Relative Abundance Of Dominant Taxa Research Articles

Bee wisdom: exploring bee control strategies for food microflora by comparing the physicochemical characteristics and microbial composition of beebread.

Bees are a valuable model for investigating the relationship between environmental factors, gut microbiota, and organismal health. Beebread, produced from collected pollen, is a natural food source and a primary reservoir of gut microorganisms. Although pollen typically has diverse bacterial species, beebread has low species richness and bacterial abundance. Consequently, considerable attention has been paid to the adaptive strategies employed by honey bees to cope with the microorganisms within their food environment during co-evolution with plants. This study identified the distribution patterns of beebread's physicochemical characteristics, showing how bees use fermentation to enrich specific microbes. These findings help understand the relationship between environmental and food-associated microbes and bee intestinal microbiota. They also bridge gaps in the literature and provide a valuable reference for studying the complex interplay between these factors.

Patterns and drivers of prokaryotic communities in thermokarst lake water across Northern Hemisphere

AbstractAimThe formation of thermokarst lakes could make a large amount of carbon accessible to microbial degradation, potentially intensifying the permafrost carbon‐climate feedback via carbon dioxide/methane emissions. Because of their diverse functional roles, prokaryotes could strongly mediate biogeochemical cycles in thermokarst lakes. However, little is known about the large‐scale patterns and drivers of these communities.LocationPermafrost regions in the Northern Hemisphere.Time periodPresent day.Major taxa studiedProkaryotes.MethodsBased on a combination of large‐scale measurements on the Tibetan Plateau and data syntheses in pan‐Arctic regions, we constructed a comprehensive dataset of 16S rRNA sequences from 258 thermokarst lakes across Northern Hemisphere permafrost regions. We also used the local contributions to beta diversity (LCBD) to characterize the variance of prokaryotic species composition and screened underlying drivers by conducting a random forest modelling analysis.ResultsProkaryotes in thermokarst lake water were dominated by the orders Burkholderiales, Micrococcales, Flavobacteriales and Frankiales. The relative abundance of dominant taxa was positively associated with dissolved organic matter (DOM) properties, especially for the chromophoric/aromatic compounds. Microbial structure differed between high‐altitude and high‐latitude thermokarst lakes, with the dominance of Flavobacterium in high‐altitude lakes, and the enrichment of Polynucleobacter in high‐latitude lakes. More importantly, climatic variables were among the main drivers shaping the large‐scale variation of prokaryotic communities. Specifically, mean annual precipitation was the best predictor for prokaryotic beta diversity across the Northern Hemisphere, as well as in the high‐altitude permafrost regions, while mean annual air temperature played a key role in the high‐latitude thermokarst lakes.Main conclusionsOur findings demonstrate significant associations between dominant taxa and DOM properties, as well as the important role of climatic factors in affecting prokaryotic communities. These findings suggest that climatic change may alter DOM conditions and induce dynamics in prokaryotic communities of thermokarst lake water in the Northern Hemisphere.

Efficient vegetation restoration in Mu Us desert reduces microbial diversity due to the transformation of nutrient requirements

Various nutrient requirements of soil microorganisms often occur in restoration ecosystems, but the responses of microbial communities in different vegetation types remain unclear. In this study, we selected four types of vegetation (grassland desert (GD), desert steppe (DS), typical steppe (TS), and artificial forest (AF)) on the Mu Us Desert, and examined the soil physicochemical properties, extracellular enzyme activities (carbon (C)-, nitrogen (N)-, and phosphorus (P)-acquisition enzymes), and community characteristics. Our results revealed that the N-requirement of microorganisms in the area was higher than that of other elements, particularly when organic C was scarce, whereas severe P requirement was detected in the presence of abundant organic matter. Compared with TS, we detected a higher diversity of microorganisms in GD, DS, and AF, and the microbial communities were dominated by a few taxa with loose internal connections and higher C and N requirements. Stronger N and P requirements reduced the diversity of microorganisms and the relative abundance of dominant taxa in TS, but increased the stability of bacterial communities. Our results further indicate that bacteria play a more active role in coping with the transformation of nutrient requirements. When C- and N-requirements of microorganisms were transformed to N and P, the abundance of dominant and sub-dominant taxa decreased and increased, respectively. Collectively, the results of this study indicate that efficient vegetation restoration in desert areas may lead to stronger nutrient requirements for microorganisms, thus reducing the diversity of microorganisms and causing unpredictable consequences for ecological sustainable development.

