Gut microbiota of homologous Chinese soft-shell turtles (Pelodiscus sinensis) in different habitats.

BACKGROUND: Chinese soft-shell turtle (Pelodiscus sinensis) is an important commercial species for their high nutritional value and unique taste, but it has been a vulnerable species due to habitat loss. In this study, homologous juvenile turtles were allocated to lake, pond and paddy field to investigate the habitat effects on turtles. RESULTS: The growth, morphology and gut microbial communities were monitored during the 4 months cultural period. It showed higher growth rate of turtles in paddy field and pond. The appearance, visceral coefficients, gut morphology and microbial communities in turtles were distinct among different habitats. The microbial community richness on Chao1 was obviously lower in initial turtle guts from greenhouses, whereas it was relative higher in turtle guts sampled from paddy fields than ponds and lake. Significant differences on dominant microbes were found among initial and subsequent samples from different habitats. Firmicutes was the most abundant phylum in the guts of turtles sampled from the greenhouse initially, while Proteobacteria was the most abundant phylum after cultivation in different habitats, followed by Bacteroidetes. The microbial composition were distinct in different habitats at 60d, and the appearance of dominant phyla and genera was more driven by sampling time than habitats at 120d. Both the sampling time and habitats affected the appearance of dominant phyla and genera during the cultivation. The functional predictions indicated that both habitat type and sampling time had significant effects on metabolic pathways, especially amino acid and carbohydrate metabolism. CONCLUSIONS: The turtles could adapt to natural lakes, artificial ponds and paddy fields. The gut microbial abundance was different among the habitats and sampling time. The species of microbes were significantly more diverse in paddy field specimens than in those from ponds and lakes. Rice-turtle coculture is a potential ecological and economic farming mode that plays important roles in wild turtle protection and food security.

Oral microbial profile variation during canine ligature-induced peri-implantitis development.

BACKGROUND: Dental implants have become well-established in oral rehabilitation for fully or partially edentulous patients. However, peri-implantitis often leads to the failure of dental implants. The aim of this study was to understand the core microbiome associated with peri-implantitis and evaluate potential peri-implantitis pathogens based on canine peri-implantitis model. RESULTS: In this study, three beagle dogs were used to build peri-implantitis models with ligature-induced strategy. The peri-implant sulcular fluids were collected at four different phases based on disease severity during the peri-implantitis development. Microbial compositions during peri-implantitis development were monitored and evaluated. The microbes were presented with operational taxonomic unit (OTU) classified at 97% identity of the high-throughput 16S rRNA gene fragments. Microbial diversity and richness varied during peri-implantitis. At the phylum-level, Firmicutes decreased and Bacteroides increased during peri-implantitis development. At the genus-level, Peptostreptococcus decreased and Porphyromonas increased, suggesting peri-implantitis pathogens might be assigned to these two genera. Further species-level and co-occurrence network analyses identified several potential keystone species during peri-implantitis development, and some OTUs were potential peri-implantitis pathogens. CONCLUSION: In summary, canine peri-implantitis models help to identify several potential keystone peri-implantitis associated species. The canine model can give insight into human peri-implantitis associated microbiota.

Regional Variation of Infectious Agents Causing Endogenous Endophthalmitis in the United States: A National Database Analysis.

OBJECTIVE: To describe regional variation in microbes causing infectious endogenous endophthalmitis (EE) in the United States. DESIGN: This is a retrospective, national database analysis utilizing the 2002-2014 National Inpatient Sample database. SUBJECTS: Using the International Classification of Disease 9 codes, we identified cases with EE. Cases were stratified regionally into Northeast, South, West, or Midwest. METHODS: Unadjusted chi-square analysis followed by adjusted multivariate logistic regression was performed to evaluate variation in demographic factors, comorbidities using the Elixhauser Comorbidity Index (ECI), microbial variation, mortality, and use of vitrectomy or enucleation by region. MAIN OUTCOME MEASURES: Proportion of microbes, mortality, and vitrectomy by region in addition to factors with significant odds ratios for mortality and for in-hospital vitrectomy. RESULTS: A total of 10 912 patients with infectious EE were identified, with 2063 cases in the Northeast (18.9%), 2145 cases in the Midwest (19.7%), 4134 cases in the South (37.9%), and 2570 cases in the West (23.6%). Chi-square analysis indicated significant regional variation in patient demographics, microbes causing the infection, ECI, mortality, and surgical intervention. The 4 most common microbes for all regions were methicillin-sensitive Staphylococcus aureus (MSSA), Streptococcus, Candida, and methicillin-resistant Staphylococcus aureus. Methicillin-sensitive S. aureus was the most common cause of EE in all regions, although the proportion of MSSA infection did not significantly vary by region (P = 0.03). Further, there was significant regional variation in the proportion of other microbes causing the infection (P < 0.001). Higher rates of vitrectomies were seen in the South and Midwest regions than that in the Northeast and West (P = 0.04). CONCLUSIONS: Regional variation exists in the infectious microbes causing EE. Further studies are needed to elucidate the etiology of these variations. FINANCIAL DISCLOSURE(S): Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Temporal profiling resolves the drivers of microbial nitrogen cycling variability in coastal sediments.

