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1.
Int J Syst Evol Microbiol ; 70(10): 5488-5496, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32886593

RESUMO

A novel Gram-stain-negative, non-motile, strictly aerobic, rod-shaped bacterium was isolated from deep-sea hydrothermal sulfide in the northwest Indian Ocean Ridge and designated as strain IOP_32T. Strain IOP_32T could grow at 4-40 °C (optimum, 37 °C), pH 5-9 (optimum, pH 7-8) and salinity of 0-12 % NaCl (w/v; optimum, 2-3 %). The 16S rRNA gene sequence of strain IOP_32T is most similar to Bizionia fulviae EM7T, Bizionia berychis RA3-3-1T, Bizionia paragorgiae KMM 6029T and Oceanihabitans sediminis S9_10T with 95.5-95.3 % similarity. The phylogenomic analysis indicated that strain IOP_32T forms a distinct lineage with Flaviramulus ichthyoenteri Th78T within the family Flavobacteriaceae. The average nucleotide identity, average amino acid identity and percentage of conserved protein values between strain IOP_32T and the type strains of close genera were 72.3-78.5 %, 67.4-76.9 % and 56.3-61.6 %, respectively. The major cellular fatty acid was anteiso-C15 : 0. The respiratory quinone was MK-6. The polar lipids were mainly composed of phosphatidylethanolamine, an unidentified aminophospholipid and five unidentified polar lipids. Strain IOP_32T is significantly different from related genera, which is reflected by the wide adaptability to temperature and salinity levels, the composition of phospholipids and fatty acids, and the results of phylogenetic analyses. The phenotypic properties and phylogenetic data suggest that the lineage represents a novel genus and species within the family Flavobacteriaceae, for which the name Wocania indica gen. sp. nov. is proposed, with the type strain IOP_32T (=MCCC 1A14017 T=KCTC 62660 T). We also propose the reclassification of Flaviramulus ichthyoenteri as Wocania ichthyoenteri comb. nov. (Th78T=DSM 26285T=JCM 18634T=KCTC 32142T).


Assuntos
Flavobacteriaceae/classificação , Fontes Hidrotermais/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/isolamento & purificação , Oceano Índico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
2.
Environ Int ; 144: 106068, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32871382

RESUMO

Atmospheric CO2 concentration is increasing, largely due to anthropogenic activities. Previous studies of individual free-air CO2 enrichment (FACE) experimental sites have shown significant impacts of elevated CO2 (eCO2) on soil microbial communities; however, no common microbial response patterns have yet emerged, challenging our ability to predict ecosystem functioning and sustainability in the future eCO2 environment. Here we analyzed 66 soil microbial communities from five FACE sites, and showed common microbial response patterns to eCO2, especially for key functional genes involved in carbon and nitrogen fixation (e.g., pcc/acc for carbon fixation, nifH for nitrogen fixation), carbon decomposition (e.g., amyA and pulA for labile carbon decomposition, mnp and lcc for recalcitrant carbon decomposition), and greenhouse gas emissions (e.g., mcrA for methane production, norB for nitrous oxide production) across five FACE sites. Also, the relative abundance of those key genes was generally increased and directionally associated with increased biomass, soil carbon decomposition, and soil moisture. In addition, a further literature survey of more disparate FACE experimental sites indicated increased biomass, soil carbon decay, nitrogen fixation, methane and nitrous oxide emissions, plant and soil carbon and nitrogen under eCO2. A conceptual framework was developed to link commonly responsive functional genes with ecosystem processes, such as pcc/acc vs. soil carbon storage, amyA/pulA/mnp/lcc vs. soil carbon decomposition, and nifH vs. nitrogen availability, suggesting that such common responses of microbial functional genes may have the potential to predict ecosystem functioning and sustainability in the future eCO2 environment.