Effects of isolation and confinement on gastrointestinal microbiota-a systematic review.

The gastrointestinal (GI) microbiota is a complex and dynamic ecosystem whose composition and function are influenced by many internal and external factors. Overall, the individual GI microbiota composition appears to be rather stable but can be influenced by extreme shifts in environmental exposures. To date, there is no systematic literature review that examines the effects of extreme environmental conditions, such as strict isolation and confinement, on the GI microbiota. We conducted a systematic review to examine the effects of isolated and confined environments on the human GI microbiota. The literature search was conducted according to PRISMA criteria using PubMed, Web of Science and Cochrane Library. Relevant studies were identified based on exposure to isolated and confined environments, generally being also antigen-limited, for a minimum of 28 days and classified according to the microbiota analysis method (cultivation- or molecular based approaches) and the isolation habitat (space, space- or microgravity simulation such as MARS-500 or natural isolation such as Antarctica). Microbial shifts in abundance, alpha diversity and community structure in response to isolation were assessed. Regardless of the study habitat, inconsistent shifts in abundance of 40 different genera, mainly in the phylum Bacillota (formerly Firmicutes) were reported. Overall, the heterogeneity of studies was high. Reducing heterogeneity was neither possible by differentiating the microbiota analysis methods nor by subgrouping according to the isolation habitat. Alpha diversity evolved non-specifically, whereas the microbial community structure remained dissimilar despite partial convergence. The GI ecosystem returned to baseline levels following exposure, showing resilience irrespective of the experiment length. An isolated and confined environment has a considerable impact on the GI microbiota composition in terms of diversity and relative abundances of dominant taxa. However, due to a limited number of studies with rather small sample sizes, it is important to approach an in-depth conclusion with caution, and results should be considered as a preliminary trend. The risk of dysbiosis and associated diseases should be considered when planning future projects in extreme environments. https://www.crd.york.ac.uk/prospero/, identifier CRD42022357589.

The microbiomes of two Singaporean corals show site-specific differentiation and variability that correlates with the seasonal monsoons

Corals host abundant microbial communities, or microbiomes, that play essential roles in the function of the coral holobiont. We examined the mucus microbiome in corals within the port of Singapore, where corals persist despite intense anthropogenic impacts. The coral mucus microbiomes of Pectinia paeonia and Platygyra sinensis at three reef sites were tracked by 16S rRNA gene amplicon sequencing from January 2019 to January 2020. Both coral species displayed spatial and temporal differences in microbiome composition, suggesting site specificity and seasonality in microbiome composition consistent with the monsoons. The temporal shifts in relative abundance of dominant taxa were different between the two coral species. Nonetheless, Proteobacteria was the most abundant phylum in both coral species and was reduced during the southwest (SW) monsoon, while Cyanobacteria and Crenarchaeota increased. The presumptive beneficial endosymbiont Endozoicomonas was only associated with corals at the reef site located the farthest from the Singapore mainland. The coral microbiomes reflected seasonal changes, while the seawater displayed distinct temporal microbial compositions and site-specific differentiation within all sampling dates. The persistence of coral reefs within the port of Singapore highlights the adaptive ability of corals to respond to stressful environments, and this study provides further evidence that a flexible microbiome could be an important part of the strategy employed by corals to remain resilient.

