Core Microbial Community Research Articles

The salivary microbiome shows a high prevalence of core bacterial members yet variability across human populations

Human saliva contains diverse bacterial communities, reflecting health status, dietary patterns and contributing to variability in the sensory perception of food. Many descriptions of the diversity of the salivary microbiome have focused on the changes induced by certain diseased states, but the commonalities and differences within healthy saliva have not been fully described. Here, we define and explore the core membership of the human salivary microbial community by collecting and re-analysing raw 16S rRNA amplicon sequencing data from 47 studies with 2206 saliva samples. We found 68 core bacterial taxa that were consistently detected. Differences induced by various host intrinsic and behaviour factors, including gender, age, geographic location, tobacco usage and alcohol consumption were evident. The core of the salivary microbiome was verified by collecting and analysing saliva in an independent study. These results suggest that the methods used can effectively define a core microbial community in human saliva. The core salivary microbiome demonstrated both stability and variability among populations. Geographic location was identified as the host factor that is most associated with the structure of salivary microbiota. The independent analysis confirmed the prevalence of the 68 core OTUs we defined from the global data and provides information about how bacterial taxa in saliva varies across human populations.

Deterministic mechanisms drive bacterial communities assembly in industrial wastewater treatment system.

Microbial communities are responsible for biological treatment of many industrial wastewater, but our knowledge of their diversity, assembly patterns, and function is still poor. Here, we analyzed the bacterial communities of wastewater and activated sludge samples taken from 11 full-scale industrial wastewater treatment plants (IWWTPs) characterized by the same process design but different wastewater types and WWTP compartments. We found significantly different diversity and compositions of bacterial assemblages among distinct wastewater types and IWWTPs compartments. IWWTPs bacterial communities exhibited a clear species abundance distribution. The dispersal-driven process was weak in shaping IWWTP communities. Meanwhile, environmental and operating conditions were important factors in regulating the structure of the activated sludge community and pollutants removal, indicating that bacterial community was largely driven by deterministic mechanisms. The core microbial community in IWWTPs was different from that in municipal wastewater treatment plants (MWWTPs), and many taxa (e.g. the genus Citreitalea) rarely were detected before, indicating IWWTPs harbored unique core bacterial communities. Furthermore, we found that bacterial community compositions were strongly linked to activated sludge function. These findings are important to both microbial ecologists and environmental engineers, who may optimize the operation strategies jointly for maintaining biodiversity, which in turn may promote a more stable performance of the IWWTP. Overall, our study enhances the mechanistic understanding of the IWWTP microbial community diversity, assembly patterns, and function, and provides important implications for microbial ecology and wastewater treatment processes.

Storage time and temperature affect microbial dynamics of yeasts and acetic acid bacteria in a kombucha beverage

Kombucha is a mildly sweet, slightly acidic fermented beverage, commercially available worldwide, that has attracted increasing consumers' interest due to its potential health benefits. Kombucha is commonly prepared using sugared black or green tea, but also other plant substrates are frequently utilised. Kombucha is obtained by fermentation using a symbiotic culture of bacteria and yeasts, whose composition varies depending on inoculum origin, plant substrates and environmental conditions. After fermentation, kombucha drinks are usually refrigerated at 4 °C, in order to maintain their biological and functional properties. There are no reports on the fate of microbial communities of kombucha in relation to long-term storage time and temperature. Here, for the first time, we monitored the diversity and dynamics of the microbial communities of a kombucha beverage fermented with different herbs during storage at 4 °C and at room temperature, for a period of 90 days, utilising culture-dependent and independent approaches. Moreover, cultivable yeasts and acetic acid bacteria (AAB) were isolated from the beverage, inoculated in pure culture, identified by molecular methods, and yeasts assessed for their functional properties. Total yeast counts were not affected by storage temperature and time, although their community composition changed, as Saccharomyces species significantly decreased after 45 days of storage at room temperature, completely disappearing after 90 days. On the other hand, Dekkera anomala (Brettanomyces anomalus), representing 52 % of the yeast isolates, remained viable up to 90 days at both storage temperatures, and was able to produce high levels of organic acids and exopolysaccharides. Data from DGGE (Denaturing Gradient Gel Electrophoresis) band sequencing confirmed that it was the dominant yeast species in all samples across storage. Other yeast isolates were represented by Saccharomyces and Zygosaccharomyces species. Among AAB, Gluconobacter oxydans, Novacetimonas hansenii and Komagataeibacter saccharivorans represented 46, 36 and 18 % of the isolates, whose occurrence remained unchanged across storage at 4 °C and did not vary up to 20 days of storage at room temperature. This work showed that the combination of culture-dependent and independent approaches is important for obtaining a complete picture of the distinctive core microbial community in kombucha beverages during storage, elucidating its diversity and composition, and preliminary characterizing yeast strains with putative functional activities.

