, JST, Japan.
| |
Collapse
|
64
|
Wang NF, Zhang T, Zhang F, Wang ET, He JF, Ding H, Zhang BT, Liu J, Ran XB, Zang JY. Diversity and structure of soil bacterial communities in the Fildes Region (maritime Antarctica) as revealed by 454 pyrosequencing. Front Microbiol 2015; 6:1188. [PMID: 26579095 PMCID: PMC4623505 DOI: 10.3389/fmicb.2015.01188] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 10/12/2015] [Indexed: 12/19/2022] Open
Abstract
This study assessed the diversity and composition of bacterial communities in four different soils (human-, penguin-, seal-colony impacted soils and pristine soil) in the Fildes Region (King George Island, Antarctica) using 454 pyrosequencing with bacterial-specific primers targeting the 16S rRNA gene. Proteobacteria, Actinobacteria, Acidobacteria, and Verrucomicrobia were abundant phyla in almost all the soil samples. The four types of soils were significantly different in geochemical properties and bacterial community structure. Thermotogae, Cyanobacteria, Fibrobacteres, Deinococcus-Thermus, and Chlorobi obviously varied in their abundance among the 4 soil types. Considering all the samples together, members of the genera Gaiella, Chloracidobacterium, Nitrospira, Polaromonas, Gemmatimonas, Sphingomonas, and Chthoniobacter were found to predominate, whereas members of the genera Chamaesiphon, Herbaspirillum, Hirschia, Nevskia, Nitrosococcus, Rhodococcus, Rhodomicrobium, and Xanthomonas varied obviously in their abundance among the four soil types. Distance-based redundancy analysis revealed that pH (p < 0.01), phosphate phosphorus (p < 0.01), organic carbon (p < 0.05), and organic nitrogen (p < 0.05) were the most significant factors that correlated with the community distribution of soil bacteria. To our knowledge, this is the first study to explore the soil bacterial communities in human-, penguin-, and seal- colony impacted soils from ice-free areas in maritime Antarctica using high-throughput pyrosequencing.
Collapse
Affiliation(s)
- Neng Fei Wang
- Key Lab of Marine Bioactive Substances, The First Institute of Oceanography, State Oceanic Administration Qingdao, China
| | - Tao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences Beijing, China
| | - Fang Zhang
- Polar Research Institute of China Shanghai, China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional Mexico, Mexico
| | - Jian Feng He
- Polar Research Institute of China Shanghai, China
| | - Hui Ding
- Chemical Engineering Institute, Qingdao University Qingdao, China
| | - Bo Tao Zhang
- Chemical Engineering Institute, Qingdao University Qingdao, China
| | - Jie Liu
- Department of Bioengineering and Biotechnology, Qingdao University of Science and Technology Qingdao, China
| | - Xiang Bin Ran
- Key Lab of Marine Bioactive Substances, The First Institute of Oceanography, State Oceanic Administration Qingdao, China
| | - Jia Ye Zang
- Key Lab of Marine Bioactive Substances, The First Institute of Oceanography, State Oceanic Administration Qingdao, China
| |
Collapse
|
65
|
Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores. Nat Commun 2015; 6:8285. [PMID: 26393325 PMCID: PMC4595633 DOI: 10.1038/ncomms9285] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 08/04/2015] [Indexed: 12/21/2022] Open
Abstract
Mammals host gut microbiomes of immense physiological consequence, but the determinants of diversity in these communities remain poorly understood. Diet appears to be the dominant factor, but host phylogeny also seems to be an important, if unpredictable, correlate. Here we show that baleen whales, which prey on animals (fish and crustaceans), harbor unique gut microbiomes with surprising parallels in functional capacity and higher level taxonomy to those of terrestrial herbivores. These similarities likely reflect a shared role for fermentative metabolisms despite a shift in primary carbon sources from plant-derived to animal-derived polysaccharides, such as chitin. In contrast, protein catabolism and essential amino acid synthesis pathways in baleen whale microbiomes more closely resemble those of terrestrial carnivores. Our results demonstrate that functional attributes of the microbiome can vary independently even given an animal-derived diet, illustrating how diet and evolutionary history combine to shape microbial diversity in the mammalian gut. Diet is a major factor determining the composition of gut microbiota in mammals, while host evolutionary history seems to play an unclear role. Here, Sanders et al. show that baleen whales, which prey on animals, harbour a unique gut microbiome with similarities to those of terrestrial herbivores.
