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Möller L, Vainshtein Y, Meyer B, Neidhardt J, Eren AM, Sohn K, Rabus R. Rich microbial and depolymerising diversity in Antarctic krill gut. Microbiol Spectr 2024; 12:e0403523. [PMID: 38466097 PMCID: PMC10986584 DOI: 10.1128/spectrum.04035-23] [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: 11/25/2023] [Accepted: 02/13/2024] [Indexed: 03/12/2024] Open
Abstract
With almost a quadrillion individuals, the Antarctic krill processes five million tons of organic carbon every day during austral summer. This high carbon flux requires a broad range of hydrolytic enzymes to decompose the diverse food-derived biopolymers. While krill itself possesses numerous such enzymes, it is unclear, to what extent the endogenous microbiota contribute to the hydrolytic potential of the gut environment. Here we applied amplicon sequencing, shotgun metagenomics, cultivation, and physiological assays to characterize the krill gut microbiota. The broad bacterial diversity (273 families, 919 genera, and 2,309 species) also included a complex potentially anaerobic sub-community. Plate-based assays with 198 isolated pure cultures revealed widespread capacities to utilize lipids (e.g., tributyrin), followed by proteins (casein) and to a lesser extent by polysaccharides (e.g., alginate and chitin). While most isolates affiliated with the genera Pseudoalteromonas and Psychrobacter, also Rubritalea spp. (Verrucomicrobia) were observed. The krill gut microbiota growing on marine broth agar plates possess 13,012 predicted hydrolyses; 15-fold more than previously predicted from a transcriptome-proteome compendium of krill. Cultivation-independent and -dependent approaches indicated members of the families Flavobacteriaceae and Pseudoalteromonadaceae to dominate the capacities for lipid/protein hydrolysis and to provide a plethora of carbohydrate-active enzymes, sulfatases, and laminarin- or porphyrin-depolymerizing hydrolases. Notably, also the potential to hydrolyze plastics such as polyethylene terephthalate and polylactatide was observed, affiliating mostly with Moraxellaceae. Overall, this study shows extensive microbial diversity in the krill gut, and suggests that the microbiota likely play a significant role in the nutrient acquisition of the krill by enriching its hydrolytic enzyme repertoire.IMPORTANCEThe Antarctic krill (Euphausia superba) is a keystone species of the Antarctic marine food web, connecting the productivity of phyto- and zooplankton with the nutrition of the higher trophic levels. Accordingly, krill significantly contributes to biomass turnover, requiring the decomposition of seasonally varying plankton-derived biopolymers. This study highlights the likely role of the krill gut microbiota in this ecosystem function by revealing the great number of diverse hydrolases that microbes contribute to the krill gut environment. The here resolved repertoire of hydrolytic enzymes could contribute to the overall nutritional resilience of krill and to the general organic matter cycling under changing environmental conditions in the Antarctic sea water. Furthermore, the krill gut microbiome could serve as a valuable resource of cold-adapted hydrolytic enzymes for diverse biotechnological applications.
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Affiliation(s)
- Lars Möller
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Yevhen Vainshtein
- In Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Stuttgart, Germany
| | - Bettina Meyer
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University Oldenburg (HIFMB), Oldenburg, Germany
- Biosciences, Alfred Wegener Institute (AWI), Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - John Neidhardt
- Department of Human Medicine, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Research Center Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - A. Murat Eren
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University Oldenburg (HIFMB), Oldenburg, Germany
- HIFMB-MPG Bridging Group for Marine Genomics, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute (AWI), Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Kai Sohn
- In Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Stuttgart, Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
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Ricci F, Leggat W, Pasella MM, Bridge T, Horowitz J, Girguis PR, Ainsworth T. Deep sea treasures - Insights from museum archives shed light on coral microbial diversity within deepest ocean ecosystems. Heliyon 2024; 10:e27513. [PMID: 38468949 PMCID: PMC10926130 DOI: 10.1016/j.heliyon.2024.e27513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 02/15/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024] Open
Abstract
Deep sea benthic habitats are low productivity ecosystems that host an abundance of organisms within the Cnidaria phylum. The technical limitations and the high cost of deep sea surveys have made exploring deep sea environments and the biology of the organisms that inhabit them challenging. In spite of the widespread recognition of Cnidaria's environmental importance in these ecosystems, the microbial assemblage and its role in coral functioning have only been studied for a few deep water corals. Here, we explored the microbial diversity of deep sea corals by recovering nucleic acids from museum archive specimens. Firstly, we amplified and sequenced the V1-V3 regions of the 16S rRNA gene of these specimens, then we utilized the generated sequences to shed light on the microbial diversity associated with seven families of corals collected from depth in the Coral Sea (depth range 1309 to 2959 m) and Southern Ocean (depth range 1401 to 2071 m) benthic habitats. Surprisingly, Cyanobacteria sequences were consistently associated with six out of seven coral families from both sampling locations, suggesting that these bacteria are potentially ubiquitous members of the microbiome within these cold and deep sea water corals. Additionally, we show that Cnidaria might benefit from symbiotic associations with a range of chemosynthetic bacteria including nitrite, carbon monoxide and sulfur oxidizers. Consistent with previous studies, we show that sequences associated with the bacterial phyla Proteobacteria, Verrucomicrobia, Planctomycetes and Acidobacteriota dominated the microbial community of corals in the deep sea. We also explored genomes of the bacterial genus Mycoplasma, which we identified as associated with specimens of three deep sea coral families, finding evidence that these bacteria may aid the host immune system. Importantly our results show that museum specimens retain components of host microbiome that can provide new insights into the diversity of deep sea coral microbiomes (and potentially other organisms), as well as the diversity of microbes writ large in deep sea ecosystems.
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Affiliation(s)
- Francesco Ricci
- University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington, NSW, Australia
- University of Melbourne, School of Biosciences, Parkville, VIC, Australia
- Monash University, Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia
| | - William Leggat
- University of Newcastle, School of Environmental and Life Sciences, Callaghan, NSW, Australia
| | - Marisa M. Pasella
- University of Melbourne, School of Biosciences, Parkville, VIC, Australia
| | - Tom Bridge
- Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, Townsville, QLD, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| | - Jeremy Horowitz
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
- Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Peter R. Girguis
- University of Harvard, Department of Organismic and Evolutionary Biology, Cambridge, MA, USA
| | - Tracy Ainsworth
- University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington, NSW, Australia
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Klose SM, Legione AR, Bushell RN, Browning GF, Vaz PK. Unveiling genome plasticity and a novel phage in Mycoplasma felis: Genomic investigations of four feline isolates. Microb Genom 2024; 10:001227. [PMID: 38546735 PMCID: PMC11004492 DOI: 10.1099/mgen.0.001227] [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: 01/09/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
Mycoplasma felis has been isolated from diseased cats and horses, but to date only a single fully assembled genome of this species, of an isolate from a horse, has been characterized. This study aimed to characterize and compare the completely assembled genomes of four clinical isolates of M. felis from three domestic cats, assembled with the aid of short- and long-read sequencing methods. The completed genomes encoded a median of 759 ORFs (range 743-777) and had a median average nucleotide identity of 98.2 % with the genome of the available equid origin reference strain. Comparative genomic analysis revealed the occurrence of multiple horizontal gene transfer events and significant genome reassortment. This had resulted in the acquisition or loss of numerous genes within the Australian felid isolate genomes, encoding putative proteins involved in DNA transfer, metabolism, DNA replication, host cell interaction and restriction modification systems. Additionally, a novel mycoplasma phage was detected in one Australian felid M. felis isolate by genomic analysis and visualized using cryo-transmission electron microscopy. This study has highlighted the complex genomic dynamics in different host environments. Furthermore, the sequences obtained in this work will enable the development of new diagnostic tools, and identification of future infection control and treatment options for the respiratory disease complex in cats.