Effect of Bacillus subtilis fortified inoculation on the microbial communities in different niches of Daqu

Daqu is the fermentation starter of Baijiu, which is one of the six most renowned distilled spirits. Studies have found that Bacillus is one of the dominant microbial genera in Daqu, and Bacillus subtilis is known to produce amylase, an important enzyme that influences the quality of Daqu. This study aims to explore the influence of B. subtilis inoculation on the microbial community structure in different niches of Daqu. We studied the microbial community structure of the natural inoculated Daqu (i.e., control Daqu) and the fortified Daqu (i.e., B. subtilis-inoculated Daqu) by amplicon sequencing. Our results showed that compared with the control Daqu rind microbial community, the relative abundance of Bacillus, Aspergillus, Thermomyces, and Rasamsonia in the fortified Daqu rind microbial community increased, and the relative abundance of Weissella, Lactobacillus, Leuconostoc, and Pichia decreased. Compared with the control Daqu core microbial community, the relative abundance of Bacillus in the fortified Daqu core microbial community also increased, but the relative abundance of Pseudomonas and Paecilomyces decreased. The effect of B. subtilis inoculation on the rind microbial community of Daqu was more significant. In addition, the bacterial community of Daqu was more susceptible to the effect of the B. subtilis inoculation than was the fungal community of Daqu. The correlation between the bacterial community of Daqu and the fungal community of Daqu increased significantly after the B. subtilis inoculation. These results provide an important theoretical basis for the production of fortified Daqu.

Characterization of the core microbial community governing acidogenic processes for the production of valuable bioproducts

Volatile fatty acids (VFAs) and alcohols generated from acidogenic processes are valuable bioresources. However, how the diversity of acidogenic microorganisms and environmental factors affect their generation are still poorly understood. In this study, 18 different inocula and 42 sludges from acidogenic lab-scale reactors were collected to analyze the microbial communities and their metabolic potential using 16S rRNA genes high throughput sequencing coupled with PICRUSt2. 23 out of 30732 distinctive amplicon sequence variants were identified as the core features and 34.8% of them (e.g., Clostridium spp.) were positively correlated with the generation of the most common product acetate. PICRUSt2 shows that an average of 27% of predicted fermentation-pathway genes was assigned to the core features, suggesting their crucial roles in acidogenesis. From the network aspect, the acidogenic network had a slightly higher number of nodes (12%), but significantly lower numbers of edges (109%) and neighbors (132%) compared with the inoculum network. A total of 28 independent subnetworks from large to small scales were extracted from the acidogenic network. The decentralized distribution of core features in these subnetworks emphasized their non-co-occurring relationships. The electrode potential was the most significant environmental variable (48.2–49.3% of the explanation), positively affecting the distribution of more than 50% of the core features and fermentation pathways. Results of this study emphasized the importance of core features rather than microbial diversity in acidogenic performance and highlighted the response of the core microbial community to environmental changes, which may be applied in practical applications to optimize acidogenic performance.

Microbial diversity and composition in acidic sediments of freshwater finfish culture ponds fed with two types of feed: a metagenomic approach.