3.
Appl Microbiol Biotechnol ; 104(15): 6813-6824, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32514755

RESUMO

A deteriorated water quality is closely associated with disease outbreaks in aquaculture, where microorganisms play indispensable roles in improving water quality and aquatic animals' health. Mangrove is known to be a natural water quality filter and microbiological buffer of pathogen and prebiotics. However, it is unclear how and to what extent Rhizophora apiculata plantation is of benefits to the gut microbiota and growth over mud crab (Scylla paramamosain) aging. To address these concerns, we explored the bacterial communities in mud crab gut and rearing water at 45, 114, and 132 days after incubation, roughly corresponding to juvenile, pre-adult, and adult stages of mud crab. Results showed that 1-year R. apiculata plantation slightly increased the body weight of mud crab and improved water quality to a certain extent. Both bacterioplankton and gut bacterial communities were highly temporal dynamic, while the two communities were significantly distinct (ANOSIM r = 0.90, P = 0.0001). Relative abundances of dominant taxa in water and gut significantly varied between the plantation and the control conditions over mud crab aging. R. apiculata plantation promoted the stability of gut microbiota, as evidenced by more diverse core species. Furthermore, R. apiculata plantation led to the dominance of Verrucomicrobiae species in water and probiotic Bacteroidetes and Lactobacillales taxa in gut. A structural equation model revealed that water variables directly constrained gut microbiota, which in turn affected the body weight of mud crab (r = 0.52, P < 0.001). In addition, functional pathways facilitating immunity and lipid metabolism significantly increased in mud crab gut under the plantation, while those involved in infectious diseases exhibited the opposing trend. These findings greatly expand our understanding of the R. apiculata plantation effects on water quality, gut microbiota, and growth feature of mud crab. Overall, R. apiculata plantation is beneficial for mud crab growth and health. KEY POINTS: • A short-term R. apiculata plantation could potentially improve water quality. • Bacterioplankton is more sensitive than mud crab gut microbiota in response to R. apiculata plantation. • R. apiculata plantation enhances mud crab resistance against pathogen invasion. • R. apiculata plantation alters mud crab gut microbiota, which in turn promotes their body weight.

4.
Microb Ecol ; 80(4): 935-945, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32494840

RESUMO

Understanding the rules that govern the successions of gut microbiota is prerequisite for testing general ecological theories and sustaining a desirable microbiota. However, the ignorance of microeukaryotes raises the question of whether gut microeukaryotes are assembled according to the same rules as bacteria. We tracked the shrimp gut bacterial and microeukaryotic communities by a longitudinal dense sampling. The successions of both domains were significantly correlated with host age, with relatively stable microeukaryotic communities in adult shrimp. Gut microeukaryotes exhibited significantly higher turnover rate, but fewer transient species, lower proportion of temporal generalists, and narrower habitat niche breadth than bacteria. The γ-diversity partitioning analysis revealed that the successions of gut microbiotas were primarily ascribed to the high dissimilarity as shrimp aged ([Formula: see text]IntraTimes), whereas the relative importance of [Formula: see text]IntraTimes was significantly higher for microeukaryotes than that for bacteria. Compared with contrasting ecological processes in governing free-living bacteria and microeukaryotes, the ecological patterns were comparable between host-associated gut counterparts. However, the gut microeukaryotes were governed more strongly by deterministic selection relative to nestedness compared with the gut bacteria, which supports the "size-plasticity" hypothesis. Our results highlight the importance of independently interpreting free-living and host-associated meta-communities for a comprehensive understanding of the processes that govern microbial successions.

5.
Microb Ecol ; 80(2): 447-458, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32307553

RESUMO

It is now recognized that some diseases of aquatic animals are attributed to polymicrobial pathogens infection. Thus, the traditional view of "one pathogen, one disease" might mislead the identification of multiple pathogens, which in turn impedes the design of probiotics. To address this gap, we explored polymicrobial pathogens based on the origin and timing of increased abundance over shrimp white feces syndrome (WFS) progression. OTU70848 Vibrio fluvialis, OTU35090 V. coralliilyticus, and OTU28721 V. tubiashii were identified as the primary colonizers, whose abundances increased only in individuals that eventually showed disease signs but were stable in healthy subjects over the same timeframe. Notably, the random Forest model revealed that the profiles of the three primary colonizers contributed an overall 91.4% of diagnosing accuracy of shrimp health status. Additionally, NetShift analysis quantified that the three primary colonizers were important "drivers" in the gut microbiotas from healthy to WFS shrimp. For these reasons, the primary colonizers were potential pathogens that contributed to the exacerbation of WFS. By this logic, we further identified a few "drivers" commensals in healthy individuals, such as OUT50531 Demequina sediminicola and OTU_74495 Ruegeria lacuscaerulensis, which directly antagonized the three primary colonizers. The predicted functional pathways involved in energy metabolism, genetic information processing, terpenoids and polyketides metabolism, lipid and amino acid metabolism significantly decreased in diseased shrimp compared with those in healthy cohorts, in concordant with the knowledge that the attenuations of these functional pathways increase shrimp sensitivity to pathogen infection. Collectively, we provide an ecological framework for inferring polymicrobial pathogens and designing antagonized probiotics by quantifying their changed "driver" feature that intimately links shrimp WFS progression. This approach might generalize to the exploring disease etiology for other aquatic animals.