Response of intestinal microbiota to saline-alkaline water in mud crab (Scylla paramamosain) based on multiple low salinity culture modes

IntroductionThe intestinal microbiota acts as an additional “organ” that performs a variety of fu\nctions for the host’s health. However, the composition and role of the intestinal microbiota in Scylla paramamosain cultivated in inland low salinity saline-alkaline water are unknown.MethodsAccordingly, from the perspective of practical production, we explored the intestinal microbiota communities and the critical bacteria of S. paramamosain in normal salinity seawater (NS), coastal low salinity seawater (CS), acute low salinity seawater (AS) and inland low salinity saline-alkaline water (IS).ResultsResults showed that there were significant differences in the diversity composition of intestinal microbiota and the relative abundance of dominant taxa in each group of cultured crabs. Firmicutes, Proteobacteria, Bacteroidota and Campilobacterota were shown to be the major phyla shared by the four groups, with Bacteroidota having the highest relative abundance (27.10%) in the inland low salinity saline-alkaline water group (IS). Fusobacteriota had the highest proportion in IS group compared with other low salinity groups. A total of 284 indicator bacteria were identified, belonging to eight phyla, and their relative abundances were varied significantly (P < 0.05). Genus Carboxylicivirga, as the indicator bacterium of the IS group, may play a critical role in the adaptation of crab to saline-alkaline water environment. Moreover, salinity may exert considerable selective pressure on the entire microbial community.DiscussionThese findings revealed the features of the intestinal microbiome in S. paramamosain in multiple low salinity patterns, and provided candidate probiotics and basic information for crab farming in saline-alkaline water, which was conducive to the development and perfection of mud crab culturing technology in inland low salinity saline-alkaline water.

Long-term integrated rice-crayfish culture disrupts the microbial communities in paddy soil

The integrated rice-crayfish culture (IRCC) mode has been developed for more than twenty years in China, but little information could be obtained on the microbial communities in paddy soil under this mode. This study used 16SrRNA and ITS Illumina high-throughput sequencing to investigate microbial communities, diversity, and function in paddy soil under different IRCC times (0, 2, 4, 6, and 10 years). With increasing culture time, IRCC mode altered the relative abundance of dominant taxa, showing a significant decrease in the relative abundance of Actinobacteria and Chytridiomycota, with an increase in Proteobacteria and Firmicutes. The species richness and diversity of bacteria/fungi in 10-year IRCC paddy soil were significantly lower than in other groups (P < 0.05). Bacterial functional potential prediction by PICRUSt2 and phenotype prediction by BugBase showed that long-term IRCC significantly reduced the relative abundance of carbohydrate metabolism and increased the relative abundance of pathogenic potential and anaerobic phenotype (P < 0.05). Saprotrophs and pathotrophs dominated the fungal communities, and higher relative abundances of the plant pathogens, fungal parasites and lichen pathogens were found in IRCC soil (2- and 4-year) (P < 0.05). Microbial communities were mainly influenced by ammonium nitrogen, nitrate nitrogen, soil moisture content, and total carbon. Long-term IRCC could significantly change microbial communities and functions, while reducing microbial diversity in paddy soil. A “resting period” is recommended to ensure the sustainable development of ecological agriculture in paddy fields.

The impact of 12 years of biological control on soil microbiome and microfauna composition and functions in tea plantations

Synthetic pesticides were introduced to China in the 1940s and have become essential to increasing crop yield. They are now commonly applied across all agricultural landscapes. However, little is known about how the long-term pesticide use is affecting belowground communities and what impact pesticide residues are having on soil health. We investigated how pest management practice influence soil biota and overall yield. Soil samples were compared across tea farms that had different levels of pest management strategies: biocontrol, pesticide use, unmanaged over 12 years. DNA was extracted from the bulk soil underneath the canopy and subjected to 16S rRNA, 18S rRNA genes, ITS amplicon sequencing, qPCR quantification of the community and functional genes involved in the N-cycle. Additionally, the abundance and diversity of soil mites were recorded using traditional methods. The results highlighted that there were significant differences in edaphic properties including total nitrogen, total organic carbon, pH, phosphorus and levels of several pesticides across all treatments. Overall, there were distinct microbial communities associated with each treatment and diversity patterns were significantly influenced by management strategies. Across all gene regions, there was variation in the relative abundance of dominant taxa across treatment. Management influenced the abundance of N-cycling genes with an increased abundance of amoA and nirK in biocontrol and unmanaged farms. Interestingly, we found an increased abundance of fungal pathotrophs in the pesticide treatment. We also found that mite compositions and densities were different across all management strategies. The overall mite density and that of Rhodacaroidea were highest in the pesticide treatment and lowest in the unmanaged farm soil. This work aims to improve our understanding of pest management strategies from a soil biota point of view, to enhance soil health and to promote sustainable tea productions.