Microbial community profile associated with acidic pond sediments (APS) (pH = 3·0-4·5) of freshwater finfish aquaculture ponds (n = 8) was investigated. Sediment DNA extracted from the eight APS were subjected to high-throughput sequencing of V3 and V4 regions which yielded 7236 operational taxonomic units (OTUs) at a similarity of 97%. Overall results showed higher proportion of bacterial OTUs than archaeal OTUs in all the APS. Euryarchaeota (23%), Proteobacteria (19%), Chloroflexi (17%), Crenarchaeota (5·3%), Bacteroidetes (4·8%), Nitrospirae (3·2%), Nanoarchaeaeota (3%) which together constituted 75% of the microbial diversity. At the genus level, there was high preponderance of methanogens namely Methanolinea (5·4%), Methanosaeta (4·5%) and methanotrops, Bathyarchaeota (5%) in APS. Moreover, the abundant phyla in the APS were not drastically affected by the administration of chicken slaughter waste (R-group ponds) and commercial fish feed (C-group ponds), since 67% of the OTUs generated remained common in the APS of both the groups of ponds. There was a minimal difference of 24-26% of OTUs between C-group and R-group ponds, suggesting the existence of a core microbial community in these ponds driven by acidic pH over the years. This study concludes that microbial diversity in pond sediment was influenced to a lesser extent by the addition of chicken slaughter waste but was majorly driven by acidic nature of the pond.

Constructed wetlands treating synthetic wastewater in response to day-night alterations: Performance and mechanisms

Constructed wetlands (CWs), as nature-based wastewater treatment systems, continuously maintain exchanges of material and energy with the natural environment. However, it is unclear how pollutant removal performance in CWs occurs in response to diurnal variation. Herein, we investigated the effects of day-night alterations on the rhizosphere microbial community in CWs. The results revealed that a dynamic alternate mechanism existed in the inner environment when the CWs were in steady operation, which was validated by rhythmic changes in the core microbial community, microbial metabolism activity, and pollutant removal shown in this study. The results showed that pollutant removal (e.g., total nitrogen) due to microbial processes was 1.31 times higher under daytime conditions than under nighttime conditions. Core microbial taxa of the rhizosphere that evolved with circadian rhythm (e.g., Chloroflexus and Beijerinckia) were mostly associated with carbon, nitrogen, phosphorus, and energy metabolism, with lower average relative abundance identified at night. Although higher activity of microbial metabolism was also observed in the daytime, nighttime conditions demonstrated higher gene levels that were related to carbon and nitrogen metabolic functions. Structural equation model (SEM) analysis further suggested that environmental factors exerted a significant influence in driving microbial processes for pollutant removal and that the microbial community played a greater role in promoting pollutant removal under nighttime conditions than under daytime conditions.

The Gut Microbiota Composition of Cnaphalocrocis medinalis and Their Predicted Contribution to Larval Nutrition.

Intestinal bacterial flora plays an important role in the nutrition, physiology, and behavior of herbivorous insects. The composition of gut microbiota may also be affected by the food consumed. Cnaphalocrocis medinalis is an oligophagous pest, feeds on rice leaves almost exclusively and causes serious damage to rice in Asian countries. Using antibiotic treatment and metagenome sequencing, we investigated the influence of the food sources (rice and maize seedlings) on the structure and functions of intestinal bacteria of C. medinalis. Firstly, food utilization indices, relative growth rate (RGR), relative consumption rate (RCR), efficiency of conversion of ingested food (ECI), and efficiency of conversion of digested food (ECD), were all significantly adversely affected in the antibiotic treatment eliminating gut bacteria, showing that the microbiota loading in the gut were essential for the larva growth and development of C. medinalis. Further, metagenome sequencing revealed that different diets caused a variation in gut microbiota composition of C. medinalis, indicating that the gut microbiota were in part driven by the diet provided. However, the larvae of C. medinalis hosted a core microbial community in the gut, which was independent from the diets changing. The dominant bacteria in the two feeding groups were highly consistent in the gut of C. medinalis larvae, with the gut bacterial community dominated by Firmicutes at the phylum level, Enterococcus at the genus level, Enterococcus sp. FDAARGOS-375, E. casseliflavus, E. gallinarum, and E. sp. CR-Ec1 accounted for more than 96% of the gut microbiota. Functional prediction analysis demonstrated that gut bacteria encoded a series of metabolism-related enzymes involved in carbohydrate metabolism and amino acid synthesis. Carbohydrate metabolism was the most enriched function in both groups and was more abundant in rice feeding group than in maize feeding group. The core dominant Enterococcus species possessed complete pathways of 14 carbohydrates metabolism, 11 amino acids biosynthesis, and two vitamins synthesize, implied to contribute an essential role to the nutrition intake and development of C. medinalis. Finally, the study may provide an in-depth analysis of the symbiont-host co-adaptation and new insights into the management of C. medinalis.