6.
Microbiome ; 8(1): 32, 2020 03 10.
Artigo em Inglês | MEDLINE | ID: mdl-32156316

RESUMO

BACKGROUND: Recently, increasing evidence supports that some complex diseases are not attributed to a given pathogen, but dysbiosis in the host intestinal microbiota (IM). The full intestinal ecosystem alterations, rather than a single pathogen, are associated with white feces syndrome (WFS), a globally severe non-infectious shrimp disease, while no experimental evidence to explore the causality. Herein, we conducted comprehensive metagenomic and metabolomic analysis, and intestinal microbiota transplantation (IMT) to investigate the causal relationship between IM dysbiosis and WFS. RESULTS: Compared to the Control shrimp, we found dramatically decreased microbial richness and diversity in WFS shrimp. Ten genera, such as Vibrio, Candidatus Bacilloplasma, Photobacterium, and Aeromonas, were overrepresented in WFS, whereas 11 genera, including Shewanella, Chitinibacter, and Rhodobacter were enriched in control. The divergent changes in these populations might contribute the observation that a decline of pathways conferring lipoic acid metabolism and mineral absorption in WFS. Meanwhile, some sorts of metabolites, especially lipids and organic acids, were found to be related to the IM alteration in WFS. Integrated with multiomics and IMT, we demonstrated that significant alterations in the community composition, functional potentials, and metabolites of IM were closely linked to shrimp WFS. The distinguished metabolites which were attributed to the IM dysbiosis were validated by feed-supplementary challenge. Both homogenous selection and heterogeneous selection process were less pronounced in WFS microbial community assembly. Notably, IMT shrimp from WFS donors eventually developed WFS clinical signs, while the dysbiotic IM can be recharacterized in recipient shrimp. CONCLUSIONS: Collectively, our findings offer solid evidence of the causality between IM dysbiosis and shrimp WFS, which exemplify the 'microecological Koch's postulates' (an intestinal microbiota dysbiosis, a disease) in disease etiology, and inspire our cogitation on etiology from an ecological perspective. Video abstract.

7.
Fish Shellfish Immunol ; 99: 176-183, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32018034

RESUMO

Large yellow croaker (Larimichthys crocea, LYC) aquaculture is being threatened by intensive infectious diseases. Relevant studies have focused on LYC immune responses to infection. By contrast, little is known how and to what extent the gut microbiota responds to infection. Here, we explored the interactions between LYC immune responses and gut bacterial communities during Pseudomonas plecoglossicida infection. P. plecoglossicida successfully colonized into LYC gut microbiota, resulting in an increasing mortality rate. Relative gene expressions of pro-inflammatory cytokines (TNF-α1, TNF-α2 and IL-1ß) and anti-inflammatory cytokine (IL-10) were consistently and significantly induced by P. plecoglossicida infection, whereas non-specific immune enzymes activities were only enhanced at the early infection stages. P. plecoglossicida infection caused an irreversible disruption in the gut microbiota, of which infection and hours post infection constrained 16.2% and 5.6% variations, respectively. In addition, top 18 discriminatory taxa that were responsible for the difference between treatments were identified, whose abundances were significantly associated with the immune activities of LYC. Using a structural equation modeling (SEM), we found that gut bacterial communities were primarily governed by the conjointly direct (-0.33) and indirect (0) effects of infection, which subsequently affect host immune responses. Our results suggest that an irreversible dysbiosis in gut microbiota could be the causality of increasing mortality. To our knowledge, this is the first study to provide an integrated overview among pathogen infection, immune response and gut microbiota of LYC.


Assuntos
Microbioma Gastrointestinal , Perciformes/imunologia , Perciformes/microbiologia , Infecções por Pseudomonas/veterinária , Animais , Aquicultura , Citocinas/imunologia , Disbiose , Doenças dos Peixes/imunologia , Interações entre Hospedeiro e Microrganismos/imunologia , Pseudomonas , Infecções por Pseudomonas/imunologia
8.
Sci Total Environ ; 696: 134015, 2019 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-31470324