Effects of Water Loss Stress under Tidal Effects on the Epiphytic Bacterial Community of Sargassum thunbergii in the Intertidal Zone.

ABSTRACTIntertidal macroalgae face periodic water loss and rehydration caused by daily tidal changes. However, the effect of water loss stress on algal epiphytic bacteria has not yet been reported. In this study, the effects of water loss stress on the epiphytic bacteria community of Sargassum thunbergii were analyzed, and the different responses of epiphytic bacteria to water loss stress were compared between male and female algae. The results showed that after water loss stress, the diversity of the epiphytic bacterial community of S. thunbergii first decreased and then increased. Among the dominant taxa, the abundance of Cyanobacteria decreased significantly, whereas the abundance of Portibacter and Aquimarina first increased and then decreased. Additionally, the indicator species and the abundance of predicted functional genes related to carbon, nitrogen, and sulfur metabolism both changed significantly. More importantly, when the epiphytic bacteria were analyzed separately according to the algal sex, the changes in algal epiphytic bacterial community structure and indicator species were more significant, and there were sexual differences. Therefore, it was concluded that water loss stress has a significant effect on the community structure and function of the epiphytic bacteria on S. thunbergii. Meanwhile, the epiphytic bacteria community of two sexes of S. thunbergii differed in the response to water loss stress.IMPORTANCE Periodic water loss caused by the tide is an important environmental factor that is faced by intertidal macroalgae, but the impact of periodic water loss on the epiphytic bacterial communities associated with macroalgae is still unknown. Through this study, we found that the diversity, the relative abundance of dominant taxa, the indicator species, and the abundance of the predicted functional genes in the epiphytic bacteria on S. thunbergii changed with the time of water loss. Moreover, male and female S. thunbergii exhibited different responses to water loss stress. This study not only paves the way for the delineation of the interactions between S. thunbergii and its epiphytic bacteria but also provides new insights for the mechanisms of the adaptation and evolution of macroalgae in the intertidal zone.

Plant Interaction Patterns Shape the Soil Microbial Community and Nutrient Cycling in Different Intercropping Scenarios of Aromatic Plant Species.

Intercropping systems improve the soil nutrient cycle through microbial community activity and then land productivity. However, their interactions mechanism underlying that the mixed aromatic plant species intercropping regulate the soil microbiome and nutrient cycling on the perennial woody orchard is still uncovered. We designed treatments with 0, 1, and 3 aromatic plant species intercropped in two scenarios of clean tillage (T model, T1, T2, and T4) and natural grass (G model, G1, G2, and G4) in apple orchards, and investigated intercrops effects at the branch growing stage (BGS) and fruit development stage (FDS), respectively. Compared with T model, G model in FDS increased alpha diversity of bacterial community and Shannon index fungal community, the relative abundance of dominant taxa, such as Acidobacteria and Actinobacteria, and also the numbers of up and down-regulated OTUs, the most of indices of co-occurrence network in both bacterial and fungal community, and then improved invertase activity and available nitrogen content. Relative to G1, G2 and G4 reduced diversity bacterial community in FDS, the relative abundance of dominant taxa, the most of indices of co-occurrence network, and then improved soil invertase activity and total phosphorus content in soil. Moreover, Shannon index of fungal community, the altered number of OTUs and the most indices of co-occurrence network were higher in G4 than those in G2 in FDS. These changes above in FDS were more markedly than those in BGS, suggesting that chemical diversity of litter from mixed species of aromatic plants in natural grass scenario led to diversity, complexity, and stability of soil microbial community and then nutrient cycling. It provided a novel highlight and method to modulate biocenosis and then improve the soil nutrient cycling.

Revisiting the effect of PCR replication and sequencing depth on biodiversity metrics in environmental DNA metabarcoding.