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Affiliation(s)
- Sara M. Klose
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
- Institute of Molecular Medicine and Experimental Immunology, Faculty of Medicine, University of Bonn, NRW, Germany
| | - Alistair R. Legione
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
| | - Rhys N. Bushell
- Department of Veterinary Clinical Sciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
| | - Glenn F. Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
| | - Paola K. Vaz
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
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Dong Y, Li Y, Ge M, Takatsu T, Wang Z, Zhang X, Ding D, Xu Q. Distinct gut microbial communities and functional predictions in divergent ophiuroid species: host differentiation, ecological niches, and adaptation to cold-water habitats. Microbiol Spectr 2023; 11:e0207323. [PMID: 37889056 PMCID: PMC10715168 DOI: 10.1128/spectrum.02073-23] [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: 05/17/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Gastrointestinal microorganisms are critical to the survival and adaptation of hosts, and there are few studies on the differences and functions of gastrointestinal microbes in widely distributed species. This study investigated the gut microbes of two ophiuroid species (Ophiura sarsii and its subspecies O. sarsii vadicola) in cold-water habitats of the Northern Pacific Ocean. The results showed that a combination of host and environmental factors shapes the intestinal microbiota of ophiuroids. There was a high similarity in microbial communities between the two groups living in different regions, which may be related to their similar ecological niches. These microorganisms played a vital role in the ecological success of ophiuroids as the foundation for their adaptation to cold-water environments. This study revealed the complex relationship between hosts and their gut microbes, providing insights into the role they play in the adaptation and survival of marine species.
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Affiliation(s)
- Yue Dong
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Yixuan Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Meiling Ge
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Tetsuya Takatsu
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Zongling Wang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Xuelei Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Dewen Ding
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Qinzeng Xu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
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Methou P, Cueff‐Gauchard V, Michel LN, Gayet N, Pradillon F, Cambon‐Bonavita M. Symbioses of alvinocaridid shrimps from the South West Pacific: No chemosymbiotic diets but conserved gut microbiomes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:614-630. [PMID: 37752716 PMCID: PMC10667644 DOI: 10.1111/1758-2229.13201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 08/31/2023] [Indexed: 09/28/2023]
Abstract
Rimicaris exoculata shrimps from hydrothermal vent ecosystems are known to host dense epibiotic communities inside their enlarged heads and digestive systems. Conversely, other shrimps from the family, described as opportunistic feeders have received less attention. We examined the nutrition and bacterial communities colonising 'head' chambers and digestive systems of three other alvinocaridids-Rimicaris variabilis, Nautilocaris saintlaurentae and Manuscaris sp.-using a combination of electron microscopy, stable isotopes and sequencing approaches. Our observations inside 'head' cavities and on mouthparts showed only a really low coverage of bacterial epibionts. In addition, no clear correlation between isotopic ratios and relative abundance of epibionts on mouthparts could be established among shrimp individuals. Altogether, these results suggest that none of these alvinocaridids rely on chemosynthetic epibionts as their main source of nutrition. Our analyses also revealed a substantial presence of several Firmicutes and Deferribacterota lineages within the foreguts and midguts of these shrimps, which closest known lineages were systematically digestive symbionts associated with alvinocaridids, and more broadly for Firmicutes from digestive systems of other crustaceans from marine and terrestrial ecosystems. Overall, our study opens new perspectives not only about chemosynthetic symbioses of vent shrimps but more largely about digestive microbiomes with potential ancient and evolutionarily conserved bacterial partnerships among crustaceans.
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Affiliation(s)
- Pierre Methou
- X‐STARJapan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaJapan
| | - Valérie Cueff‐Gauchard
- Univ BrestIfremer, CNRS, Unité Biologie des Environnements Extrêmes marins ProfondsPlouzanéFrance
| | - Loïc N. Michel
- Univ BrestIfremer, CNRS, Unité Biologie des Environnements Extrêmes marins ProfondsPlouzanéFrance
- Laboratory of Oceanology, Freshwater, and Oceanic Sciences Unit of reSearch (FOCUS)University of LiègeLiègeBelgium
| | - Nicolas Gayet
- Univ BrestIfremer, CNRS, Unité Biologie des Environnements Extrêmes marins ProfondsPlouzanéFrance
| | - Florence Pradillon
- Univ BrestIfremer, CNRS, Unité Biologie des Environnements Extrêmes marins ProfondsPlouzanéFrance
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Kakakhel MA, Narwal N, Kataria N, Johari SA, Zaheer Ud Din S, Jiang Z, Khoo KS, Xiaotao S. Deciphering the dysbiosis caused in the fish microbiota by emerging contaminants and its mitigation strategies-A review. ENVIRONMENTAL RESEARCH 2023; 237:117002. [PMID: 37648194 DOI: 10.1016/j.envres.2023.117002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/01/2023]
Abstract
The primary barrier to nutrient absorption in fish is the intestinal epithelium, followed by a community of microorganisms known as the gut microbiota, which can be thought of as a hidden organ. The gastrointestinal microbiota of fish plays a key role in the upholding of overall health by maintaining the homeostasis and disease resistance of the host. However, emerging contaminants as the result of anthropogenic activities have significantly led to disruptions and intestinal dysbiosis in fish. Which probably results in fish mortalities and disrupts the balance of an ecosystem. Therefore, we comprehensively seek to compile the effects and consequences of emerging contaminations on fish intestinal microbiota. Additionally, the mitigation strategies including prebiotics, probiotics, plant-based diet, and Biofloc technology are being outlined. Biofloc technology (BFT) can treat toxic materials, i.e., nitrogen components, and convert them into a useful product such as proteins and demonstrated promising elevating technique for the fish intestinal bacterial composition. However, it remains unclear whether the bacterial isolate is primarily responsible for the BFT's removal of nitrate and ammonia and the corresponding removal mechanism. To answer this, real time polymerase chain reaction (RT-PCR) with metagenomics, transcriptomics, and proteomics techniques probably provides a possible solution.
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Affiliation(s)
- Mian Adnan Kakakhel
- Hubei International Science and Technology Cooperation Base of Fish Passage, Three Gorges University, Yichang, 443002, Hubei, China; College of Hydraulic & Environmental Engineering, Three Gorges University, Yichang, 443002, Hubei, China
| | - Nishita Narwal
- University School of Environment Management, Guru Gobind Singh Indraprastha University, New Delhi, 110078, India
| | - Navish Kataria
- Department of Environmental Sciences, J.C. Bose University of Science and Technology, YMCA, Faridabad, Haryana, 121006, India
| | - Seyed Ali Johari
- Department of Fisheries, Faculty of Natural Resources, University of Kurdistan, Sanandaj, Kurdistan, Iran
| | - Syed Zaheer Ud Din
- International School for Optoelectronic Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Zewen Jiang
- Hubei International Science and Technology Cooperation Base of Fish Passage, Three Gorges University, Yichang, 443002, Hubei, China; College of Hydraulic & Environmental Engineering, Three Gorges University, Yichang, 443002, Hubei, China
| | - Kuan Shiong Khoo
- Department of Chemical Engineering and Materials Science, Yuan Ze University, Taoyuan, Taiwan
| | - Shi Xiaotao
- Hubei International Science and Technology Cooperation Base of Fish Passage, Three Gorges University, Yichang, 443002, Hubei, China; College of Hydraulic & Environmental Engineering, Three Gorges University, Yichang, 443002, Hubei, China.