RESUMO

Increasing intensity and frequency of coastal pollutions are the trajectory to be expected due to anthropogenic pressures. However, it is still unclear how and to what extent bacterioplankton communities respond to the two factors, despite the functional importance of bacterioplankton in biogeochemical cycles. In this study, significant organic pollution index (OPI) and offshore distance gradients, as respective proxies of disturbance intensity and disturbance frequency, were detected in a regional scale across the East China Sea. A multiple regression on matrices (MRM) revealed that the biogeography of bacterioplankton community depended on spatial scale, which was governed by local characters. Bacterioplankton community compositions (BCCs) were primarily governed by the conjointly direct (-0.28) and indirect (-0.48) effects of OPI, while offshore distance contributed a large indirectly effect (0.52). A SEGMENTED analysis depicted non-linear responses of BCCs to increasing disturbance intensity and disturbance frequency, as evidenced by significant tipping points. This was also true for the dominant bacterial phyla. Notably, we screened 30 OPI-discriminatory taxa that could quantitatively diagnose coastal OPI levels, with an overall 79.3% accuracy. Collectively, the buffer capacity of bacterioplankton communities to increasing disturbance intensity and disturbance frequency is limited, of which the significant tipping points afford a warning line for coastal management. In addition, coastal pollution level can be accurately diagnosed by a few OPI-discriminatory taxa.


Assuntos
Organismos Aquáticos , Bactérias , Monitoramento Ambiental , Plâncton , Biodiversidade , China , Ecologia
9.
Environ Microbiol ; 21(4): 1383-1394, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30828926

RESUMO

Aquatic animals encounter suites of novel planktonic microbes during their development. Although hosts have been shown to exert strong selection on their gut microbiota from surrounding environment, to what extent and the generality that the gut microbiota and the underlying ecological processes are affected by biotic and abiotic variations are largely unclear. Here, these concerns were explored by coupling spatiotemporal data on gut and rearing water bacterial communities with environmental variables over shrimp life stages at spatially distant locations. Shrimp gut microbiotas significantly changed mirroring their development, as evidenced by gut bacterial signatures of shrimp life stage contributing 95.5% stratification accuracy. Shrimp sourced little (2.6%-15.8%) of their gut microbiota from their rearing water. This microbial resistance was reflected by weak compositional differences between shrimp farming spatially distinct locations where species pools were distinct. Consistently, the assembly of shrimp gut microbiota was not adequately explained by the rearing water variables and bacterial community, but rather by host-age-associated biotic features. The successions of shrimp gut microbiota were droved by replacement (ßsim), rather than by nestedness (ßnes), while those of bacterioplankton communities were equally governed by replacement and nestedness. Our study highlights how shrimp gut bacterial community assembly is coupled to their development, rearing species pool, and that the successional pattern of host-associated communities is differed from that of free-living bacteria.


Assuntos
Fenômenos Fisiológicos Bacterianos , Biodiversidade , Microbioma Gastrointestinal/fisiologia , Penaeidae/microbiologia , Animais , Aquicultura , Ecologia , Fatores de Tempo
10.
Sci Total Environ ; 651(Pt 2): 2059-2067, 2019 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-30321727

RESUMO

Climate change-induced glacial melting is a global phenomenon. The effects of climate change-induced melting on the microbial ecology in different glacial-fed aquatic systems have been well illuminated, but the resolution of seasonal dynamics was still limited. Here, we studied bacterial community composition and diversity in a glacial-fed Tibetan lake, Lake Ranwu, to elucidate how glacial-fed aquatic ecosystems respond to the seasonal glacial melting. Obvious seasonal variations of bacterial dominant groups were found in Lake Ranwu and inlet rivers. In April, the majority of OTUs belonged to the Bacteroidetes, Actinobacteria and Proteobacteria. The Proteobacteria increased to the most abundant phylum in July and November, while the Bacteroidetes and Actinobacteria decreased about 50% over seasons. Most key discriminant taxa of each season's community strongly associated with specific environmental variables, suggesting their adaptation to seasonal environments. Bacterial alpha diversity varied among seasons and exhibited strongly negative correlations with conductivity. Conductivity was the major driving force in determining the seasonal variation of bacterial community composition. Fluctuated conductivity was one of the consequences of seasonal melting of glaciers. This study offered evidence for the unique seasonal dynamics pattern of bacterial communities responding to glacial melting. Moreover, this study may provide a reference for assessing the long-term effects of glacial retreat on glacial-fed aquatic ecosystems.


