16S rDNA High-throughput Sequencing Research Articles

Simultaneous nitrification-denitrification (SND) using a thermoplastic gel as support: pollutants removal and microbial community in a pilot-scale biofilm membrane bioreactor

ABSTRACT In this study, experiments were carried out to treat sanitary wastewater in a biofilm membrane bioreactor using a thermoplastic gel as a support to assist the nitrification-denitrification process. For this purpose, the system was operated in two different dissolved oxygen concentrations (2.3 ± 0.2 and 0.9 ± 0.3 mg O2/L for Phases I and II, respectively) and the removal of organic compounds and nitrogen, as well as the microbial community in suspended biomass and biofilm were evaluated. The MB-MBR system was able to withstand raw wastewater variations and maintaining a low permeate COD concentration (18 mg/L) even at low DO concentrations. On the other hand, it was found that oxygen concentration significantly influenced the process of nitrogen conversion. In Phase I the average removal of total nitrogen was 18 ± 8%, while in Phase II it increased to 66 ± 11%. The denitrification rate was two times higher (7.8 mg NO3 --N/h) at low dissolved oxygen, with a significant contribution of the biofilm (41%). Additionally, the high-throughput 16S rDNA sequencing showed that the oxygen concentration was determinant for arrangement patterns of the samples and not the sampling site (suspended biomass and support material). Thiothrix, Comamonas, Rhodobacter, Mycobacterium, Thermomonas, Sphingobium, Sphigopyxis, Pseudoxanthomonas, Nitrospira and, Novosphingobium were the main genera regarding the nitrogen cycle.

Toxic effects of ammonia on the intestine of the Asian clam (Corbicula fluminea)

Intestines contain a large number of microorganisms that collectively play a vital role in regulating physiological and biochemical processes, including digestion, water balance, and immune function. In this study, we explored the effects of ammonia stress on intestinal inflammation, the antioxidant system, and the microbiome of the Asian clam (Corbicula fluminea). Exposure to varying ammonia concentrations (10 and 25 mg N/L) and exposure times (7 and 14 days) resulted in damage to C. fluminea intestinal tissue, according to histological analysis. Furthermore, intestinal inflammatory responses and damage to the antioxidant system were revealed through qPCR, ELISA, and biochemical analysis experiments. Inflammatory responses were more severe in the treatment group exposed to a lower concentration of ammonia. High-throughput 16S rDNA sequencing showed that ammonia stress under different conditions altered intestinal bacterial diversity and microbial community composition, particularly impacting the dominant phylum Proteobacteria and genus Aeromonas. These results indicate that ammonia stress can activate intestinal inflammatory reactions, damage the intestinal antioxidant system, and alter intestinal microbial composition, thereby impeding intestinal physiological function and seriously threatening the health of C. fluminea.

Profiling of Diagnostic Information of and Latent Susceptibility to Bacterial Keratitis From the Perspective of Ocular Bacterial Microbiota.

The ocular surface possesses its own bacterial microbiota. Once given a chance, opportunistic pathogens within ocular microbiota may lead to corneal infection like bacterial keratitis (BK). To reveal the possible factor that makes people vulnerable to BK from the perspective of ocular bacterial microbiota, as well as to compare diagnostic information provided by high-throughput 16S rDNA sequencing and bacterial culture, 20 patients with BK and 42 healthy volunteers were included. Conjunctival swabs and corneal scrapings collected from the diseased eyes of BK patients were subjected for both high-throughput 16S rDNA sequencing and bacterial culture. Conjunctival swabs collected from the normal eyes of BK patients and healthy volunteers were sent only for sequencing. For identifying the pathogens causing BK, high-throughput 16S rDNA sequencing presented a higher positive rate than bacterial culture (98.04% vs. 17.50%), with 92.11% reaching the genus level (including 10.53% down to the species level). However, none of the sequencing results was consistent with the cultural results. The sequencing technique appears to challenge culture, and could be a complement for pathogen identification. Moreover, compared to the eyes of healthy subjects, the ocular microbiota of three sample groups from BK patients contained significantly less Actinobacteria and Corynebacteria (determinate beneficial symbiotic bacteria), but significantly more Gammaproteobacteria, Pseudomonas, Bacteroides, and Escherichia-Shigella (common ocular pathogenic bacteria). Therefore, it is speculated that the imbalance of protective and aggressive bacteria in the ocular microbiota of healthy people may trigger susceptibility to BK. Based on this speculation, it seems promising to prevent and treat infectious oculopathy through regulating ocular microbiota.