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Cicala F, Cisterna-Céliz JA, Paolinelli M, Moore JD, Sevigny J, Rocha-Olivares A. The Role of Diversity in Mediating Microbiota Structural and Functional Differences in Two Sympatric Species of Abalone Under Stressed Withering Syndrome Conditions. MICROBIAL ECOLOGY 2023; 85:277-287. [PMID: 35064808 DOI: 10.1007/s00248-022-01970-5] [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: 06/25/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Withering syndrome (WS) is a gastro-intestinal (GI) infectious disease likely affecting all abalone species worldwide. Structural and functional changes in abalone GI microbiotas under WS-stressed conditions remain poorly investigated. It is unclear if interspecific microbiota differences, such as the presence of certain microbes, their abundance, and functional capabilities, may be involved in the occurrence of this disease. Bacterial microbiotas of healthy Haliotis fulgens and Haliotis corrugata are mainly composed by Tenericutes, Proteobacteria, Fusobacteria, and Spirochaetes. We previously reported species-specific structural and functional profiles of those communities and suggested that they are of consequence to the different susceptibility of each species to WS. Here, we address this question by comparing the structure and function of healthy and dysbiotic microbiota through 454 pyrosequencing and PICRUSt 2, respectively. Our findings suggest that the extent to which WS-stressed conditions may explain structural and functional differences in GI microbiota is contingent on the microbiota diversity itself. Indeed, microbiota differences between stressed and healthy abalone were marginal in the more complex bacterial communities of H. corrugata, in which no significant structural or functional changes were detected. Conversely, significant structural changes were observed in the less complex bacterial microbiota of H. fulgens. Moreover, structural alterations led to a significant downregulation of some metabolic activities conducted by GI bacteria. Accordingly, results suggest that gastro-intestinal bacterial diversity appears to be related with both the health of abalone and the etiology of WS.
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Affiliation(s)
- Francesco Cicala
- Department of Biological Oceanography, CICESE, Carretera Tijuana-Ensenada km 3918, 22860, Ensenada, Baja CA, Mexico
- Department of Biomedical Innovation, CICESE, Carretera Tijuana-Ensenada km 3918, 22860, Ensenada, Baja CA, Mexico
| | | | - Marcos Paolinelli
- National Council of Scientific and Technical Research (CONICET), Av. Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina
- National Institute of Agricultural Technology INTA EEA Mendoza, San Martin 3853, Luján de Cuyo, 5507, Mendoza, Argentina
| | - James D Moore
- Bodega Marine Laboratory, University of California at Davis, P.O. Box 247, Bodega Bay, CA, USA
| | - Joseph Sevigny
- Hubbard Center for Genome Studies, University of New Hampshire, 35 Colovos Rd, Durham, NH, 03824, USA
| | - Axayácatl Rocha-Olivares
- Department of Biological Oceanography, CICESE, Carretera Tijuana-Ensenada km 3918, 22860, Ensenada, Baja CA, Mexico.
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Plante CJ, Hill-Spanik KM, Emerson R. Inputs don't equal outputs: bacterial microbiomes of the ingesta, gut, and feces of the keystone deposit feeder Ilyanassa obsoleta. FEMS Microbiol Ecol 2022; 99:6887277. [PMID: 36496168 DOI: 10.1093/femsec/fiac152] [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: 04/19/2022] [Revised: 11/22/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Bacteria drive energy fluxes and geochemical processes in estuarine sediments. Deposit-feeding invertebrates alter the structure and activity of microbial communities through sediment ingestion, gut passage, and defecation. The eastern mud snail, Ilyanassa obsoleta, is native to estuaries of the northwestern Atlantic, ranging from Nova Scotia, Canada, to Florida in the USA. Given extremely high densities, their deposit-feeding and locomotory activities exert ecological influence on other invertebrates and microbes. Our aim was to characterize the bacterial microbiome of this 'keystone species' and determine how its feeding alters the native bacterial microbiota. We gathered snails from both mudflat and sandflat habitats and collected their fresh fecal pellets in the laboratory. Dissection of these same snails allowed us to compare bacterial assemblages of ingested sediments, shell surfaces, gut sections (esophagus, stomach, intestine), and feces using DNA metabarcoding. Our findings indicate a diverse, resident gut microbiota. The stomach and intestines were dominated by bacteria of the genus Mycoplasma. Comparison of ingesta and feces revealed digestion of several bacterial taxa, introduction of gut residents during passage, in addition to unique bacterial taxa within the feces of unknown provenance. Our results demonstrate that I. obsoleta has the potential to modify microbial community structure in estuarine sediments.
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Affiliation(s)
- Craig J Plante
- Grice Marine Laboratory, College of Charleston, Charleston, SC 29412, United States
| | | | - Rowan Emerson
- Grice Marine Laboratory, College of Charleston, Charleston, SC 29412, United States
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A
Mollicutes
Metagenome-Assembled Genome from the Gut of the Pteropod
Limacina rangii. Microbiol Resour Announc 2022; 11:e0075222. [DOI: 10.1128/mra.00752-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A nearly complete genome of an uncultured
Mollicutes
sp. was obtained from the metagenome of the gut of
Limacina rangii
(open-ocean snail), an important grazer and prey for higher trophic animals along the rapidly warming region of the western Antarctic Peninsula.
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Aubé J, Cambon-Bonavita MA, Velo-Suárez L, Cueff-Gauchard V, Lesongeur F, Guéganton M, Durand L, Reveillaud J. A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata. MICROBIOME 2022; 10:189. [PMID: 36333777 PMCID: PMC9636832 DOI: 10.1186/s40168-022-01380-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND In deep-sea hydrothermal vent areas, deprived of light, most animals rely on chemosynthetic symbionts for their nutrition. These symbionts may be located on their cuticle, inside modified organs, or in specialized cells. Nonetheless, many of these animals have an open and functional digestive tract. The vent shrimp Rimicaris exoculata is fueled mainly by its gill chamber symbionts, but also has a complete digestive system with symbionts. These are found in the shrimp foregut and midgut, but their roles remain unknown. We used genome-resolved metagenomics on separate foregut and midgut samples, taken from specimens living at three contrasted sites along the Mid-Atlantic Ridge (TAG, Rainbow, and Snake Pit) to reveal their genetic potential. RESULTS We reconstructed and studied 20 Metagenome-Assembled Genomes (MAGs), including novel lineages of Hepatoplasmataceae and Deferribacteres, abundant in the shrimp foregut and midgut, respectively. Although the former showed streamlined reduced genomes capable of using mostly broken-down complex molecules, Deferribacteres showed the ability to degrade complex polymers, synthesize vitamins, and encode numerous flagellar and chemotaxis genes for host-symbiont sensing. Both symbionts harbor a diverse set of immune system genes favoring holobiont defense. In addition, Deferribacteres were observed to particularly colonize the bacteria-free ectoperitrophic space, in direct contact with the host, elongating but not dividing despite possessing the complete genetic machinery necessary for this. CONCLUSION Overall, these data suggest that these digestive symbionts have key communication and defense roles, which contribute to the overall fitness of the Rimicaris holobiont. Video Abstract.