Environmental DNA (eDNA) metabarcoding is an increasingly popular tool for measuring and cataloguing biodiversity. Because the environments and substrates in which DNA is preserved differ considerably, eDNA research often requires bespoke approaches to generating eDNA data. Here, we explore how two experimental choices in eDNA study design—the number of PCR replicates and the depth of sequencing of PCR replicates—influence the composition and consistency of taxa recovered from eDNA extracts. We perform 24 PCR replicates from each of six soil samples using two of the most common metabarcodes for Fungi and Viridiplantae (ITS1 and ITS2), and sequence each replicate to an average depth of ~84,000 reads. We find that PCR replicates are broadly consistent in composition and relative abundance of dominant taxa, but that low abundance taxa are often unique to one or a few PCR replicates. Taxa observed in one out of 24 PCR replicates make up 21–29% of the total taxa detected. We also observe that sequencing depth or rarefaction influences alpha diversity and beta diversity estimates. Read sampling depth influences local contribution to beta diversity, placement in ordinations, and beta dispersion in ordinations. Our results suggest that, because common taxa drive some alpha diversity estimates, few PCR replicates and low read sampling depths may be sufficient for many biological applications of eDNA metabarcoding. However, because rare taxa are recovered stochastically, eDNA metabarcoding may never fully recover the true amplifiable alpha diversity in an eDNA extract. Rare taxa drive PCR replicate outliers of alpha and beta diversity and lead to dispersion differences at different read sampling depths. We conclude that researchers should consider the complexity and unevenness of a community when choosing analytical approaches, read sampling depths, and filtering thresholds to arrive at stable estimates.

EDNA revealed in situ microbial community changes in response to Trapa japonica in Lake Qionghai and Lake Erhai, southwestern China

Trapa japonica was observed to have inhibiting effects and could be used as a potential environment-friendly control strategy for cyanobacterial blooms in freshwater. However, the changes and effecting mechanisms in eukaryotic and prokaryotic communities by T. japonica are not yet clear. In this study, the effects of T. japonica on microbial communities were assessed in Lake Qionghai and Lake Erhai by 18S rRNA and 16S rRNA amplicon sequencing, respectively. The results showed that T. japonica can improve biodiversity and change the microbial community structures to varying degrees in both lakes. The alpha diversity indexes of microbial communities (e.g., Shannon, Sobs, Ace and Chao 1) were higher in the water inhabited by T. japonica (TJ group) than the water uninhabited by T. japonica (control) (P < 0.05). The PCoA results suggested that the microbial community compositions differed between the two groups (PERMANOVA P = 0.001). In Lake Qionghai, the relative abundances of dominant taxa and nutrients level showed little differences between the two groups. These may result from the homogenous water condition in Lake Qionghai. While the genera Cyanobium_PCC-6307, the majority of Cyanobacteria, decreased significantly in TJ group than control according to 16S rRNA gene sequencing. In Lake Erhai, environmental variables were distinctly affected by T. japonica, which was found to drive Cryptophyceae to become the main taxa through taxonomic analysis of 18S rRNA. Based on 16S rRNA gene sequencing, T. japonica reduced the relative abundance of Cyanobacteria, such as Planktothrix_NIVA-CYA_15 and Cyanobium_PCC-6307, by enriching cyanobactericidal bacteria and growth-inhibiting bacteria (e.g., Limnohabitans and Flavobacterium) and changing environmental parameters. Our results revealed that T. japonica acts in shaping microbial communities in lakes on the community level, shedding new lights on eutrophication mitigation, one of the most serious global ecological problems we are facing.

Similar heterotrophic communities but distinct interactions supported by red and green-snow algae in the Antarctic Peninsula.

Snow algae are predicted to expand in polar regions due to climate warming, which can accelerate snowmelt by reducing albedo. Green snow frequently occurs near penguin colonies, and red snow distributes widely along ocean shores. However, the mechanisms underpinning the assemblage of algae and heterotrophs in colored snow remain poorly characterized. We investigated algal, bacterial, and fungal communities and their interactions in red and green snows in the Antarctic Peninsula using a high-throughput sequencing method. We found distinct algal community structure in red and green snows, and the relative abundance of dominant taxa varied, potentially due to nutrient status differences. Contrastingly, red and green snows exhibited similar heterotrophic communities (bacteria and fungi), whereas the relative abundance of fungal pathogens was substantially higher in red snow by 3.8-fold. Red snow exhibited a higher network complexity, indicated by a higher number of nodes and edges. Red snow exhibited a higher proportion of negative correlations among heterotrophs (62.2% vs 3.4%) and stronger network stability, suggesting the red-snow network is more resistant to external disturbance. Our study revealed that the red snow microbiome exhibits a more stable microbial network than the green snow microbiome.