Host-Adapted Strains of Spodoptera frugiperda Hold and Share a Core Microbial Community Across the Western Hemisphere.

The fall armyworm Spodoptera frugiperda is an important polyphagous agricultural pest in the Western Hemisphere and currently invasive to countries of the Eastern Hemisphere. This species has two host-adapted strains named "rice" and "corn" strains. Our goal was to identify the occurrence of core members in the gut bacterial community of fall armyworm larvae from distinct geographical distribution and/or host strain. We used next-generation sequencing to identify the microbial communities of S. frugiperda from corn fields in Brazil, Colombia, Mexico, Panama, Paraguay, and Peru, and rice fields from Panama. The larval gut microbiota of S. frugiperda larvae did not differ between the host strains nor was it affected by the geographical distribution of the populations investigated. Our findings provide additional support for Enterococcus and Pseudomonas as core members of the bacterial community associated with the larval gut of S. frugiperda, regardless of the site of collection or strain. Further investigations are required for a deeper understanding of the nature of this relationship.

Towards heat tolerant metagenome functional prediction, coral microbial community composition, and enrichment analysis

Coral reefs represent one of the most biodiverse marine ecosystems on our planet. These consist of colonies of very small sea animals belonging to the phylum named Cnidaria, and of more complex, yet not so well-known microbial communities. Despite the fact that they occupy only a tiny portion of the oceans' surface, coral reefs are swarming with life, providing food and shelter to a wide number of marine species, ranging from mollusks to numerous fish species. There is a number of factors that can affect their sustainability and likelihood of developing diseases, including increased seawater temperature, acidity, salinity, and human impact. It is crucial to study the relationship between corals and microbial communities linked to them. This work analyzes the overall microbial community composition of the different coral species found in the Australian waters and identifies the most abundant Operational Taxonomic Units (OTUs) on different taxonomic levels. Additionally, heat specific coral core microbiome found across at least 20% of the investigated coral host species was identified and thoroughly analyzed. Lastly, metagenome functional prediction was carried out and the most abundant heat tolerance related genes were highlighted.

Temperature Affects Antagonism Among Coral-Associated Bacteria

Reef-building corals are invertebrate animals that associate with diverse microorganisms, including Symbiodiniaceae, bacteria, fungi, and archaea. This symbiotic consortium, called the holobiont, is a dynamic system and rapidly responds to environmental temperatures. At present, the effects of temperature on bacteria-bacteria interactions in the coral-associated bacterial community are not clear. Antagonism is considered one of the potential structuring forces in coral microbial communities. Here, we examined the antagonistic interactions among 32 coral-associated bacteria and the physiological and biochemical characteristics of these isolates at different temperatures. The results showed that the antagonism breadth (i.e. the total number of antagonistic interactions) increased but antagonism intensity (i.e. the size of the inhibition zone) decreased at 32°C. The antagonistic interaction network was nested and sender-determined both at 25°C and 32°C, suggesting that the competition networks of coral-associated bacteria were more influenced by the antagonist strains than sensitive strains. Furthermore, we found that the elevated temperature increased the complexity of the antagonistic network. By evaluating the correlations between antagonism and the phylogenetic and phenotypic distances, we demonstrated that the antagonism probability correlated with the phylogenetic distance rather than phenotypic distance. Moreover, the antagonist strains have a wider metabolic niche space, i.e., grew on more carbon sources, than the antagonized strains at 25°C, while there was no difference at 32°C, suggesting the trade-off between antagonism and resource exploitation shifted in the antagonistic interactions under the higher temperature. These findings will be helpful for understanding the bacterial interactions in coral holobionts and the assembly of bacterial community in altered environments, especially under heat stress.