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Affiliation(s)
- Johanne Aubé
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Marie-Anne Cambon-Bonavita
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Lourdes Velo-Suárez
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
- Univ Brest, INSERM, EFS, UMR 1078, GGB, F-29200 Brest, France and Centre Brestois d’Analyse du Microbiote (CBAM), Brest University Hospital, Brest, France
| | - Valérie Cueff-Gauchard
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Françoise Lesongeur
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Marion Guéganton
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Lucile Durand
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Julie Reveillaud
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
- MIVEGEC, Univ. Montpellier, INRAe, CNRS, IRD, Montpellier, France
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Kivistik C, Käiro K, Tammert H, Sokolova IM, Kisand V, Herlemann DPR. Distinct stages of the intestinal bacterial community of Ampullaceana balthica after salinization. Front Microbiol 2022; 13:767334. [PMID: 36110301 PMCID: PMC9468257 DOI: 10.3389/fmicb.2022.767334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 07/19/2022] [Indexed: 12/15/2022] Open
Abstract
Environmental disturbances influence bacterial community structure and functioning. To investigate the effect of environmental disturbance caused by changes in salinity on host-protected bacterial communities, we analyzed the microbiome within the gastrointestinal tract of Ampullaceana balthica in different salinities. A. balthica is a benthic gastropod found in fresh- and mesohaline waters. Whereas the total energy reserves of A. balthica were unaffected by an increase of salinity to 3, a high mortality rate was detected after a shift from freshwater to salinity 6 suggesting a major disruption of energy homeostasis. The shift to salinity 6 also caused a change in the gastrointestinal bacterial community composition. At salinity 3, the bacterial community composition of different host individuals was related either to the freshwater or salinity 6 gastrointestinal bacterial community, indicating an ambivalent nature of salinity 3. Since salinity 3 represents the range where aquatic gastropods are able to regulate their osmolarity, this may be an important tipping point during salinization. The change in the intestinal microbiome was uncoupled from the change in the water bacterial community and unrelated to the food source microbiome. Our study shows that environmental disturbance caused by salinity acts also on the host-protected microbiome. In light of the sea-level rise, our findings indicate that salinization of the near-shore freshwater bodies will cause changes in organisms' intestinal microbiomes if a critical salinity threshold (presumably ∼3) is exceeded.
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Affiliation(s)
- Carmen Kivistik
- Estonian University of Life Sciences, Center for Limnology, Tartu, Estonia
| | - Kairi Käiro
- Estonian University of Life Sciences, Center for Limnology, Tartu, Estonia
| | - Helen Tammert
- Estonian University of Life Sciences, Center for Limnology, Tartu, Estonia
| | - Inna M. Sokolova
- Department of Marine Biology, Institute for Biological Sciences, University of Rostock, Rostock, Germany
- Department of Maritime Systems, Interdisciplinary Faculty, University of Rostock, Rostock, Germany
| | - Veljo Kisand
- Estonian University of Life Sciences, Center for Limnology, Tartu, Estonia
- Institute of Technology, University of Tartu, Tartu, Estonia
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12
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Chan J, Geng D, Pan B, Zhang Q, Xu Q. Gut Microbial Divergence Between Three Hadal Amphipod Species from the Isolated Hadal Trenches. MICROBIAL ECOLOGY 2022; 84:627-637. [PMID: 34545412 DOI: 10.1007/s00248-021-01851-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Amphipods are the dominant scavenging metazoan species in the hadal trenches at water depths below 6,000 m. The gut microbiota have been considered to be contribution to the adaptation of deep-sea organisms; however, few comparative analyses of animal gut microbiota between different isolated hadal environments have been done so far. Here, we employed high-throughput 16S rRNA sequencing to compare the gut microbial taxonomic composition and functional potential diversity of three hadal amphipod species, Hirondellea gigas, Bathycallisoma schellenbergi, and Alicella gigantea, collected from the Mariana Trench, Marceau Trench, and New Britain Trench in the Pacific Ocean, respectively. Results showed that different community compositions were detected across all the amphipod specimens based on the analyses of alpha-diversity, hierarchical cluster tree, and PCoA (principal coordinate analysis). Moreover, almost no correlation was observed between genera overrepresented in different amphipods by microbe-microbe correlations analysis, which suggested that the colonization of symbionts were host-specific. At genus level, Psychromonas was dominant in H. gigas, and Candidatus Hepatoplasma was overall dominant in A. gigantea and B. schellenbergi. Comparison of the functional potential showed that, though three hadal amphipod species shared the same predominant functional pathways, the abundances of those most shared pathways showed distinct differences across all the specimens. These findings pointed to the enrichment of particular functional pathways in the gut microbiota of the different isolated trench amphipods. Moreover, in terms of species relative abundance, alpha-diversity and beta-diversity, there was high similarity of gut microbiota between the two A. gigantea populations, which dwelled in two different localities of the same hadal trench. Altogether, this study provides an initial investigation into the gut-microbial interactions and evolution at the hadal depths within amphipod. Each of these three amphipod species would be a model taxa for future studies investigating the influence habitat difference and geography on gut-microbial communities.
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Affiliation(s)
- Jiulin Chan
- Shanghai Engineering Research Center of Hadal Science & Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China
| | - Daoqiang Geng
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China
| | - Binbin Pan
- Shanghai Engineering Research Center of Hadal Science & Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China
| | - Qiming Zhang
- Shanghai Rainbowfish Ocean Technology Co., Ltd., Lingang New City, Shanghai, 201306, People's Republic of China
| | - Qianghua Xu
- Shanghai Engineering Research Center of Hadal Science & Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China.
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China.
- National Distant-water Fisheries Engineering Research Center, Shanghai Ocean University, Shanghai, 201306, People's Republic of China.
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13
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Millar EN, Kidd KA, Surette MG, Bennett CJ, Salerno J, Gillis PL. Effects of municipal wastewater effluents on the digestive gland microbiome of wild freshwater mussels (Lasmigona costata). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 241:113774. [PMID: 35777341 DOI: 10.1016/j.ecoenv.2022.113774] [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: 03/01/2022] [Revised: 06/07/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023]
Abstract
Gut microbial communities are vital for maintaining host health, and are sensitive to diet, environment, and chemical exposures. Wastewater treatment plants (WWTPs) release effluents containing antimicrobials, pharmaceuticals, and other contaminants that may negatively affect the gut microbiome of downstream organisms. This study investigated changes in the diversity and composition of the digestive gland microbiome of flutedshell mussels (Lasmigona costata) from upstream and downstream of two large (service >100,000) WWTPs. Mussel digestive gland microbiome was analyzed following the extraction, PCR amplification, and sequencing of bacterial DNA using the V3-V4 hypervariable regions of the 16 S rRNA gene. Bacterial alpha diversity decreased at sites downstream of the second WWTP and these sites were dissimilar in beta diversity from sites upstream and downstream of the first upstream WWTP. The microbiomes of mussels collected downstream of the first WWTP had increased relative abundances of Actinobacteria, Bacteroidetes, and Firmicutes, with a decrease in Cyanobacteria, compared to upstream mussels. Meanwhile, those collected downstream of the second WWTP increased in Proteobacteria and decreased in Actinobacteria, Bacteroidetes, and Tenericutes. Increased Proteobacteria has been linked to adverse effects in mammals, but their functions in mussels is currently unknown. Finally, effluent-derived bacteria were found in the microbiome of mussels downstream of both WWTPs but not in those from upstream. Overall, results show that the digestive gland microbiome of mussels collected upstream and downstream of WWTPs differed, which has implications for altered host health and the transport of WWTP-derived bacteria through aquatic ecosystems.