Impact of the Gut Microbiome on the Progression of Hepatitis B Virus Related Acute-on-Chronic Liver Failure.

The relationship between the progression of hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF) and the gut microbiota is poorly understood, and an HBV-ACLF-related microbiome has yet to be identified. In this study alterations in the fecal microbiome of 91 patients with HBV-ACLF (109 stool samples), including a cohort of nine patients at different stages of HBV-ACLF, were determined by high-throughput 16S rDNA sequencing. The operational taxonomic units and Shannon indexes indicated that the diversity and abundance of the gut microbiome significantly decreased with the progression of HBV-ACLF (p <0.05). The relative abundance of the Bacteroidetes phylum in the microbiome was significantly reduced, whereas the abundance of potentially pathogenic bacteria, such as Veilonella, Streptococcus, Enterococcus, and Klebsiella, was highly enriched in the HBV-ACLF group compared with the healthy control group. The abundance of Bacteroidetes was negatively correlated with the level of serum alpha fetoprotein, and the abundance of Veilonella was positively correlated with serum total bilirubin (TBIL). Furthermore, the abundance of Coprococcus was significantly negatively correlated with the level of serum TBIL and the international normalized ratio and positively correlated with prothrombin time activity. Our findings suggest that the gut microbiota plays an important role in the development of HBV-ACLF.

Characteristics of soil bacterial and fungal communities on interval seawater covering Linchang Island, China.

Characterization of microbial communities is important for understanding the soil biodiversity distribution affected by environmental factors. Here, we combined high-throughput sequencing of 16S rDNA and ITS to investigate the composition of bacterial and fungal communities in interval seawater covering Linchang Island, China. We compared the microbial communities in the soil of three sample points from the southern part to the northern part. No difference was observed in microbial abundance, richness and diversity in those three different locations. In addition, weighted and unweighted UniFrac distances revealed that three soil samples could not be separated from each other, even if the LCNS sample had significantly lower organic matter (OM), sodium and sulfate contents than the LCSS and LCMS samples. This result indicated that the microbial community of the soil may be influenced more strongly by interval seawater than by soil chemical characteristics. The bacterial phyla Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroidetes were the four most abundant phyla in all samples, accounting for 83.22% of the microbial community. Escherichia-Shigella and Vibrio were abundant in the samples and accounted for 1.17% and 0.27%, respectively. Fungal structure, phylogenetic diversity, richness, and bacterial structure had a significant negative relationship with Vibrio abundance. In addition, Vibrio showed negative correlations with the genera Simiduia, Microbulbifer and Haliangium. The results reveal that the re-shaped microbiome and introduced typical microbes could be strategies for inhibiting Vibrio in the soil of Linchang Island.

Bacterial community profiling of floating plastics from South Mediterranean sites: First evidence of effects on mussels as possible vehicles of transmission

Plastic wastes accumulation in marine environments is becoming a crucial issue; while the toxicity to biota is quite well explored, a gap of knowledge still exists on the role that plastics play in shaping bacterial community structures in marine conditions and their possible transmission to humans. The present study intended first to profile bacterial community structure in floating plastic particles (FP) biofilms and seawater from four Tunisian coastal areas using high-throughput sequencing (HTS) of 16S rDNA. Subsequently, mussels (Mytilus galloprovincialis) as filter feeding organisms were exposed to the FP to broaden the knowledge on the potential role played by environmental plastic particles in shaping bacterial community structures and on their possibility to act as vehicles of bacteria through the food web. The mussels’ microbiota was microbiologically analyzed through HTS, and the Histidine Rich Glycoprotein (HRG) gene expression level was investigated as the main immune response. Our results clearly showed a great variation in the composition of bacterial communities of FP and seawater from different geographical areas. Moreover, the gills of mussels exposed to sterilized seawater and native FP from each site exhibited a wider bacterial biodiversity. The gene expression level of HRG was found to be significantly higher in animals exposed to native FP when compared to sterilized FP. Our results should be carefully considered in view of the Trojan horse effects of FP toward bacteria and its potential toxicity.