Assuntos
Bactérias/isolamento & purificação , Aquecimento Global , Lagos/microbiologia , Microbiota , Actinobacteria/classificação , Actinobacteria/isolamento & purificação , Bactérias/classificação , Bacteroidetes/classificação , Bacteroidetes/isolamento & purificação , Mudança Climática , Camada de Gelo , Proteobactérias/classificação , Proteobactérias/isolamento & purificação , RNA Bacteriano/análise , RNA Ribossômico 16S/análise , Estações do Ano , Tibet
11.
Appl Microbiol Biotechnol ; 103(2): 633-641, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30465305

RESUMO

Microorganisms contribute diverse and fundamental roles in biogeochemical processes. In a given microbial community, individuals interact with one another to form complex regulatory networks in which gatekeepers contribute disproportional roles in sustaining stability, dynamics, and function. Owing to the ecological and functional importance of microbial gatekeeper, this review provides an overview on its history, identification, roles, application in biological sciences, and clinical diagnostics. The roles of microbial gatekeepers can be beneficial or detrimental, which depends on our purpose. As the field is rather new, some limitations are raised, and further efforts devoted to solving these concerns are proposed. Collectively, gatekeepers provide promising targets for sustaining and re-establishing a desired microbial community. However, substantial obstacles, such as factors governing gatekeepers, must be overcome to manipulate gatekeepers as positive guys.


Assuntos
Interações Microbianas , Microbiota , Viabilidade Microbiana
12.
Zool Res ; 40(2): 70-76, 2019 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-29976843

RESUMO

Intensive aquaculture has increased the severity and frequency of fish diseases. Given the functional importance of gut microbiota in various facets of host physiology, modulation of this microbiota is a feasible strategy to mitigate emerging diseases in aquaculture. To achieve this, a fundamental understanding of the interplay among fish health, microbiota, and invading pathogens is required. This mini-review focuses on current knowledge regarding the associations between fish diseases, dysbiosis of gut microbiota, and immune responses. Furthermore, updated research on fish disease from an ecological perspective is discussed, including colonization resistance imposed by commensals and strategies used by pathogens to overcome resistance. We also propose several directions for future research, such as exploration of the causal links between fish diseases and specific taxa, and identification of universal gut microbial biomarkers for rapid disease diagnosis.


Assuntos
Doenças dos Peixes/microbiologia , Peixes/microbiologia , Microbioma Gastrointestinal , Trato Gastrointestinal/microbiologia , Animais , Doenças dos Peixes/imunologia
13.
FEMS Microbiol Ecol ; 94(10)2018 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-30124839

RESUMO

Increasing evidence indicates that dysbiosis in the gut microbiota contributes to disease pathogenesis. However, whether certain taxa are universally indicative of diverse shrimp diseases is unclear thus far. We conducted a meta-analysis to explore the divergences in gut microbiota between healthy and diseased shrimp. The gut bacterial communities of healthy shrimp varied significantly (P < 0.05 in each comparison) over ontogenetic stages, and were distinct from the corresponding diseased cohorts at each life stage. Both phylogenetic-based mean nearest taxon distance analysis and multivariate dispersion testing revealed that shrimp disease weakened the relative importance of deterministic processes in governing the gut microbiota. Partitioning beta diversity analysis indicated that temporal turnover governed the gut microbiota as healthy shrimp aged, whereas this trend was retarded in disease cohorts, concurrent with an increased nestedness. After ruling out the age-discriminatory and disease-specific orders, a high diagnosed accuracy (85.9%) of shrimp health status was achieved by using the profiles of the 11 universal disease-discriminatory orders as independent variables. These findings improve current understanding of how disease alters the ecological processes that govern the shrimp gut microbiota assembly, and exemplifies the potential application of universal bacterial signatures to diagnose the incidence of diverse shrimp diseases, irrespective of causal pathogens.


Assuntos
Doenças dos Animais/diagnóstico , Microbioma Gastrointestinal , Penaeidae/microbiologia , Frutos do Mar/microbiologia , Doenças dos Animais/microbiologia , Animais , Disbiose , Estágios do Ciclo de Vida , Metanálise como Assunto , Penaeidae/genética , Penaeidae/crescimento & desenvolvimento , Filogenia
14.
Mol Ecol ; 27(18): 3686-3699, 2018 09.
Artigo em Inglês | MEDLINE | ID: mdl-30070062