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Affiliation(s)
- Elise N Millar
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Karen A Kidd
- Department of Biology, McMaster University, Hamilton, Ontario, Canada; School of Earth, Environment and Society, McMaster University, Hamilton, Ontario, Canada.
| | - Michael G Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada; Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - C James Bennett
- Aquatic Contaminants Research Division, Water Science and Technology Directorate, Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Joseph Salerno
- Aquatic Contaminants Research Division, Water Science and Technology Directorate, Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Patricia L Gillis
- Aquatic Contaminants Research Division, Water Science and Technology Directorate, Environment and Climate Change Canada, Burlington, Ontario, Canada
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Ramirez-Delgado D, Cicala F, Gonzalez-Sanchez RA, Avalos-Tellez R, Solana-Arellano E, Licea-Navarro A. Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México. PeerJ 2022; 10:e13235. [PMID: 35833012 PMCID: PMC9272818 DOI: 10.7717/peerj.13235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/17/2022] [Indexed: 01/13/2023] Open
Abstract
Background The gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the use of a single hypervariable region (HR) of 16S rRNA, which may result in misleading structural interpretations and limit comparisons among studies. Here, we considered a multi-locus analysis by targeting six HRs of 16S rRNA with the aims of (i) comprehensively assessing the GI bacterial consortium in rectal samples from Zalophus californianus pups and (ii) elucidating structural variations among the tested HRs. In addition, we evaluated which HRs may be most suitable for identifying intrinsic, structurally related microbiome characteristics, such as geographic variations or functional capabilities. Methods We employed a Short MUltiple Regions Framework (SMURF) approach using the Ion 16S™ Metagenomic Kit. This kit provides different proprietary primers designed to target six HRs of the 16S rRNA gene. To date, the only analytical pipeline available for this kit is the Ion Reporter™ Software of Thermo Fisher Scientific. Therefore, we propose an in-house pipeline to use with open-access tools, such as QIIME2 and PICRUSt 2, in downstream bioinformatic analyses. Results As hypothesized, distinctive bacterial community profiles were observed for each analyzed HR. A higher number of bacterial taxa were detected with the V3 and V6-V7 regions. Conversely, the V8 and V9 regions were less informative, as we detected a lower number of taxa. The synergistic information of these HRs suggests that the GI microbiota of Zalophus californianus pups is predominated by five bacterial phyla: Proteobacteria (~50%), Bacteroidetes (~20%), Firmicutes (~18%), Fusobacteria (~7%), and Epsilonbacteraeota (~4%). Notably, our results differ at times from previously reported abundance profiles, which may promote re-evaluations of the GI bacterial compositions in sea lions and other pinniped species that have been reported to date. Moreover, consistent geographic differences were observed only with the V3, V4, and V6-V7 regions. In addition, these HRs also presented higher numbers of predicted molecular pathways, although no significant functional changes were apparent. Together, our results suggests that multi-locus analysis should be encouraged in GI microbial surveys, as single-locus approaches may result in misleading structural results that hamper the identification of structurally related microbiome features.
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Affiliation(s)
| | - Francesco Cicala
- Biomedical Innovation Department, CICESE, Ensenada, Baja California, México
| | | | - Rosalia Avalos-Tellez
- Comisión Nacional de Areas Naturales Protegidas, Secretaría de Medio Ambiente y Recursos Naturales, Bahia de los Angeles, Baja California, México
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15
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Crosstalk between gut microbiota and lung inflammation in murine toxicity models of respiratory exposure or co-exposure to carbon nanotube particles and cigarette smoke extract. Toxicol Appl Pharmacol 2022; 447:116066. [PMID: 35595072 DOI: 10.1016/j.taap.2022.116066] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/08/2022] [Accepted: 05/11/2022] [Indexed: 11/23/2022]
Abstract
Carbon nanotubes (CNTs) are emerging environmental and occupational toxicants known to induce lung immunotoxicity. While the underlying mechanisms are evolving, it is yet unknown whether inhaled CNTs would cause abnormalities in gut microbiota (dysbiosis), and if such microbiota alteration plays a role in the modulation of CNT-induced lung immunotoxicity. It is also unknown whether co-exposure to tobacco smoke will modulate CNT effects. We compared the effects of lung exposure to multi-wall CNT, cigarette smoke extract (CSE), and their combination (CNT + CSE) in a 4-week chronic toxicity mouse model. The exposures induced differential perturbations in gut microbiome as evidenced by altered microbial α- and β- diversity, indicating a lung-to-gut communication. The gut dysbiosis due to CNTs, unlike CSE, was characterized by an increase in Firmicutes/Bacteroidetes ratio typically associated with proinflammatory condition. Notably, while all three exposures reduced Proteobacteria, the CNT exposure and co-exposure induced appearance of Tenericutes and Cyanobacteria, respectively, implicating them as potential biomarkers of exposure. CNTs differentially induced certain lung proinflammatory mediators (TNF-α, IL-1β, CCL2, CXCL5) whereas CNTs and CSE commonly induced other mediators (CXCL1 and TGF-β). The co-exposure showed either a component-dominant effect or a summative effect for both dysbiosis and lung inflammation. Depletion of gut microbiota attenuated both the differentially-induced and commonly-induced (TGF-β) lung inflammatory mediators as well as granulomas implying gut-to-lung communication and a modulatory role of gut dysbiosis. Taken together, the results demonstrated gut dysbiosis as a systemic effect of inhaled CNTs and provided the first evidence of a bidirectional gut-lung crosstalk modulating CNT lung immunotoxicity.
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16
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Abstract
Microbial communities associated with deep-sea animals are critical to the establishment of novel biological communities in unusual environments. Over the past few decades, rapid exploration of the deep sea has enabled the discovery of novel microbial communities, some of which form symbiotic relationships with animal hosts. Symbiosis in the deep sea changes host physiology, behavior, ecology, and evolution over time and space. Symbiont diversity within a host is often aligned with diverse metabolic pathways that broaden the environmental niche for the animal host. In this review, we focus on microbiomes and obligate symbionts found in different deep-sea habitats and how they facilitate survival of the organisms that live in these environments. In addition, we discuss factors that govern microbiome diversity, host specificity, and biogeography in the deep sea. Finally, we highlight the current limitations of microbiome research and draw a road map for future directions to advance our knowledge of microbiomes in the deep sea. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Eslam O Osman
- Biology Department, Eberly College, Pennsylvania State University, State College, Pennsylvania, USA; .,Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Marine Biology Lab, Zoology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Alexis M Weinnig
- Biology Department, Temple University, Philadelphia, Pennsylvania, USA
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17
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Liu G, Guo Z, Liu D, Meng H, Zheng Y, Zhao X, Gu L, Chen Z, Chen X, Li M, Sun J, Ma Z, He H, Yu X, Hu F. Does gut microbiota regulate brooding in geese? ANIM BIOL 2021. [DOI: 10.1163/15707563-bja10059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Domestic geese can reduce the amount of food intake when brooding. Because of the reduction in food intake, the total number of microorganisms in the gut is also reduced. Will this affect the goose’s thinking and make the goose stop brooding and eat food? We hypothesize that gut microbiota affects the brain through a brain–gut peptide and further regulates the breeding behavior of geese. In this study, we evaluated the microbiome related to the goose and transcription groups of brooding and egg production periods. The changes and differences in gut microbiota and gene expression of female geese in different reproduction periods were analyzed, and the possible interaction between them was explored. The results showed that the relative abundance of Faecalibacterium with a growth-promoting effect in the cecum was higher in the egg production group than in the brooding group. Microbial metabolic pathways with significant differences between the two groups were also enriched in the secondary functional groups with different gut microbiota metabolism. The downregulated genes in the egg production group were mainly related to energy metabolism, such as ATP synthesis-related genes. These results suggest that the brooding group’s gut microbiota can make relevant changes according to the reproduction stage of the goose. Since the amount of food taken in is reduced, it can promote the decomposition of the host’s fat. Simultaneously, insulin is also used to deliver messages to the brain; it is necessary to end the brooding behavior at an appropriate time and for eating to start.