Lime addition significantly attenuates tetracycline resistance genes and class 1 integrons in dewatered sludge by affecting bacterial profiles

To verify the hypothesis that adding lime can remove antibiotic resistance genes (ARGs) in excess activated sludge (EAS), in this study, we explored the effects of lime addition at different ratios on the removal of tetracycline resistance genes (TRGs, tetW/tetS/tetZ/tetC/tetX) and class 1 integrons (intI1) in dewatered EAS. The microbial community succession was also analyzed. Drying without lime addition for 7 d significantly reduced the total content of TRGs and intI1 with a removal efficiency of 72.88%, and lime addition further promoted the removal effect and achieved a removal efficiency exceeding 98.54%. A higher L/S ratio did not result in more effective removal of TRGs. The fate of TRGs did not correlate with their resistance mechanism. Lime addition promoted the removal of TRGs by enhancing the decrease in moisture content and changing the microbial community structure. Principal component analysis suggested that the core microbial community was significantly distinct and clustered more by the treatment stage than the method used. Spearman correlation and network analyses indicated that 17 genera belonging to five phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Nitrospirae) were significantly positively or negatively correlated (|R| > 0.6, p < 0.05) with TRGs and intI1. These findings increase our understanding of the benefits of lime addition treatment for attenuating TRGs and intI1 in EAS. Adding lime to EAS is straightforward and cost-effective and contributes toward preventing the release of TRGs and intI1 into the total environment.

Elaeagnus angustifolia can improve salt-alkali soil and the health level of soil: Emphasizing the driving role of core microbial communities

Saline-alkali environments are widely distributed in China and significantly hinder the development of agriculture. This study characterizes the long-term effects of planting Elaeagnus angustifolia (E. angustifolia) on the physical and chemical properties, enzyme activities and microbial community characteristics of saline-alkali soil in the Songnen Plain (1, 2 and 3 years). The results showed that planting E. angustifolia reduced soil pH and electrical conductivity (EC) and increased soil total phosphorus (TP), total nitrogen (TN), nitrate nitrogen (Nni), total potassium (TK), dissolved organic C (DOC), dissolved organic matter (DOM) and available potassium (AK) content and catalase, urease, polyphenol oxidase, phosphatase, sucrase and cellulase enzyme activities, and the results peaked in the 3 year. High-throughput sequencing showed that the bacterial abundance and diversity were as follows (from high to low) y3 > y2 > y1 > CK. E. angustifolia resulted in an increase in the relative abundance of the dominant bacteria. Proteobacteria and Pseudomonas were the major phylum and genus, respectively. Redundancy analysis showed that changes in the soil microbial community significantly affect the physical and chemical properties of the soil, with Proteobacteria members being the key microorganisms that reduce soil salinity. Network analysis showed that Pseudomonas (Proteobacteria) participated in the synthesis of key soil enzymes. 16S rRNA sequencing predicted that the expression of genes related to carbon (rbcL, acsA, acsB, Pcc and accA) and nitrogen (amoA/B, nxrA, hao, gdh, ureC and nosZ) transformation increased, and Pseudomonas members were key regulators of carbon and nitrogen dynamics. In conclusion, the planting of E. angustifolia could improve the physical and chemical properties of the soil by releasing root exudates into the soil and increasing the diversity and richness of soil microbial communities to improve saline-alkali soil, providing a theoretical basis for improving saline-alkali soil and promoting the sustainable development of modern agriculture.

Re-evaluation of the environmental hazards of nZnO to denitrification: Performance and mechanism

Numerous studies have shown that zinc oxide nanoparticles (nZnO) have an inhibitory effect on wastewater biotreatment, where doses exceeding ambient concentrations are used. However, the effect of ambient concentrations of ZnO (<1 mg/L) on anaerobic digestion processes is not clear. Herein, this study comprehensively explored the impact of nZnO on the denitrification performance and core microbial community of activated sludge under ambient concentrations. Results showed that only 0.075 mg/L nZnO had shown a beneficial effect on nitrogen removal by activated sludge. When nZnO concentration reached 0.75 mg/L, significant enhancement of nitrate reduction and mitigation of nitrite accumulation were observed, indicating a remarkable stimulatory effect on nitrogen removal. Simultaneously, nZnO could weaken the sludge surface charge and improve the secretion of extracellular polymeric substances, thus enhancing sludge flocculation for denitrification. Microbial community analysis revealed that nZnO exposure increased the relative abundance of denitrifying bacteria, which could contribute to the reinforcement of traditional denitrification. Furthermore, exogenous addition of NH4+ significantly inhibited the accumulation of nitrite, implying that nZnO had a potential to improve the denitrification process via a partial denitrification-anammox pathway. Considering current ambient concentration, the stimulatory effect shown in our work may better represent the actual behavior of ZnO in wastewater biotreatment.