RESUMO

The host-associated microbiota is increasingly recognized to facilitate host fitness, but the understanding of the underlying ecological processes that govern the host-bacterial colonization over development and, particularly, under disease remains scarce. Here, we tracked the gut microbiota of shrimp over developmental stages and in response to disease. The stage-specific gut microbiotas contributed parallel changes to the predicted functions, while shrimp disease decoupled this intimate association. After ruling out the age-discriminatory taxa, we identified key features indicative of shrimp health status. Structural equation modelling revealed that variations in rearing water led to significant changes in bacterioplankton communities, which subsequently affected the shrimp gut microbiota. However, shrimp gut microbiotas are not directly mirrored by the changes in rearing bacterioplankton communities. A neutral model analysis showed that the stochastic processes that govern gut microbiota tended to become more important as healthy shrimp aged, with 37.5% stochasticity in larvae linearly increasing to 60.4% in adults. However, this defined trend was skewed when disease occurred. This departure was attributed to the uncontrolled growth of two candidate pathogens (over-represented taxa). The co-occurrence patterns provided novel clues on how the gut commensals interact with candidate pathogens in sustaining shrimp health. Collectively, these findings offer updated insight into the ecological processes that govern the host-bacterial colonization in shrimp and provide a pathological understanding of polymicrobial infections.


Assuntos
Bactérias/classificação , Crustáceos/microbiologia , Microbioma Gastrointestinal , Animais , Infecções Bacterianas/imunologia , Técnicas de Tipagem Bacteriana , Crustáceos/crescimento & desenvolvimento , Crustáceos/imunologia , DNA Bacteriano/genética , Meio Ambiente , RNA Ribossômico 16S/genética
15.
Appl Microbiol Biotechnol ; 102(17): 7343-7350, 2018 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-29982924

RESUMO

It is now recognized that gut microbiota contributes indispensable roles in safeguarding host health. Shrimp is being threatened by newly emerging diseases globally; thus, understanding the driving factors that govern its gut microbiota would facilitate an initial step to reestablish and maintain a "healthy" gut microbiota. This review summarizes the factors that assemble the shrimp gut microbiota, which focuses on the current progresses of knowledge linking the gut microbiota and shrimp health status. In particular, I propose the exploration of shrimp disease pathogenesis and incidence based on the interplay between dysbiosis in the gut microbiota and disease severity. An updated research on shrimp disease toward an ecological perspective is discussed, including host-bacterial colonization, identification of polymicrobial pathogens and diagnosing disease incidence. Further, a simple conceptual model is offered to summarize the interplay among the gut microbiota, external factors, and shrimp disease. Finally, based on the review, current limitations are raised and future studies directed at solving these concerns are proposed. This review is timely given the increased interest in the role of gut microbiota in disease pathogenesis and the advent of novel diagnosis strategies.


Assuntos
Fenômenos Fisiológicos Bacterianos , Microbioma Gastrointestinal , Penaeidae/microbiologia , Animais , Disbiose , Interações Hospedeiro-Patógeno
16.
Huan Jing Ke Xue ; 39(8): 3640-3648, 2018 Aug 08.
Artigo em Chinês | MEDLINE | ID: mdl-29998670

RESUMO

Hangzhou Bay suffers from intensive anthropogenic disturbances and a huge amount of terrestrial inputs, and thus has become one of the most seriously contaminated coastal zones in China. There is evidence that microbes play a dominant role in pollutant biodegradation and serve as biomarkers for pollution levels. However, it remains unclear how the bacterioplankton communities respond to organic contaminants. To fill this knowledge gap, we collected surface water samples (0.5 m below the surface layer) from 13 sites across Hangzhou Bay and 8 control sites across its adjacent offshore areas. Using Illumina sequencing based on analysis of the bacterial 16S rRNA gene, we explored the effects of increasing organic pollution levels on the bacterioplankton community compositions (BCCs). The results revealed that the organic pollution level (A) in Hangzhou Bay (13.2±1.6) was significantly (P<0.001) higher than in the control zone (5.4±3.0). The distribution and diversity of bacterioplankton communities were significantly distinct between the two zones. The dominant bacterioplankton lineages in Hangzhou Bay were γ-Proteobacteria (24.4%±5.5%), α-Proteobacteria (16.5%±7.7%), and Planctomycetes (13.9%±8.6%), whereas those in the adjacent zones were Cyanobacteria (20.1%±7.5%), Bacteroidetes (18.4%±1.5%), Actinobacteria (17.5%±4.2%), γ-Proteobacteria (16.6%±1.2%), and α-Proteobacteria (14.3%±1.7%). Multivariate regression tree (MRT) analysis showed that the bacterioplankton community diversity was primarily affected by suspended particulates (SP), nitrite, oil, and organic pollutants, which respectively explained 22.0%, 6.5%, 6.0%, and 5.5% of the variance in diversity. Redundancy analysis (RDA) illustrated that the bacterioplankton community distribution was controlled by organic pollutants, COD, Chla, TN, nitrate, and salinity, which cumulatively governed 71.0% of the variation in BCCs. Organic pollutants alone controlled 6.5% variance, which was higher than any other single factor. Additionally, 35 sensitive species were identified via the indicator value method and their relative abundances were significantly associated (P<0.05 in each case) with the organic pollution level, thereby indicating their potential for evaluating coastal pollution. Collectively, our work demonstrates that BCCs are sensitive to coastal pollution and provides biomarkers for elevated pollution levels.