Comparison of productive and biological characteristics of indigenous and imported cattle in Yakutia

The aim of this research was evaluation of the rumen and faecal bacterial communities with high-throughput sequencing of 16S rDNA in indigenous Yakut and transferred Kalmyk cows, which have potentially valuable gene pools for beef cattle breeding. The obtained results showed a similar composition of the microbiomes in the rumens of Yakut and Kalmyk cows. The dominant bacterial phyla in the rumen microbiocenoses were Firmicutes and Bacteroidetes represented mainly by the Prevotellaceae, Porphyromonadaceae, Ruminococccaceae and Lachnospiraceae families. In the faeces of the cow breeds, compared families Bacteroidaceae, Clostridiaceae, Ruminococcaceae and Verrucomicrobiaceae were the most numerous. Further work is necessary to reveal the role of the identified bacterial taxa in changes of the rumen fermentation.

Impact of land use on soil function and bacterial community in the Brazilian savanna

Land use systems have a great impact on soil function and microbial diversity in tropical soils. Our study aimed to evaluate soil biochemical indicators and community composition and to assess the relationship between soil biochemical and microbial indicators and bacterial diversity of three agroecosystems (pine forest, soya and sugarcane) and native Cerrado forest in the Brazilian savanna. Soil biochemical indicators (soil organic matter and enzymes) and high-throughput sequencing of 16S rDNA were performed in two topsoil depths (0-5 cm and 5-10 cm). Soil microbial and enzyme activity showed that agricultural soil usage has a negative impact on soil function compared to native and pine forests. Results also revealed higher enzyme activities in 0-5 cm depth compared to 5-10 cm depth, but enzymatic activities depend on land use systems. Soil bacterial community was affected by land use systems and depth, revealing changes in structure and abundance of bacterial composition. Alpha-diversity indexes were higher in the agricultural systems than in the forests, however they showed a significant negative correlation with most of the studied soil microbial and biochemical indicators. Our research had brought new relevant information about the relationship between the soil biochemical indicators and the bacterial diversity in the Brazilian Cerrado.

Dietary Ginsenoside T19 Supplementation Regulates Glucose and Lipid Metabolism via AMPK and PI3K Pathways and Its Effect on Intestinal Microbiota.

Ginseng, as a functional food, is widely used worldwide because of its multifarious benefits. Studies have verified that 25-hydroxyl-protopanaxatriol (T19) is a new ginsenoside from ginseng, which had an important inhibitory effect on α-glucosidase and protein tyrosine phosphatase 1B in vitro. This study aims to assess the regulation of T19 against glycolipid metabolism by insulin-resistant HepG2 cells and diabetes mice induced with high-fat diet combined with streptozotocin (STZ). T19 effectively lowered the levels of blood glucose and lipid, alleviated insulin resistance, and improved histological pathology of liver and pancreas. Further study demonstrated that regulation of AMP-activated protein kinase- and phosphoinositide-3-kinase-signaling pathways was involved in the potential mechanism of T19 efficiency. Simultaneously, high-throughput sequencing of 16S rDNA revealed that T19 remarkably ameliorated the high-fat diet/STZ-induced disorders of intestinal microbiota by decreasing the value of Firmicutes/Bacteroidetes, and remarkably raised the relative abundance of the Lachnospiraceae family, which are the beneficial bacteria that can regulate glucose and lipid metabolism. The results may provide clues for further understanding the mechanism of T19 in regulating glycolipid metabolism, and may provide a scientific basis for ginseng as a potential dietary food to prevent metabolic diseases.

Alterations of the Gut Microbiome Composition and Lipid Metabolic Profile in Radiation Enteritis.