Microbial Communities of the Hydrothermal Scaly-Foot Snails From Kairei and Longqi Vent Fields

The microbial communities of the hydrothermal Scaly-foot Snails (SFSs) from independent hydrothermal vent fields have not been investigated in depth. In this study, we collected SFSs from two different hydrothermal environments located on the Central Indian Ridge (CIR) and the Southwest Indian Ridge (SWIR), the Kairei and Longqi vent fields, respectively. Additionally, one SFS collected from the Kairei vent field was reared for 16 days with in situ deep-sea seawater. The epibiotic and internal samples of SFSs, including ctenidium, esophageal gland, visceral mass, shells, and scales, were examined for microbial community compositions based on the 16S rRNA gene. Our results revealed significant differences in microbial community composition between SFSs samples collected from Kairei and Longqi vent fields. Moreover, the microbial communities of epibiotic and internal SFS samples also exhibited significant differences. Epibiotic SFS samples were dominated by the bacterial lineages of Sulfurovaceae, Desulfobulbaceae, Flavobacteriaceae, and Campylobacteraceae. While in the internal SFS samples, the genus Candidatus Thiobios, affiliated with the Chromatiaceae, was the most dominant bacterial lineage. Furthermore, the core microbial communities of all samples, which accounted for 78 ∼ 92% of sequences, were dominated by Chromatiaceae (27 ∼ 49%), Sulfurovaceae (10 ∼ 35%), Desulfobulbaceae (2 ∼ 7%), and Flavobacteriaceae (3 ∼ 7%) at the family level. Based on the results of random forest analysis, we also found the genera Desulfobulbus and Sulfurovum were the primary bacterial lineages responsible for the dissimilarity of microbial communities between the SFS samples collected from the Kairei and Longqi vent fields. Our results indicated that the microbial lineages involved in the sulfur cycle were the key microorganisms, playing a crucial role in the hydrothermal vent ecosystems. Our findings expand current knowledge on microbial diversity and composition in the epibiotic and internal microbial communities of SFS collected from different hydrothermal vent fields.

PSIX-28 Parity and lactation stage affect the sow milk microbiome

Abstract The milk microbiome in swine has been recently demonstrated to develop and alter the growing gut microbiome in offspring. Milk is the primary nutritional source for piglets and the established microbial communities from initial diet remain stable over time, thus being critical for long-term effects on the animal. Since little is known about the ontogeny of the milk microbiome, the objective of this study was to determine differences in the sow milk microbiome among multiple parities and days in lactation. A total of 32 sows were grouped by parity, 1–4, with 8 sows per parity. Sows were on the same diet and had ad libitum access to water. At sampling, teats were cleaned and stripped. Milk samples were manually collected on one side from a fore, mid, and hind teat, then combined for one whole milk sample per animal. Milk was sampled on days 2 and 16 to determine differences between days in lactation. Samples were sequenced using an Illumina MiSeq for V1-V3 regions of the bacterial 16S rRNA gene and downstream analyses were conducted in the R environment using ‘phyloseq’ and ‘DADA2’ packages. Statistical analyzes utilized a completely randomized design and a mixed model analysis of variance, with fixed effects of parity and days in lactation and examining a parity by day interaction. The genera Corynebacterium were greater (P &amp;lt; 0.05) abundance in parity 4. There was an increase (P &amp;lt; 0.05) in Staphylococcus at day 2 compared to day 16. Core microbial communities, Lactobacillus and Romboutsia increased (P &amp;lt; 0.05) by day 16. Identifying microbial communities present in the milk microbiome in sows can allow producers to understand how these microbes may influence the gut microbiome in growing piglets to augment gain. USDA is an equal opportunity provider and employer.