Assuntos
Bactérias/classificação , Baías/microbiologia , Biodiversidade , Plâncton/classificação , Poluentes da Água/análise , China , Monitoramento Ambiental , Material Particulado , RNA Ribossômico 16S , Vitamina B 12/análogos & derivados
17.
Appl Environ Microbiol ; 84(18)2018 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-30006395

RESUMO

There is evidence that gut microbial signatures are indicative of host health status. However, few efforts have been devoted to establishing an applicable technique for determining disease incidence by using gut microbial signatures. Herein, we established a quantitative PCR (qPCR)-based approach to detect the relative abundances of gut disease-discriminatory phyla, which in turn afforded independent variables for quantitatively determining the incidence of shrimp disease. Given the temporal dynamics of gut bacterial communities as healthy shrimp aged, we identified disease-discriminatory phyla after ruling out age-discriminatory phyla. The top 10 disease-discriminatory phyla contributed to an overall 93.2% accuracy in diagnosis (n = 103 samples from shrimp that were determined with high confidence to be healthy or that exhibited apparent disease symptoms and subsequent death), with 70% diagnosis accuracy at the disease onset stage, when symptoms or signs of disease were not apparent. 16S rRNA gene-targeted group-specific primers of five disease-discriminatory phyla were then designed according to their compositions within shrimp gut microbiota, and other primers were borrowed from previous studies. The relative abundances of the 10 disease-discriminatory phyla assayed by qPCR exhibited a high consistency (r = 0.946, P < 0.001) with those detected by Illumina sequencing. Notably, using the profiles of disease-discriminatory phyla assayed by qPCR and the corresponding weight coefficients as independent variables, we were able to accurately estimate the incidences of future disease outcome. This work establishes an applicable technique to quantitatively determine the incidence and onset of shrimp disease, which is a valuable attempt to translate scientific research into a practical application.IMPORTANCE Current studies have identified gut microbial signatures of host health using high-throughput sequencing (HTS) techniques. However, HTS is still expensive and time-consuming and requires a high technical ability, thereby impeding its application in routine monitoring in aquaculture. Hence, it is necessary to seek an alternative strategy to overcome these shortcomings. Herein, we establish a qPCR-based approach to detect the relative abundances of gut disease-discriminatory phyla, which in turn afford independent variables to quantitatively determine the incidence and onset of shrimp disease. Notably, there is a high consistency between the accuracies of disease diagnosis achieved by qPCR and HTS. This applicable technique makes important progress toward defining a diseased state in shrimp and toward solving an important animal health management-driven economic problem.


Assuntos
Bactérias/isolamento & purificação , Microbioma Gastrointestinal , Penaeidae/imunologia , Penaeidae/microbiologia , Animais , Bactérias/classificação , Bactérias/genética , DNA Bacteriano/genética , Resistência à Doença , Reação em Cadeia da Polimerase , RNA Ribossômico 16S/genética
18.
Genes Genomics ; 40(6): 603-613, 2018 06.
Artigo em Inglês | MEDLINE | ID: mdl-29892942

RESUMO

Quantitative real-time PCR (qRT-PCR) is a standard method to measure gene expression in function exploring. Accurate and reproducible data of qRT-PCR requires appropriate reference genes, which are stably expressed under different experimental conditions. However, no housekeeping genes were validated as internal controls for qRT-PCR in Sinonovacula constricta. In this study, we classified the transcriptome data of two tissues for Vibrio infection and Cd2+ stress into ten clusters based on the gene expression patterns. Among them, cluster 5 had the most stable gene expression patterns regardless of tissues and treatments as the database for candidate reference genes. A total of 55 orthologs of classical housekeeping genes in the clam transcriptome were annotated. Combined the expression profiles and housekeeping genes in S. constricta, we chose eight candidate reference genes and validated their expression in Vibrio-infected samples and different tissues by qRT-PCR. Their expression stability was analyzed by three different algorithms geNorm, NormFinder and BestKeeper. Although the rank of the eight candidate reference genes is different in different treatments using different software, RS9 could be the best reference genes for normalization of qRT-PCR expression data in S. constricta under various treatments considering the above analysis. Meanwhile, the ranking of genes based on the CV values of transcriptomic data was similar to the validation results. This study provides for the first time a list of suitable reference genes for S. constricta and a valuable resource for further studies of clam immune defense systems.