Radiation enteritis (RE) is a common complication in cancer patients receiving radiotherapy. Although studies have shown the changes of this disease at clinical, pathological and other levels, the dynamic characteristics of local microbiome and metabolomics are hitherto unknown. We aimed to examine the multi-omics features of the gut microecosystem, determining the functional correlation between microbiome and lipid metabolites during RE activity. By delivering single high-dose irradiation, a RE mouse model was established. High-throughput 16S rDNA sequencing and global lipidomics analysis were performed to examine microbial and lipidomic profile changes in the gut microecosystem. Spearman correlation analysis was used to determine the functional correlation between bacteria and metabolites. Clinical samples were collected to validate the above observations. During RE activity, the intestinal inflammation of the mice was confirmed by typical signs, symptoms, imaging findings and pathological evidences. 16S datasets revealed that localized irradiation dramatically altered the gut microbial composition, resulting in a decrease ratio of Bacteroidetes to Firmicutes. Lipidomics analysis indicated the remarkable lipidomic profile changes in enteric epithelial barrier, determining that glycerophospholipids metabolism was correlated to RE progression with the highest relevance. Spearman correlation analysis identified that five bacteria-metabolite pairs showed the most significant functional correlation in RE, including Alistipes-PC(36:0e), Bacteroides-DG(18:0/20:4), Dubosiella-PC(35:2), Eggerthellaceae-PC(35:6), and Escherichia-Shigella-TG(18:2/18:2/20:4). These observations were partly confirmed in human specimens. Our study provided a comprehensive description of microbiota dysbiosis and lipid metabolic disorders in RE, suggesting strategies to change local microecosystem to relieve radiation injury and maintain homeostasis.

Effect of sodium bisulfate amendments on bacterial populations in broiler litter

The accumulation of ammonia in poultry houses is of concern to bird and human health. Acidification of the litter by application of acidifying amendments such as sodium bisulfate (SBS) retains ammonia generated by microbial degradation of uric acid as harmless ammonium in the litter. Although some studies on the effects of litter amendments on specific bacteria and groups of bacteria have been carried out previously, wide gaps in knowledge remain. In the present study, 2 types of samples were prepared and either left unamended or amended with 2.5 or 10% SBS. One set of samples consisted of a 1:1 mixture of built-up litter and fresh poultry manure (L/M); the other of fresh wood shavings and fresh poultry manure (S/M). The samples were kept in the laboratory at room temperature for 35 d. The pH of unamended mixtures increased to 7.3 and 6.9 for L/M and S/M, respectively. A pH of 6.7 and 3.9 on day 35 was observed for L/M and SM with 2.5% SBS, respectively. The corresponding values for LM and SM amended with 10% SBS were 3.5 and 2.5, respectively. Plating data indicated that coliforms became less numerous in the unamended samples than the SBS-amended samples. This difference was also seen in data obtained by high-throughput sequencing of 16S rDNA. The sequencing data also indicated that sequences from the genus Oceanisphaera accounted for as much as 80% of the sequences from L/M and about 40% of those from S/M samples early on. Sequences from members of the order Clostridiales were enriched in L/M and S/M amended with 10% SBS as were sequences from the genus Turicibacter. Weisella species sequences were more prevalent in SBS-amended samples than in unamended ones. Sequences from the genus Corynebacterium, Brachybacterium, and Arthrobacter were more common in L/M samples than in S/M samples regardless of the SBS content. The data indicate that litter amendments affect some bacteria populations and not others. Further studies are required to determine if the observed population changes such as increased survival of coliforms warrant actions to improve the microbial quality of litter to be reused.

Colonic Mucosal Microbiota and Association of Bacterial Taxa with the Expression of Host Antimicrobial Peptides in Pediatric Ulcerative Colitis.