Here we describe the potential for sediment microbial nitrogen-cycling gene (DNA) and activity (RNA) abundances to spatially resolve coastal areas impacted by seasonal variability in external nutrient inputs. Three sites were chosen within a nitrogen-limited embayment, Port Phillip Bay (PPB), Australia that reflect variability in both proximity to external nutrient inputs and the dominant form of available nitrogen. At three sediment depths (0-1; 1-5; 5-10 cm) across a 2 year study key genes involved in nitrification (archaeal amoA and bacterial ß-amoA), nitrite reduction (clade I nirS and cluster I nirK, archaeal nirK-a), anaerobic oxidation of ammonium (anammox 16S rRNA phylogenetic marker) and nitrogen fixation (nifH) were quantified. Sediments impacted by a dominance of organic nitrogen inputs were characterised at all time-points and to sediment depths of 10 cm by the highest transcript abundances of archaeal amoA and archaeal nirk-a. Proximity to a dominance of external nitrate inputs was associated with the highest transcript abundances of nirS which temporally co-varied with seasonal changes in sediment nitrate. Sediments isolated from external inputs displayed the greatest depth-specific decrease in quantifiable transcript abundances. In these isolated sediments bacterial ß-amoA transcripts were temporally associated with increased sediment ammonium levels. Across this nitrogen limited system variability in the abundance of bacterial ß-amoA, archaeal amoA, archaeal nirk-a or nirS transcripts from the sediment surface (0-1 and 5 cm) demonstrated a capacity to improve our ability to monitor coastal zones impacted by anthropogenic nitrogen inputs. Specifically, the spatial detection sensitivity of bacterial ß-amoA transcripts could be developed as a metric to determine spatiotemporal impacts of large external loading events. This temporal study demonstrates a capacity for microbial activity metrics to facilitate coastal management strategies through greater spatial resolution of areas impacted by external nutrient inputs.

Gut microbial community structure and function of Przewalski's horses varied across reintroduced sites in China.

Host-associated microbiota can significantly impact host fitness. Therefore, naturally occurring variations in microbiota may influence the health and persistence of their hosts. This finding is particularly important in reintroduced animals, as they typically experience habitat changes during translocations. However, little is known about how microbiomes are altered in response to conservation translocation. Here, we accessed the gut microbiome of Przewalski's horse (Equus przewalskii) populations in China from three nature reserves (i.e. Xinjiang Kalamaili Nature Reserve, KNR; Dunhuang Xihu National Nature Reserve, DXNNR; and Anxi Extreme-arid Desert Nature Reserve, AENR) using 16s rRNA gene and metagenome sequencing. The results showed that the microbial composition and function differed significantly across locations, while a subset of core taxa was consistently present in most of the samples. The abundance of genes encoding microbe-produced enzymes involved in the metabolism of carbohydrates, especially for glycoside hydrolases, was significantly higher in open-spaced KNR populations than in more confined AENR individuals. This study offers detailed and significant differential characters related to the microbial community and metabolic pathways in various reintroduced sites of Przewalski's horse, which might provide a basis for future microecological and conservation research on endangered reintroduced animals.

Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress.

Introduction: Soil salinization is a serious abiotic stress for grapevines. The rhizosphere microbiota of plants can help counter the negative effects caused by salt stress, but the distinction between rhizosphere microbes of salt-tolerant and salt-sensitive varieties remains unclear. Methods: This study employed metagenomic sequencing to explore the rhizosphere microbial community of grapevine rootstocks 101-14 (salt tolerant) and 5BB (salt sensitive) with or without salt stress. Results and Discussion: Compared to the control (treated with ddH2O), salt stress induced greater changes in the rhizosphere microbiota of 101-14 than in that of 5BB. The relative abundances of more plant growth-promoting bacteria, including Planctomycetes, Bacteroidetes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes, Chloroflexi, and Firmicutes, were increased in 101-14 under salt stress, whereas only the relative abundances of four phyla (Actinobacteria, Gemmatimonadetes, Chloroflexi, and Cyanobacteria) were increased in 5BB under salt stress while those of three phyla (Acidobacteria, Verrucomicrobia, and Firmicutes) were depleted. The differentially enriched functions (KEGG level 2) in 101-14 were mainly associated with pathways related to cell motility; folding, sorting, and degradation functions; glycan biosynthesis and metabolism; xenobiotics biodegradation and metabolism; and metabolism of cofactors and vitamins, whereas only the translation function was differentially enriched in 5BB. Under salt stress, the rhizosphere microbiota functions of 101-14 and 5BB differed greatly, especially pathways related to metabolism. Further analysis revealed that pathways associated with sulfur and glutathione metabolism as well as bacterial chemotaxis were uniquely enriched in 101-14 under salt stress and therefore might play vital roles in the mitigation of salt stress on grapevines. In addition, the abundance of various sulfur cycle-related genes, including genes involved in assimilatory sulfate reduction (cysNC, cysQ, sat, and sir), sulfur reduction (fsr), SOX systems (soxB), sulfur oxidation (sqr), organic sulfur transformation (tpa, mdh, gdh, and betC), increased significantly in 101-14 after treatment with NaCl; these genes might mitigate the harmful effects of salt on grapevine. In short, the study findings indicate that both the composition and functions of the rhizosphere microbial community contribute to the enhanced tolerance of some grapevines to salt stress.