Assuntos
Bivalves/genética , Perfilação da Expressão Gênica/métodos , Animais , Reação em Cadeia da Polimerase em Tempo Real/métodos , Padrões de Referência , Reprodutibilidade dos Testes , Transcriptoma
19.
Fish Shellfish Immunol ; 80: 191-199, 2018 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-29803665

RESUMO

Aquatic animals are frequently suffered from starvation due to restricted food availability or deprivation. It is currently known that gut microbiota assists host in nutrient acquisition. Thus, exploring the gut microbiota responses would improve our understanding on physiological adaptation to starvation. To achieve this, we investigated how the gut microbiota and shrimp digestion and immune activities were affected under starvation stress. The results showed that the measured digestion activities in starved shrimp were significantly lower than in normal cohorts; while the measured immune activities exhibited an opposite trend. A structural equation modeling (SEM) revealed that changes in the gut bacterial community were directly related to digestive and immune enzyme activities, which in turn markedly affected shrimp growth traits. Notably, several gut bacterial indicators that characterized the shrimp nutrient status were identified, with more abundant opportunistic pathogens in starved shrimp, although there were no statistical differences in the overall diversity and the structures of gut bacterial communities between starved and normal shrimp. Starved shrimp exhibited less connected and cooperative interspecies interaction as compared with normal cohorts. Additionally, the functional pathways involved in carbohydrate and protein digestion, glycan biosynthesis, lipid and enzyme metabolism remarkably decreased in starved shrimp. These attenuations could increase the susceptibility of starved shrimp to pathogens infection. In summary, this study provides novel insights into the interplay among shrimp digestion, immune activities and gut microbiota in response to starvation stress.


Assuntos
Digestão , Microbioma Gastrointestinal , Penaeidae , Inanição , Estresse Fisiológico , Fosfatase Ácida/metabolismo , Amilases/metabolismo , Animais , Bactérias/genética , Digestão/imunologia , Digestão/fisiologia , Hepatopâncreas/enzimologia , Lipase/metabolismo , Muramidase/metabolismo , Penaeidae/imunologia , Penaeidae/microbiologia , Penaeidae/fisiologia , Pepsina A/metabolismo , RNA Ribossômico 16S/genética , Inanição/imunologia , Inanição/microbiologia , Estômago/enzimologia , Estresse Fisiológico/imunologia , Estresse Fisiológico/fisiologia , Superóxido Dismutase/metabolismo
20.
Appl Microbiol Biotechnol ; 102(7): 3315-3326, 2018 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-29497796

RESUMO

One common notion is emerging that gut eukaryotes are commensal or beneficial, rather than detrimental. To date, however, surprisingly few studies have been taken to discern the factors that govern the assembly of gut eukaryotes, despite growing interest in the dysbiosis of gut microbiota-disease relationship. Herein, we firstly explored how the gut eukaryotic microbiotas were assembled over shrimp postlarval to adult stages and a disease progression. The gut eukaryotic communities changed markedly as healthy shrimp aged, and converged toward an adult-microbiota configuration. However, the adult-like stability was distorted by disease exacerbation. A null model untangled that the deterministic processes that governed the gut eukaryotic assembly tended to be more important over healthy shrimp development, whereas this trend was inverted as the disease progressed. After ruling out the baseline of gut eukaryotes over shrimp ages, we identified disease-discriminatory taxa (species level afforded the highest accuracy of prediction) that characteristic of shrimp health status. The profiles of these taxa contributed an overall 92.4% accuracy in predicting shrimp health status. Notably, this model can accurately diagnose the onset of shrimp disease. Interspecies interaction analysis depicted how the disease-discriminatory taxa interacted with one another in sustaining shrimp health. Taken together, our findings offer novel insights into the underlying ecological processes that govern the assembly of gut eukaryotes over shrimp postlarval to adult stages and a disease progression. Intriguingly, the established model can quantitatively and accurately predict the incidences of shrimp disease.


Assuntos
Crustáceos/microbiologia , Eucariotos/fisiologia , Microbioma Gastrointestinal/fisiologia , Animais , Disbiose , Eucariotos/genética
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