Alterations of amino acid metabolism and intestinal microbiota in Chinese mitten crab (Eriocheir sinensis) fed on formulated diet and iced trash fish

Formulated diet (FD) and iced trash fish (ITF) are common diets during E. sinensis farming. However, whether FD can completely replace ITF during long-term E. sinensis farming is still unclear. Thus this study was conducted to compare the differences in amino acid metabolism and intestinal microbiota of the E. sinensis fed on different diets. The crabs were randomly divided into three groups fed on FD, ITF and mixed diet (MD, FD: ITF = 1:1), respectively. The results showed that there were no significant differences in amino acid composition among FD, MD and ITF groups. The activities of AST and ALT, and the mRNA levels of amino acid metabolism-related genes were significantly up-regulated in FD or/and MD groups compared with ITF group. The diversity of intestinal bacterial community was similar between the FD and ITF groups, but the relative abundance of dominant taxa showed marked differences between the two groups. At the phylum level, the relative abundance of Firmicutes was significantly higher, but the relative abundance of Proteobacteria was significantly lower in the FD group than that in ITF group. Meanwhile, at genus level, the relative abundance of Candidatus_Hepatoplasma in FD was higher than that in ITF group. Data related to functional prediction demonstrated that the significantly differenced pathways between the two groups were observed in metabolism (Pyrimidine metabolism, Glycolysis/Gluconeogenesis and Citrate cycle) and environmental information processing (transporters). The overall results indicated that replacement of ITF by FD did not affect amino acid composition, but altered amino acid metabolism and the relative abundance of intestinal microbiota. Our data provided a valuable reference for FD application replacing ITF during long-term E. sinensis farming.

Differential Impacts of Water Table and Temperature on Bacterial Communities in Pore Water From a Subalpine Peatland, Central China.

The level of water table and temperature are two environmental variables shaping soil bacterial communities, particularly in peatland ecosystems. However, discerning the specific impact of these two factors on bacterial communities in natural ecosystems is challenging. To address this issue, we collected pore water samples across different months (August and November in 2017 and May 2018) with a gradient of water table changes and temperatures at the Dajiuhu peatland, Central China. The samples were analyzed with 16S rRNA high-throughput sequencing and Biolog EcoMicroplates. Bacterial communities varied in the relative abundances of dominant taxa and harbored exclusive indicator operational taxonomic units across the different months. Despite these differences, bacterial communities showed high similarities in carbon utilization, with preferences for esters (pyruvic acid methyl ester, Tween 40, Tween 80, and D-galactonic acid γ-lactone), amino acids (L-arginine and L-threonine), and amines (phenylethylamine and putrescine). However, rates of carbon utilization (as indicated by average well-color development) and metabolic diversity (McIntosh and Shannon index) in May and August were higher than those in November. Redundancy analysis revealed that the seasonal variations in bacterial communities were significantly impacted by the level of the water table, whereas the temperature had a fundamental role in bacterial carbon utilization rate. Co-occurrence analysis identified Sphingomonas, Mucilaginibacter, Novosphingobium, Lacunisphaera, Herminiimonas, and Bradyrhizobium as keystone species, which may involve in the utilization of organic compounds such as amino acids, phenols, and others. Our findings suggest that bacterial community functions were more stable than their compositions in the context of water table changes. These findings significantly expand our current understanding of the variations of bacterial community structures and metabolic functions in peatland ecosystems in the context of global warming and fluctuation of the water table.