Inflammatory bowel diseases (IBD), ulcerative colitis (UC) and Crohn’s disease (CD), are chronic debilitating disorders of unknown etiology. Over 200 genetic risk loci are associated with IBD, highlighting a key role for immunological and epithelial barrier functions. Environmental factors account for the growing incidence of IBD, and microbiota are considered as an important contributor. Microbiota dysbiosis can lead to a loss of tolerogenic immune effects and initiate or exacerbate inflammation. We aimed to study colonic mucosal microbiota and the expression of selected host genes in pediatric UC. We used high-throughput 16S rDNA sequencing to profile microbiota in colonic biopsies of pediatric UC patients (n = 26) and non-IBD controls (n = 27). The expression of 13 genes, including five for antimicrobial peptides, in parallel biopsies was assessed with qRT-PCR. The composition of microbiota between UC and non-IBD differed significantly (PCoA, p = 0.001). UC children had a decrease in Bacteroidetes and an increase in several family-level taxa including Peptostreptococcaceae and Enterobacteriaceae, which correlated negatively with the expression of antimicrobial peptides REG3G and DEFB1, respectively. Enterobacteriaceae correlated positively with the expression siderophore binding protein LCN2 and Betaproteobacteria negatively with DEFB4A expression. The results indicate that reciprocal interaction of epithelial microbiota and defense mechanisms play a role in UC.

Modern urbanization has reshaped the bacterial microbiome profiles of house dust in domestic environments

BackgroundThe prevalence of allergy and other common chronic diseases is higher in developed than developing countries, and higher in urban than rural regions. Urbanization through its modification of environmental microbiomes may play a predominant role in the development of these conditions. However, no studies have been conducted to compare the microbiome in house dust among areas with different urbanization levels. MethodsHouse dust from Xinxiang rural area (XR, n = 74), Xinxiang urban area (XU, n = 33), and Zhengzhou urban area (ZU, n = 32) in central China, and from Australia (AU, n = 58 [with pets AUP, n = 15, without pets AUNP, n = 43]) were collected during a summer season in China and Australia. High-throughput sequencing of 16S rDNA was employed to profile house dust bacterial communities. ResultsSettled dust collected in China was dominant with 2 bacterial phyla: Proteobacteria and Actinobacteria, while floor dust collected in Australia had a higher proportion of phylum Proteobacteria, Firmicutes, and Actinobacteria. XR dust samples presented higher bacterial richness and diversity compared with XU or ZU samples. Urbanization level (r2 = 0.741 P < 0.001) had a significant correlation with the distribution of house dust bacterial community. At the genus level, there was a positive correlation (r coefficient > 0.5) between urbanization level and bacterial genera Streptococcus, Bartonella, Staphylococcus, Pseudomonas, Acinetobacter, Bacteroides, Corynebacterium_1,and Enhydrobacter and a negative correlation (r coefficient < −0.5) with Rhodanobacter. ConclusionThere was a significant difference in house dust microbiota among different urbanization areas. The areas with a lower urbanization level presented higher dust-borne bacterial richness and diversity. Modern urbanization has a significant influence on the bacterial microbiome profiles of indoor dust.

Effects of oligochitosan on the growth, immune responses and gut microbes of tilapia (Oreochromis niloticus)

The immunomodulatory effects of oligochitosan have been demonstrated in several fish. However, the underlying mechanisms are not well characterized. The profound interplay between gut microbes and aquaculture has received much scientific attention but understanding the alternations of microbes populating in gut of tilapia (Oreochromis niloticus) fed with oligochitosan remains enigmatic. In this study, the effects of oligochitosan on the growth, immune responses and gut microbes of tilapia were investigated. The feeding trial was conducted in triplicates with the control diet supplemented with oligochitosan at different concentrations (0, 100, 200, 400 or 800 mg/kg). Following a six-week feeding trial, body weights of the fish supplemented with 200 mg/kg and 400 mg/kg oligochitosan were significantly higher than that of the control group. To address the immune responses stimulated by oligochitosan, by the quantitative real time PCR (qRT-PCR), the mRNA expression levels of CSF, IL-1β, IgM, TLR2 and TLR3 genes from head kidney were all significantly up-regulated in the 400 mg/kg group compared to the control. To characterize the gut microbes, bacterial samples were collected from the foregut, midgut, and hindgut, respectively and were subjected to high-throughput sequencing of 16S rDNA. The results showed that significantly lower abundance of Fusobacterium was detected in the hindgut of 400 mg/kg group compared to the control. Additionally, beta-diversity revealed that both gut habitat and oligochitosan had effects on the gut bacterial assembly. To further elucidate the mechanism underlying the effects of oligochitosan on bacterial assembly, the results showed that difference dosages of dietary oligochitosan could alter the specific metabolic pathways and functions of the discriminatory bacterial taxa, resulting in the different bacterial assemblies. To test the antibacterial ability of tilapia fed with oligochitosan, when the tilapias were challenged with Aeromonas hydrophila, the mortality of groups fed with dietary oligochitosan was significantly lower than that of the control. Taken together, appropriate dietary oligochitosan could improve growth, immune responses and alter the bacterial flora in the intestine of tilapia, so as to play a role in fighting against the bacterial infection.