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Affiliation(s)
- Guojun Liu
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, No. 368 Xuefu Road, Harbin 150086, P.R. China
| | - Zhenhua Guo
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, No. 368 Xuefu Road, Harbin 150086, P.R. China
| | - Di Liu
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, No. 368 Xuefu Road, Harbin 150086, P.R. China
| | - He Meng
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, P.R. China
| | - Yuming Zheng
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, P.R. China
| | - Xiuhua Zhao
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, No. 368 Xuefu Road, Harbin 150086, P.R. China
| | - Lihong Gu
- Hainan Academy of Agricultural Sciences, Institute of Animal Science and Veterinary Medicine, 14 Xingdan Road, Qiongshan District, Haikou, 570203, P.R. China
| | - Zhifeng Chen
- Heilongjiang Academy of Agricultural Sciences, Qiqihare Branch Academy, No. 2 Heyi Road, Qiqihare 161005, P.R. China
| | - Xingyong Chen
- College of Animal Science and Technology, Anhui Agricultural University, No. 130 Changjiangxi Road, Hefei, 230036, P.R. China
| | - Manyu Li
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, No. 368 Xuefu Road, Harbin 150086, P.R. China
| | - Jinyan Sun
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, No. 368 Xuefu Road, Harbin 150086, P.R. China
| | - Zhigang Ma
- Heilongjiang Academy of Agricultural Sciences, Qiqihare Branch Academy, No. 2 Heyi Road, Qiqihare 161005, P.R. China
| | - Haijuan He
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, No. 368 Xuefu Road, Harbin 150086, P.R. China
| | - Xiaolong Yu
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, No. 368 Xuefu Road, Harbin 150086, P.R. China
| | - Fanghong Hu
- Agricultural and Rural Bureau, Longhexi Road, Liuan, 237006, P.R. China
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Alghetaa H, Mohammed A, Zhou J, Singh N, Nagarkatti M, Nagarkatti P. Resveratrol-mediated attenuation of superantigen-driven acute respiratory distress syndrome is mediated by microbiota in the lungs and gut. Pharmacol Res 2021; 167:105548. [PMID: 33722710 PMCID: PMC10116750 DOI: 10.1016/j.phrs.2021.105548] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 02/23/2021] [Accepted: 03/09/2021] [Indexed: 12/17/2022]
Abstract
Acute Respiratory Distress Syndrome (ARDS) is triggered by a variety of agents, including Staphylococcal Enterotoxin B (SEB). Interestingly, a significant proportion of patients with COVID-19, also develop ARDS. In the absence of effective treatments, ARDS results in almost 40% mortality. Previous studies from our laboratory demonstrated that resveratrol (RES), a stilbenoid, with potent anti-inflammatory properties can attenuate SEB-induced ARDS. In the current study, we investigated the role of RES-induced alterations in the gut and lung microbiota in the regulation of ARDS. Our studies revealed that SEB administration induced inflammatory cytokines, ARDS, and 100% mortality in C3H/HeJ mice. Additionally, SEB caused a significant increase in pathogenic Proteobacteria phylum and Propionibacterium acnes species in the lungs. In contrast, RES treatment attenuated SEB-mediated ARDS and mortality in mice, and significantly increased probiotic Actinobacteria phylum, Tenericutes phylum, and Lactobacillus reuteri species in both the colon and lungs. Colonic Microbiota Transplantation (CMT) from SEB-injected mice that were treated with RES as well as the transfer of L. reuteri into recipient mice inhibited the production of SEB-mediated induction of pro-inflammatory cytokines such as IFN-γ and IL-17 but increased that of anti-inflammatory IL-10. Additionally, such CMT and L. reuteri recipient mice exposed to SEB, showed a decrease in lung-infiltrating mononuclear cells, cytotoxic CD8+ T cells, NKT cells, Th1 cells, and Th17 cells, but an increase in the population of regulatory T cells (Tregs) and Th3 cells, and increase in the survival of mice from SEB-mediated ARDS. Together, the current study demonstrates that ARDS induced by SEB triggers dysbiosis in the lungs and gut and that attenuation of ARDS by RES may be mediated, at least in part, by alterations in microbiota in the lungs and the gut, especially through the induction of beneficial bacteria such as L. reuteri.
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Affiliation(s)
- Hasan Alghetaa
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
| | - Amira Mohammed
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
| | - Juhua Zhou
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
| | - Narendra Singh
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
| | - Prakash Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA.
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Turgay E, Steinum TM, Eryalçın KM, Yardımcı RE, Karataş S. The influence of diet on the microbiota of live-feed rotifers (Brachionus plicatilis) used in commercial fish larviculture. FEMS Microbiol Lett 2021; 367:5719568. [PMID: 32005987 DOI: 10.1093/femsle/fnaa020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/29/2020] [Indexed: 12/21/2022] Open
Abstract
Live-feed is indispensable to commercial fish larviculture. However, high bacterial loads in rotifers could pose a biosecurity risk. While this may be true, live-feed associated bacteria could also be beneficial to fish larvae through improved feed utilization or pathogen inhibition following host microbiota modification. The study objective was to elucidate the largely unexplored microbiota of rotifers propagated on five different diets through bacterial community profiling by 16S rRNA gene amplicon sequencing. Investigated rotifer samples had a median observed alpha-diversity of 338 ± 87 bacterial species. Alpha- and Gamma-Proteobacteria dominated the rotifer microbiota followed by members of classes Flavobacteriia, Cytophagia, Mollicutes, Phycisphaerae and Bacteroidia. Different diets significantly altered the bacterial communities associated with rotifers according to PERMANOVA test results and beta dispersion calculations. A common core rotifer microbiome included 31 bacterial species present in relative abundances over 0.01%. We discuss the functional role of some microbiome members. Our data suggested the presence of several known fish pathogens in stock rotifers. However, we found no evidence for increased loads of these presumptive taxa in propagated live-feed rotifers during this field trial.
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Affiliation(s)
- Emre Turgay
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
| | - Terje Marken Steinum
- Department of Molecular Biology and Genetics, Faculty of Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
| | - Kamil Mert Eryalçın
- Fish Nutrition & Phytoplankton-Zooplankton Culture Laboratory, Aquaculture Department, Faculty of Aquatic Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
| | - Remziye Eda Yardımcı
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
| | - Süheyla Karataş
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
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Microbiota of the Digestive Gland of Red Abalone ( Haliotis rufescens) Is Affected by Withering Syndrome. Microorganisms 2020; 8:microorganisms8091411. [PMID: 32933183 PMCID: PMC7565822 DOI: 10.3390/microorganisms8091411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/28/2020] [Accepted: 09/03/2020] [Indexed: 12/30/2022] Open
Abstract
Withering syndrome (WS), an infectious disease caused by intracellular bacteria Candidatus Xenohaliotis californiensis, has provoked significant economic losses in abalone aquaculture. The pathogen infects gastroenteric epithelia, including digestive gland, disrupting the digestive system and causing a progressive wilting in abalone. Nonetheless, our knowledge about WS implications in digestive gland microbiota, and its role in diseases progress remains largely unknown. This study aims to determine whether digestive gland-associated microbiota differs between healthy red abalone (Haliotis rufescens) and red abalone affected with WS. Using high-throughput sequencing of the V4 region of the 16S rRNA gene, our results revealed differences in microbiota between groups. Bacterial genera, including Mycoplasma, Lactobacillus, Cocleimonas and Tateyamaria were significantly more abundant in healthy abalones, whilst Candidatus Xenohaliotis californiensis and Marinomonas were more abundant in WS-affected abalones. Whilst Mycoplasma was the dominant genus in the healthy group, Candidatus Xenohaliotis californiensis was dominant in the WS group. However, Candidatus Xenohaliotis californiensis was present in two healthy specimens, and thus the Mycoplasma/Candidatus Xenohaliotis californiensis ratio appears to be more determinant in specimens affected with WS. Further research to elucidate the role of digestive gland microbiota ecology in WS pathogenesis is required.