Structure and function of the fecal-associated microbiome in qi stagnation constitution

To clarify the structural and functional characteristics of the gut microbiota in individuals with qi stagnation constitution (QSC) and identify the potential biomarkers related to QSC. This cross-sectional study involved individuals with QSC and balanced constitution (BC) confirmed by TCM clinicians. The clinical features were recorded, and fecal samples were collected for 16S rDNA sequencing. The structure of the fecal-associated microbiome (FAM) was described by the alpha-diversity indexes, beta-distances, and relative abundances of dominant taxa. The differences in FAM distribution were analyzed by the Wilcoxon rank-sum test, MetagenomeSeq, and LEfSe analysis. The 16S rDNA gene sequences were assigned to the KEGG dataset to predict the functional information of bacterial metabolic pathways by using PICRUSt. Differences in functional pathways between groups were assessed with the Wilcoxon rank-sum test. The ROC curve based on specific operational taxonomic units (OTUs) was constructed, and the AUC was calculated. Twenty-two individuals with BC and 8 with QSC were recruited. Significant differences between the two groups were found in body mass index, health status, and low-density lipoprotein, etc . There was no significant difference in the alpha-diversity index. PCoA showed no evident clustering of bacterial communities according to constitutions. Bacteroidaceae, Lachnospiraceae, Ruminococcaceae, and Prevotellaceae were the four common bacteria with high abundances. Notably, MetagenomeSeq, LEfSe analysis, and the Wilcoxon rank-sum test identified significantly different distributions of 66, 42, and 36 OTUs, respectively. Predictive function analysis showed that 13 metabolic pathways were significantly differentially distributed, including those related to fatty acid synthesis. Five specific OTUs were selected as potential biomarkers of a QSC, and the AUC was 0.94. Individuals with QSC have unique FAM structure and related functional characteristics. Five specific OTUs were identified to serve as potentially effective biomarkers related to QSC.

Recovery of Soil-Denitrifying Community along a Chronosequence of Sand-Fixation Forest in a Semi-Arid Desertified Grassland

Revegetation on moving sand dunes is a widely used approach for restoring the degraded sandy land in northeastern China. The development of sand-fixation forest might improve the structures of soil microbial communities and affect soil N cycle. In the present study, the diversities of nitrite (nirS and nirK) and nitrous oxide (nosZ) reductase genes were investigated under a chronosequence of Caragana microphylla sand-fixation shrub forest (9- and 19-year), adjacent non-vegetated shifting sand-dune, and a natural forest dominated by C. microphylla. The dominant compositions and gene abundance were analyzed by a clone library technique and quantitative polymerase chain reaction, respectively. The compositions and dominant taxa of nirK, nirS, and nosZ communities under forest soil were all similar to those in the shifting sand-dune. However, the three gene abundances all linearly increased across forest age. Clones associated with known denitrifiers carrying nosZ, nirK, or nirS genes, such as members of Pseudomonas, Mesorhizobium, Rhizobium, Rhodopseudomonas, Azospirillum, and Cupriavidus, were detected. These denitrifiers were found to be abundant in soil and dominant in soil denitrification. Soil pH, total N, and available N affected the denitrifying communities by altering the relative abundance of dominant taxa. Overall, although soil attributes and forest age had no significant effects on the dominant constituents of nirK, nirS, and nosZ communities, revegetation on shifting sand-dunes facilitated the quantitative restoration of soil denitrifiers due to the increase in soil nutrients.

Alterations of Gastric Microbiota in Gastric Cancer and Precancerous Stages.

ObjectiveMicrobial infections have been shown to contribute to gastric carcinogenesis, the knowledge of gastric microbiota alteration in this process may provide help in early diagnosis of gastric cancer. The aim of this study was to characterize the microbial changes and identify taxonomic biomarkers across stages of gastric carcinogenesis.MethodsThe gastric microbiota was investigated by 16S rRNA gene analysis in gastric mucosal specimens from 47 patients including superficial gastritis (SG), atrophic gastritis (AG), gastric intraepithelial neoplasia (GIN), and gastric cancer (GC). Differences in microbial composition across the disease stages, especially in GIN and GC were assessed using linear discriminant analysis effect size.ResultsThere was no gradual changing trend in the richness or diversity of the gastric microbiota across stages of gastric carcinogenesis. The relative abundance of dominant taxa at phylum and genus levels didn’t show a gradual shift pattern, and the only four taxa that continuously enriched from SG to GC were Slackia, Selenomonas, Bergeyella, and Capnocytophaga, all of which were oral bacteria. The most representative taxa which were enriched in GC patients were oral bacteria including Parvimonas, Eikenella and Prevotella-2, and environmental bacteria including Kroppenstedtia, Lentibacillus, and Oceanobacillus. The gastric microbiota in GIN patients were characterized by enrichment of intestinal commensals including Romboutsia, Fusicatenibacter, Prevotellaceae-Ga6A1-group, and Intestinimonas. Gastric cardia cancer and non-cardia cancer patients had significantly different microbiota profiles characterized by a higher abundance of Helicobacter in the cardia cancer patients.ConclusionsOur results provide insights on potential taxonomic biomarkers for gastric cancer and precancerous stages, and suggest that gastric microbiota might play different roles in the carcinogenesis of cardia cancer and non-cardia cancer.