Effects of sediment physicochemical factors and heavy metals on the diversity, structure, and functions of bacterial and fungal communities from a eutrophic river.

Urbanization has destroyed river ecosystems, leading to eutrophication. Heavy metals are frequently observed in urban rivers, and the joint effects of eutrophication and heavy metals on microbial communities, especially on fungal communities, have not been adequately explored. In this study, we explored the effect of sediment physicochemical factors and heavy metals on the microbial diversity, community structure, and functions of bacterial and fungal communities from a black-odorous river in Wuhu, China. Twenty-four samples were collected, and the diversity and structure of fungal and bacterial communities were determined by high-throughput sequencing. Proteobacteria and Rozellomycota were the main phyla in the bacterial and fungal communities, respectively. The results showed different distribution patterns of bacterial and fungal communities along the river. Physicochemical factors and heavy metals exhibited different effects on microbial variation. Specifically, pH and Cr negatively affected bacterial α-diversity, whereas total phosphorus and Cr significantly affected fungal α-diversity. Variance partitioning analysis revealed that physicochemical factors explained more of the bacterial community structure than heavy metals (49.5% vs. 36.6%), with pH and total phosphorus being the dominant factors. Opposite patterns were observed for fungal community structure, with heavy metals contributing the most (48.0%). A similar influence pattern was observed for the predicted functions of the two communities. This study suggests that heavy metals in eutrophication rivers are essential factors that shift the microbial variation and should be considered in urban river evaluation and remediation.

The synergy of environmental and microbial variations caused by hydrologic management affects the carbon emission in the Three Gorges Reservoir.

The synergy of environmental and microbiological changes caused by hydrologic management on carbon emissions of river reservoirs remains unknown. Here, we investigated physiochemistry parameters, compositions of dissolved organic matter (DOM), carbon fluxes (CH4 and CO2), and microbial communities in the surface waters of the Three Gorges Reservoir (TGR) within one whole hydrological year. The results showed that hydrologic management significantly changed physiochemistry and DOM composition of the TGR water, and further influenced microbial community composition and functions. DOM content during the drainage period was much lower than during the impoundment period. During the impoundment period, humification extent of DOM became decreasing, while biotransformation extent became increasing compared with the drainage period. DOM composition and water pH exhibited significant correlation with the fluxes of CH4 and CO2, respectively. Microbial community composition and function significantly differed between the drainage and impoundment periods. Most of the differential microbial taxa were affiliated with functional groups involved in carbon cycle such as methanotrophy and phototrophy, which showed significant correlation with carbon fluxes. CH4 and CO2 fluxes can be mostly explained by synergy of microbial function with DOM composition and water pH, respectively. Such synergistic effect may account for the observed temporal variations of CH4 fluxes and spatial variations of CO2, and for the relatively low annual carbon emissions in the TGR. In summary, the synergy of environmental and microbial variations caused by hydrologic management affects carbon emissions from river reservoirs.

Pollution adaptive responses of root-associated microbiomes induced the promoted but different attenuation of soil residual lindane: Differences between maize and soybean.

Microorganisms colonize plant-associated environments and constitute complex communities aided in key functions for nutrient acquisition, disease suppression and abiotic stress resistance. In this study, we evaluated the variation of root-associated microbiomes of two typical farmland crops, maize (Zea mays L.) and soybean (Glycine max L. Merr.) respond to organochlorine pesticide stress, taking lindane as an example. Results showed that there were promoted but different attenuation rates of residual lindane in rhizosphere soils during maize and soybean growth, and the differential is due to the comprehensive effects of plant characters and microbial activities. Organochlorine pollution did not have significant impact on the microbial diversity and populations in all rhizo-compartments, but mostly stimulated the microbial connectivity. The multistep and decreasing processes for root-associated microbiomes of both maize and soybean were spatially different and mainly dependent on the shaping roles of host plants. These results expand our understandings of the organochlorine influence on the underground ecological system in crop-dependent soils.

Customizing laboratory mice by modifying gut microbiota and host immunity in an early "window of opportunity".

We recently investigated how post-natal microbial gut colonization is important for the development of the immune system, especially in the systemic compartments. This addendum presents additional data which in accordance with our previous findings show that early life microbial colonization is critical for a fine-tuned immune homeostasis to develop also in the intestinal environment. A generalized reduction in the expression of immune signaling related genes in the small intestine may explain previously shown increased systemic adaptive immune reactivity, if the regulatory cross-talk between intra- and extra-intestinal immune cells is immature following a neonatal germ-free period. These findings are furthermore discussed in the context of recently published results on how lack of microbial exposure in the neonatal life modifies disease expression in rodents used as models mimicking human inflammatory diseases. In particular, with a focus on how these interesting findings could be used to optimize the use of rodent models.