Different fertilization treatments in coal mining-affected soils change bacterial populations and enable soil reclamation

PurposeCoal mining activities result in large-scale soil degradation and ecosystem imbalances in many countries. Fertilization is an effective way to improve soil fertility and microbial activity. However, the effect of different fertilizers and remediation time on the subsided soil is not clear. The aim of this study is to explore the effects on soil fertility and the bacterial community.MethodsIn this study, we compared three fertilization regimes (inorganic, organic, and combined) applied over a 5-year period for the purpose of rehabilitating subsoil through measurement of soil’s chemical properties and microbial biomass. Bacterial diversity was evaluated in different reclaimed soils via high-throughput 16S rDNA sequencing; 1,938,561 total sequences were obtained.ResultsThe results showed that fertilization improved various soil properties, including the concentrations of available phosphorus, available potassium, and alkali-hydrolysable nitrogen, therefore, increasing microbial biomass. A significant increase in soil microbial diversity was observed in fertilized soils compared to the initial conditions. A positive correlation between microbial diversity and soil properties was observed. Regarding an improvement in soil properties and crop yields, the organic fertilizer demonstrated significantly more effectiveness compared to the inorganic fertilizer. Meanwhile, the relative abundance of Proteobacteria, Bacteroidetes, and Verrucomicrobia increased, but the relative abundance of Chloroflexi and Nitrospirae decreased. More specifically, we found that several Proteobacteria subgroups, such as Rhizobiales, Myxococcales, Sphingomonadales, Rhodospirillales, Xanthomonadales, and Burkholderiales, increased after the restoration. Additionally, the composition of the bacterial community in the 5-year groups (M5, O5, and MO5) was similar to the composition of the FS group, and the yield of the maize test crop following the 5-year restoration period was close to the average in China.ConclusionThis result indicates that soil reclamation via fertilization can contribute to soil recovery over time. Therefore, we concluded that fertilization is an effective strategy for the restoration of soil properties and bacterial communities in mining soil.

Diversity and Function of Endo-Bacteria in Bursaphelenchus xylophilus from Pinus massoniana Lamb. in Different Regions

The pine wood nematode (PWN) Bursaphelenchus xylophilus is the pathogen that causes pine wilt disease (PWD), a devastating forest disease. PWN-associated bacteria may play a role in PWD. However, little is known about the endo-bacteria in PWN. We analyzed the diversity of endo-bacteria in nine isolates of PWNs from Pinus massoniana Lamb. in nine epidemic areas from three Chinese provinces by high-throughput sequencing of 16S rDNA and isolated and identified culturable endo-bacteria through construction of a 16S rDNA phylogenetic tree and Biolog microbial identification. We also examined the effects of endo-bacteria on PWN fecundity, antioxidant capacity, and virulence using sterile nematodes as a control. While the dominant endo-bacteria in PWNs from different regions exhibited no significant difference in the classification levels of class and genus, their proportions differed. Pseudomonas and Stenotrophomonas were highly abundant in all PWN isolates. A total of 15 endo-bacterial strains were successfully isolated and identified as six species: Stenotrophomonas maltophilia, Pseudomonas fluorescens, Kocuria palustris, Microbacterium testaceum, Rhizobium radiobacter, and Leifsonia aquatica. We also found that P. fluorescens significantly increased the egg production of PWN, and that both P. fluorescens and S. maltophilia enhanced the mobility of PWN under oxidative stress and reduced the content of reactive oxygen species by increasing antioxidant enzyme activity in PWN. These strains also accelerated the development of PWD, and P. fluorescens had a more beneficial effect on PWN than S. maltophilia. Diversity exists among the endo-bacteria in PWNs from different regions, and some endo-bacteria can promote PWN infestation by enhancing the fecundity and antioxidant capacity of the nematode. Our study contributes to clarifying the interaction between endo-bacteria and PWN.