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21
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Wang Y, Huang JM, Zhou YL, Almeida A, Finn RD, Danchin A, He LS. Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli. BMC Genomics 2020; 21:408. [PMID: 32552739 PMCID: PMC7301438 DOI: 10.1186/s12864-020-06807-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/05/2020] [Indexed: 12/28/2022] Open
Abstract
Background The metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies have been largely focused on pathogenic species. In this study, we expanded analyses on Tenericutes lineages that inhabit various environments using a collection of 840 genomes. Results Several environmental lineages were discovered inhabiting the human gut, ground water, bioreactors and hypersaline lake and spanning the Haloplasmatales and Mycoplasmatales orders. A phylogenomics analysis of Bacilli and Tenericutes genomes revealed that some uncultured Tenericutes are affiliated with novel clades in Bacilli, such as RF39, RFN20 and ML615. Erysipelotrichales and two major gut lineages, RF39 and RFN20, were found to be neighboring clades of Mycoplasmatales. We detected habitat-specific functional patterns between the pathogenic, gut and the environmental Tenericutes, where genes involved in carbohydrate storage, carbon fixation, mutation repair, environmental response and amino acid cleavage are overrepresented in the genomes of environmental lineages, perhaps as a result of environmental adaptation. We hypothesize that the two major gut lineages, namely RF39 and RFN20, are probably acetate and hydrogen producers. Furthermore, deteriorating capacity of bactoprenol synthesis for cell wall peptidoglycan precursors secretion is a potential adaptive strategy employed by these lineages in response to the gut environment. Conclusions This study uncovers the characteristic functions of environmental Tenericutes and their relationships with Bacilli, which sheds new light onto the pathogenicity and evolutionary processes of Mycoplasmatales.
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Affiliation(s)
- Yong Wang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.
| | - Jiao-Mei Huang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ying-Li Zhou
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.,University of Chinese Academy of Sciences, Beijing, China
| | - Alexandre Almeida
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Antoine Danchin
- Kodikos, Department of Infection, Immunity and Inflammation, Institut Cochin INSERM U1016 - CNRS UMR8104 - Université Paris Descartes, 24 rue du Faubourg Saint-Jacques, 75014, Paris, France.,Li Kashing Faculty of Medicine, School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong, SAR, China
| | - Li-Sheng He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China
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22
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Lian CA, Yan GY, Huang JM, Danchin A, Wang Y, He LS. Genomic Characterization of a Novel Gut Symbiont From the Hadal Snailfish. Front Microbiol 2020; 10:2978. [PMID: 31998265 PMCID: PMC6965317 DOI: 10.3389/fmicb.2019.02978] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/10/2019] [Indexed: 01/30/2023] Open
Abstract
Hadal trenches are characterized by not only high hydrostatic pressure but also scarcity of nutrients and high diversity of viruses. Snailfishes, as the dominant vertebrates, play an important role in hadal ecology. Although studies have suggested possible reasons for the tolerance of hadal snailfish to high hydrostatic pressure, little is known about the strategies employed by hadal snailfish to cope with low-nutrient and virus-rich conditions. In this study, the gut microbiota of hadal snailfish was investigated. A novel bacterium named "Candidatus Mycoplasma liparidae" was dominant in the guts of three snailfish individuals from both the Mariana and Yap trenches. A draft genome of "Ca. Mycoplasma liparidae" was successfully assembled with 97.8% completeness by hybrid sequencing. A set of genes encoding riboflavin biosynthesis proteins and a clustered regularly interspaced short palindromic repeats (CRISPR) system was present in the genome of "Ca. Mycoplasma liparidae," which was unusual for Mycoplasma. The functional repertoire of the "Ca. Mycoplasma liparidae" genome is likely set to help the host in riboflavin supplementation and to provide protection against viruses via a super CRISPR system. Remarkably, genes encoding common virulence factors usually exist in Tenericutes pathogens but were lacking in the genome of "Ca. Mycoplasma liparidae." All of these characteristics supported an essential role of "Ca. Mycoplasma liparidae" in snailfish living in the hadal zone. Our findings provide further insights into symbiotic associations in the hadal biosphere.
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Affiliation(s)
- Chun-Ang Lian
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Guo-Yong Yan
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiao-Mei Huang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Antoine Danchin
- Department of Infection, Immunity and Inflammation, Institut Cochin, INSERM U1016 – CNRS UMR 8104 – Université Paris Descartes, Paris, France
| | - Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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23
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Wang Y, Zhu FC, He LS, Danchin A. Unique tRNA gene profile suggests paucity of nucleotide modifications in anticodons of a deep-sea symbiotic Spiroplasma. Nucleic Acids Res 2019; 46:2197-2203. [PMID: 29390076 PMCID: PMC5861454 DOI: 10.1093/nar/gky045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/18/2018] [Indexed: 12/22/2022] Open
Abstract
The position 34 of a tRNA is always modified for efficient recognition of codons and accurate integration of amino acids by the translation machinery. Here, we report genomics features of a deep-sea gut symbiotic Spiroplasma, which suggests that the organism does not require tRNA(34) anticodon modifications. In the genome, there is a novel set of tRNA genes composed of 32 species for recognition of the 20 amino acids. Among the anticodons of the tRNAs, we witnessed the presence of both U34- and C34-containing tRNAs required to decode NNR (A/G) 2:2 codons as countermeasure of probable loss of anticodon modification genes. In the tRNA fragments detected in the gut transcriptome, mismatches expected to be caused by some tRNA modifications were not shown in their alignments with the corresponding genes. However, the probable paucity of modified anticodons did not fundamentally change the codon usage pattern of the Spiroplasma. The tRNA gene profile that probably resulted from the paucity of tRNA(34) modifications was not observed in other symbionts and deep-sea bacteria, indicating that this phenomenon was an evolutionary dead-end. This study provides insights on co-evolution of translation machine and tRNA genes and steric constraints of codon-anticodon interactions in deep-sea extreme environment.
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Affiliation(s)
- Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Fang-Chao Zhu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Antoine Danchin
- Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié-Salpêtrière, 47 boulevard de l'Hôpital, 75013 Paris, France.,School of Biomedical Sciences, Li Kashing Faculty of Medicine, University of Hong Kong, 21 Sassoon Road, SAR Hong Kong, China
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24
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Bolaños LM, Rosenblueth M, Manrique de Lara A, Migueles-Lozano A, Gil-Aguillón C, Mateo-Estrada V, González-Serrano F, Santibáñez-López CE, García-Santibáñez T, Martínez-Romero E. Cophylogenetic analysis suggests cospeciation between the Scorpion Mycoplasma Clade symbionts and their hosts. PLoS One 2019; 14:e0209588. [PMID: 30625167 PMCID: PMC6326461 DOI: 10.1371/journal.pone.0209588] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/08/2018] [Indexed: 11/19/2022] Open
Abstract
Scorpions are predator arachnids of ancient origin and worldwide distribution. Two scorpion species, Vaejovis smithi and Centruroides limpidus, were found to harbor two different Mollicutes phylotypes: a Scorpion Mycoplasma Clade (SMC) and Scorpion Group 1 (SG1). Here we investigated, using a targeted gene sequencing strategy, whether these Mollicutes were present in 23 scorpion morphospecies belonging to the Vaejovidae, Carboctonidae, Euscorpiidae, Diplocentridae, and Buthidae families. Our results revealed that SMC is found in a species-specific association with Vaejovidae and Buthidae, whereas SG1 is uniquely found in Vaejovidae. SMC and SG1 co-occur only in Vaejovis smithi where 43% of the individuals host both phylotypes. A phylogenetic analysis of Mollicutes 16S rRNA showed that SMC and SG1 constitute well-delineated phylotypes. Additionally, we found that SMC and scorpion phylogenies are significantly congruent, supporting the observation that a cospeciation process may have occurred. This study highlights the phylogenetic diversity of the scorpion associated Mollicutes through different species revealing a possible cospeciation pattern.