Collapse
|
66
|
Waite DW, Taylor MW. Exploring the avian gut microbiota: current trends and future directions. Front Microbiol 2015; 6:673. [PMID: 26191057 PMCID: PMC4490257 DOI: 10.3389/fmicb.2015.00673] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 06/19/2015] [Indexed: 01/16/2023] Open
Abstract
Birds represent a diverse and evolutionarily successful lineage, occupying a wide range of niches throughout the world. Like all vertebrates, avians harbor diverse communities of microorganisms within their guts, which collectively fulfill crucial roles in providing the host with nutrition and protection from pathogens. Across the field of avian microbiology knowledge is extremely uneven, with several species accounting for an overwhelming majority of all microbiological investigations. These include agriculturally important birds, such as chickens and turkeys, as well as birds of evolutionary or conservation interest. In our previous study we attempted the first meta-analysis of the avian gut microbiota, using 16S rRNA gene sequences obtained from a range of publicly available data sets. We have now extended our analysis to explore the microbiology of several key species in detail, to consider the avian microbiota within the context of what is known about other vertebrates, and to identify key areas of interest in avian microbiology for future study.
Collapse
Affiliation(s)
| | - Michael W. Taylor
- Centre for Microbial Innovation, School of Biological Sciences, University of AucklandAuckland, New Zealand
| |
Collapse
|
67
|
Keenan SW, Elsey RM. The Good, the Bad, and the Unknown: Microbial Symbioses of the American Alligator. Integr Comp Biol 2015; 55:972-85. [DOI: 10.1093/icb/icv006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
|
68
|
Miura T, Kita A, Okamura Y, Aki T, Matsumura Y, Tajima T, Kato J, Nakashimada Y. Improved methane production from brown algae under high salinity by fed-batch acclimation. BIORESOURCE TECHNOLOGY 2015; 187:275-281. [PMID: 25863204 DOI: 10.1016/j.biortech.2015.03.142] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/27/2015] [Accepted: 03/29/2015] [Indexed: 06/04/2023]
Abstract
Here, a methanogenic microbial community was developed from marine sediments to have improved methane productivity from brown algae under high salinity. Fed-batch cultivation was conducted by adding dry seaweed at 1wt% total solid (TS) based on the liquid weight of the NaCl-containing sediment per round of cultivation. The methane production rate and level of salinity increased 8-fold and 1.6-fold, respectively, at the 10th round of cultivation. Moreover, the rate of methane production remained high, even at the 10th round of cultivation, with accumulation of salts derived from 10wt% TS of seaweed. The salinity of the 10th-round culture was equivalent to 5% NaCl. The improved methane production was attributed to enhanced acetoclastic methanogenesis because acetate became rapidly converted to methane during cultivation. The family Fusobacteriaceae and the genus Methanosaeta, the acetoclastic methanogen, predominated in bacteria and archaea, respectively, after the cultivation.
Collapse
Affiliation(s)
- Toyokazu Miura
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan; CREST, JST, Japan
| | - Akihisa Kita
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan; CREST, JST, Japan
| | - Yoshiko Okamura
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan; CREST, JST, Japan
| | - Tsunehiro Aki
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan; CREST, JST, Japan
| | - Yukihiko Matsumura
- Division of Energy and Environmental Engineering, Institute of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima 739-8527, Japan; CREST, JST, Japan
| | - Takahisa Tajima
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan; CREST, JST, Japan
| | - Junichi Kato
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Yutaka Nakashimada
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan; CREST, JST, Japan.
| |
Collapse
|