Spatial variation of the soil bacterial community in major apple producing regions of China.

In China, apple production areas are largely from the coastal to inland areas and across varied climate zones. However, the relationship among soil micro-organisms, environmental factors and fruit quality has not been clearly confirmed in orchards. Here we attempted to identify the variation of soil bacteria in the main apple producing regions and reveal the relationship among climatic factor, soil properties, soil bacterial community and fruit quality. Sixty soil samples were collected from six main apple producing areas in China. We examined the soil bacteria using bacterial 16S rRNA gene amplicon profiling. The results show that the soil bacterial diversity of apple orchards varied from the Bohai Bay Region to the Loess Plateau Region. Proteobacteria, Acidobacteria and Actinobacteria were the predominant taxa at the phylum level for all six areas. In the Bohai Bay and the Loess Plateau region, which are the two largest apple producing areas, Proteobacteria and Actinobacteria had the highest relative abundance, respectively. Furthermore, soil bacterial diversity showed positive correlation with the mean annual temperature (MAT), soil organic matter (SOM) and pH. Excluding a direct effect on the apple fruit quality, MAT exerted an indirect influence through soil SOM and pH to alter the relative abundance of dominant taxa and shift the bacterial diversity, which affects the apple fruit titratable acids and soluble solids. Geographic variables underlie apple orchard soil bacterial communities vary according to spatial scale. Environmental factors exert an indirect effect on apple fruit quality via shaping soil bacterial community. This study provides a list of bacteria associated with environmental factors and the ecological attributes of their interactions in apple orchards, which will improve our ability to promote soil bacterial functional capabilities in order to reduce the fertilizer input and enhance the fruit quality.

Structural and functional characteristics of the fecal-associated microbiome in dampness-heat constitution

IntroductionSusceptibility to lipid metabolic dysfunction are more frequent in individuals with dampness-heat (DH) constitution, which might be caused by the changes in the gut microbiome. This study is to explore the structural and functional characteristics of the fecal-associated microbiome (FAM) in DH constitution and screen FAM-related biomarkers of DH constitution. MethodsFecal samples were collected. The FAM structure was described with alpha/beta diversity indexes and relative abundances of dominant taxa; the distribution/functional differences of the FAM between DH and balanced constitutions were analyzed by Wilcoxon rank-sum test, MetagenomeSeq and LEfSe analysis, and the specific OTUs were screened to construct ROC curve. ResultsThere was a significant difference between the groups in the sweet preference, ACE and Chao1 indexes. In PCoA and PLS-DA, the bacterial communities in the balanced samples and DH samples clustered separately. Notably, there were 115 differentially distributed OTUs between groups identified in the MetagenomeSeq analysis and 213 OTUs identified with the Wilcoxon rank-sum test. Predicted functions showed that 12 metabolic pathways were differentially distributed between groups, including the pathway related to glycerolipid metabolism. The AUC of ROC curve based on the 4 screened specific OTUs was 0.91, and the relative abundance of these 4 OTUs could result in changes in lipid metabolism. ConclusionUnique FAM structural characteristics were identified in DH constitution, which might involve in changes in lipid metabolism and susceptibility to lipid metabolic dysfunction. The 4 screened specific OTUs could be used as potential biomarkers of DH constitution to assist clinical diagnosis.