Gut microbiota regulation of P-glycoprotein in the intestinal epithelium in maintenance of homeostasis

BackgroundP-glycoprotein (P-gp) plays a critical role in protection of the intestinal epithelia by mediating efflux of drugs/xenobiotics from the intestinal mucosa into the gut lumen. Recent studies bring to light that P-gp also confers a critical link in communication between intestinal mucosal barrier function and the innate immune system. Yet, despite knowledge for over 10 years that P-gp plays a central role in gastrointestinal homeostasis, the precise molecular mechanism that controls its functional expression and regulation remains unclear. Here, we assessed how the intestinal microbiome drives P-gp expression and function.ResultsWe have identified a “functional core” microbiome of the intestinal gut community, specifically genera within the Clostridia and Bacilli classes, that is necessary and sufficient for P-gp induction in the intestinal epithelium in mouse models. Metagenomic analysis of this core microbial community revealed that short-chain fatty acid and secondary bile acid production positively associate with P-gp expression. We have further shown these two classes of microbiota-derived metabolites synergistically upregulate P-gp expression and function in vitro and in vivo. Moreover, in patients suffering from ulcerative colitis (UC), we find diminished P-gp expression coupled to the reduction of epithelial-derived anti-inflammatory endocannabinoids and luminal content (e.g., microbes or their metabolites) with a reduced capability to induce P-gp expression.ConclusionOverall, by means of both in vitro and in vivo studies as well as human subject sample analysis, we identify a mechanistic link between cooperative functional outputs of the complex microbial community and modulation of P-gp, an epithelial component, that functions to suppress overactive inflammation to maintain intestinal homeostasis. Hence, our data support a new cross-talk paradigm in microbiome regulation of mucosal inflammation.E5eiP3AkGcyQ2ZEhk_J1qbVideo abstract

Characterizing the interaction relationship of the microbial communities between Zaopei and pit mud disturbing by Daqu.

The online version contains supplementary material available at 10.1007/s10068-021-00975-z.

Local versus site-level effects of algae on coral microbial communities.

Microbes influence ecological processes, including the dynamics and health of macro-organisms and their interactions with other species. In coral reefs, microbes mediate negative effects of algae on corals when corals are in contact with algae. However, it is unknown whether these effects extend to larger spatial scales, such as at sites with high algal densities. We investigated how local algal contact and site-level macroalgal cover influenced coral microbial communities in a field study at two islands in French Polynesia, Mo'orea and Mangareva. At 5 sites at each island, we sampled prokaryotic microbial communities (microbiomes) associated with corals, macroalgae, turf algae and water, with coral samples taken from individuals that were isolated from or in contact with turf or macroalgae. Algal contact and macroalgal cover had antagonistic effects on coral microbiome alpha and beta diversity. Additionally, coral microbiomes shifted and became more similar to macroalgal microbiomes at sites with high macroalgal cover and with algal contact, although the microbial taxa that changed varied by island. Our results indicate that coral microbiomes can be affected by algae outside of the coral's immediate vicinity, and local- and site-level effects of algae can obscure each other's effects when both scales are not considered.

Spatial and Species Variations of Bacterial Community Structure and Putative Function in Seagrass Rhizosphere Sediment.

Seagrasses are an important part of the coral reef ecosystem, and their rhizosphere microbes are of great ecological importance. However, variations in diversity, composition, and potential functions of bacterial communities in the seagrass rhizosphere of coral reef ecosystems remain unclear. This study employed the high-throughput sequencing based on 16S rDNA gene sequences and functional annotation of prokaryotic taxa (FAPROTAX) analysis to investigate these variations based on seagrass species and sampling locations, respectively. Results demonstrated that the seagrass rhizosphere microbial community was mainly dominated by phylum Proteobacteria (33.47%), Bacteroidetes (23.33%), and Planctomycetes (12.47%), while functional groups were mainly composed of sulfate respiration (14.09%), respiration of sulfur compounds (14.24%), aerobic chemoheterotrophy (20.87%), and chemoheterotrophy (26.85%). Significant differences were evident in alpha diversity, taxonomical composition and putative functional groups based on seagrass species and sampling locations. Moreover, the core microbial community of all investigated samples was identified, accounting for 63.22% of all obtained sequences. Network analysis indicated that most microbes had a positive correlation (82.41%), and two module hubs (phylum Proteobacteria) were investigated. Furthermore, a significant positive correlation was found between the OTUs numbers obtained and the functional groups assigned for seagrass rhizosphere microbial communities (p < 0.01). Our result would facilitate future investigation of the function of seagrass rhizosphere microbes.