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Affiliation(s)
- Luis M. Bolaños
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Mónica Rosenblueth
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Amaranta Manrique de Lara
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Analí Migueles-Lozano
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Citlali Gil-Aguillón
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Valeria Mateo-Estrada
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Francisco González-Serrano
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Carlos E. Santibáñez-López
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Tonalli García-Santibáñez
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Esperanza Martínez-Romero
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
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25
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Cicala F, Cisterna-Céliz JA, Moore JD, Rocha-Olivares A. Structure, dynamics and predicted functional role of the gut microbiota of the blue ( Haliotis fulgens) and yellow ( H. corrugata) abalone from Baja California Sur, Mexico. PeerJ 2018; 6:e5830. [PMID: 30405968 PMCID: PMC6216945 DOI: 10.7717/peerj.5830] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 09/25/2018] [Indexed: 12/21/2022] Open
Abstract
The GI microbiota of abalone contains a highly complex bacterial assemblage playing an essential role in the overall health of these gastropods. The gut bacterial communities of abalone species characterized so far reveal considerable interspecific variability, likely resulting from bacterial interactions and constrained by the ecology of their abalone host species; however, they remain poorly investigated. Additionally, the extent to which structural changes in the microbiota entail functional shifts in metabolic pathways of bacterial communities remains unexplored. In order to address these questions, we characterized the gut microbiota of the northeast Pacific blue (Haliotis fulgens or HF) and yellow (Haliotis corrugata or HC) abalone by 16S rRNA gene pyrosequencing to shed light on: (i) their gut microbiota structure; (ii) how bacteria may interact among them; and (iii) predicted shifts in bacterial metabolic functions associated with the observed structural changes. Our findings revealed that Mycoplasma dominated the GI microbiome in both species. However, the structure of the bacterial communities differed significantly in spite of considerable intraspecific variation. This resulted from changes in predominant species composition in each GI microbiota, suggesting host-specific adaptation of bacterial lineages to these sympatric abalone. We hypothesize that the presence of exclusive OTUs in each microbiota may relate to host-specific differences in competitive pressure. Significant differences in bacterial diversity were found between species for the explored metabolic pathways despite their functional overlap. A more diverse array of bacteria contributed to each function in HC, whereas a single or much fewer OTUs were generally observed in HF. The structural and functional analyses allowed us to describe a significant taxonomic split and functional overlap between the microbiota of HF and HC abalone.
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Affiliation(s)
- Francesco Cicala
- Molecular Ecology Laboratory, Department of Biological Oceanography, CICESE, Ensenada, Baja California, Mexico
| | | | - James D Moore
- Bodega Marine Laboratory, University of California, Davis, Bodega Bay, CA, United States of America
| | - Axayácatl Rocha-Olivares
- Molecular Ecology Laboratory, Department of Biological Oceanography, CICESE, Ensenada, Baja California, Mexico
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26
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Molecular Characterization of a Novel N-Acetylneuraminate Lyase from a Deep-Sea Symbiotic Mycoplasma. Mar Drugs 2018; 16:md16030080. [PMID: 29510563 PMCID: PMC5867624 DOI: 10.3390/md16030080] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/19/2018] [Accepted: 02/26/2018] [Indexed: 12/01/2022] Open
Abstract
N-acetylneuraminic acid (Neu5Ac) based novel pharmaceutical agents and diagnostic reagents are highly required in medical fields. However, N-acetylneuraminate lyase(NAL)for Neu5Ac synthesis is not applicable for industry due to its low catalytic efficiency. In this study, we biochemically characterized a deep-sea NAL enzyme (abbreviated form: MyNal) from a symbiotic Mycoplasma inhabiting the stomach of a deep-sea isopod, Bathynomus jamesi. Enzyme kinetic studies of MyNal showed that it exhibited a very low Km for both cleavage and synthesis activities compared to previously described NALs. Though it favors the cleavage process, MyNal out-competes the known NALs with respect to the efficiency of Neu5Ac synthesis and exhibits the highest kcat/Km values. High expression levels of recombinant MyNal could be achieved (9.56 mol L−1 culture) with a stable activity in a wide pH (5.0–9.0) and temperature (40–60 °C) range. All these features indicated that the deep-sea NAL has potential in the industrial production of Neu5Ac. Furthermore, we found that the amino acid 189 of MyNal (equivalent to Phe190 in Escherichia coli NAL), located in the sugar-binding domain, GX189DE, was also involved in conferring its enzymatic features. Therefore, the results of this study improved our understanding of the NALs from different environments and provided a model for protein engineering of NAL for biosynthesis of Neu5Ac.
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27
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He LS, Zhang PW, Huang JM, Zhu FC, Danchin A, Wang Y. The Enigmatic Genome of an Obligate Ancient Spiroplasma Symbiont in a Hadal Holothurian. Appl Environ Microbiol 2018; 84:e01965-17. [PMID: 29054873 PMCID: PMC5734040 DOI: 10.1128/aem.01965-17] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/15/2017] [Indexed: 11/20/2022] Open
Abstract
Protective symbiosis has been reported in many organisms, but the molecular mechanisms of the mutualistic interactions between the symbionts and their hosts are unclear. Here, we sequenced the 424-kbp genome of "Candidatus Spiroplasma holothuricola," which dominated the hindgut microbiome of a sea cucumber, a major scavenger captured in the Mariana Trench (6,140 m depth). Phylogenetic relationships indicated that the dominant bacterium in the hindgut was derived from a basal group of Spiroplasma species. In this organism, the genes responsible for the biosynthesis of amino acids, glycolysis, and sugar transporters were lost, strongly suggesting endosymbiosis. The highly decayed genome consists of two chromosomes and harbors genes coding for proteolysis, microbial toxin, restriction-methylation systems, and clustered regularly interspaced short palindromic repeats (CRISPRs), composed of three cas genes and 76 CRISPR spacers. The holothurian host is probably protected against invading viruses from sediments by the CRISPRs/Cas and restriction systems of the endosymbiotic spiroplasma. The protective endosymbiosis indicates the important ecological role of the ancient Spiroplasma symbiont in the maintenance of hadal ecosystems.IMPORTANCE Sea cucumbers are major inhabitants in hadal trenches. They collect microbes in surface sediment and remain tolerant against potential pathogenic bacteria and viruses. This study presents the genome of endosymbiotic spiroplasmas in the gut of a sea cucumber captured in the Mariana Trench. The extreme reduction of the genome and loss of essential metabolic pathways strongly support its endosymbiotic lifestyle. Moreover, a considerable part of the genome was occupied by a CRISPR/Cas system to provide immunity against viruses and antimicrobial toxin-encoding genes for the degradation of microbes. This novel species of Spiroplasma is probably an important protective symbiont for the sea cucumbers in the hadal zone.
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Affiliation(s)
- Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Pei-Wei Zhang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Jiao-Mei Huang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Fang-Chao Zhu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Antoine Danchin
- Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
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