Cover Crop Impact on Soil Organic Carbon, Nitrogen Dynamics and Microbial Diversity in a Mediterranean Semiarid Vineyard

Cover crop (CC) management in vineyards increases sustainability by improving soil chemical and biological fertility, but knowledge on its effects in semiarid soils is lacking. This study evaluated the effect of leguminous CC management on soil organic carbon (SOC) sequestration, soil nitrate content and microbial diversity in a semiarid vineyard, in comparison to conventional tillage (CT). SOC and nitrate were monitored during vine-growing season; soil respiration, determined by incubation experiments, microbial biomass and diversity was analyzed after CC burial. The microbial diversity was evaluated by bacterial and fungal automated ribosomal intergenic spacer analysis (ARISA) and high-throughput sequencing of 16SrDNA. CC increased nitrate content and, although it had no relevant effect on SOC, almost doubled its active microbial component, which contributes to SOC stabilization. An unexpected stability of the microbial communities under different soil managements was assessed, fungal diversity being slightly enhanced under CT while bacterial diversity increased under CC. The complete nitrifying genus Nitrospira and plant growth-promoting genera were increased under CC, while desiccation-tolerant genera were abundant in CT. Findings showed that temporary CC applied in semiarid vineyards does not optimize the provided ecosystem services, hence a proper management protocol for dry environments should be set up.

Assessment of endophytic bacterial diversity in rose by high-throughput sequencing analysis.

The endophytic bacterial diversity of rose was analyzed by high-throughput sequencing of 16S rDNA and functional prediction of the bacterial community. The number of bacterial sequence reads obtained from 18 rose samples ranged from 63,951 to 114,833, and reads were allocated to 1982 OTUs based on sequences of the V3-V4 region. The highest Shannon Index was found in Luogang rose (1.93), while the lowest was found in Grasse rose (0.35). The bacterial sequence reads were grouped into three different phyla: Firmicutes, Proteobacteria, and Actinobacteria. At the genus level, Bacillus and Staphylococcus had the highest abundance across all 18 samples; Bacillus was particularly abundant in Daguo rose (99.09%), Rosa damascena (99.65%), and Fenghua rose (99.58%). Unclassified OTUs were also found in all samples. PICRUSt gene prediction revealed that each endophyte sample contained multiple KEGG functional modules related to human metabolism and health. A high abundance of functional genes were involved in (1) Amino Acid Metabolism, (2) Carbohydrate Metabolism, (3) Cellular Processes and Signaling, (4) Energy Metabolism, and (5) Membrane Transport, indicating that the endophytic community comprised a wide variety of microorganisms and genes that could be used for further studies. The rose endophytic bacterial community is rich in diversity; community composition varies among roses and contains functional information related to human health.

Epigallocatechin-3-O-gallate modulates the diversity of gut microbiota in ovariectomized rats.

Epigallocatechin‐3‐O‐gallate (EGCG) exists as one of the major active components of green tea and has been studied extensively; however, the relationship between EGCG and the changes in the gut microflora of ovariectomized (OVX) rats as a model of menopause women have not yet been studied. Female Wistar rats were fed on a maintenance material diet and underwent either ovariectomy or SHAM surgery. The ovariectomized rats were divided into OVX group with the treatment of placebo or EGCG group which was treated with EGCG by oral gavage. After 8 weeks of treatment, anxiety‐like behaviors were assessed using elevated plus maze test (EMP) and open field test (OFT). The serum estradiol concentration was assayed through ELISA. High‐throughput V3–V4 16S rDNA sequencing was conducted to assess the microbial diversity in fecal samples collected from all rats. EGCG, at a concentration of 10 mg/kg, caused behavioral changes in rats similar to anxiety. In EPM, OVX rats spent less time in open arms than SHAM group rats and EGCG group rats (F = 16.043, p < .01). In OFT, the total travelled distance and the number of entries for EGCG group were higher compared with OVX group (F = 30.939, H = 13.107, respectively; p < .01). In addition, the distribution and composition of intestinal microflora in rats changed after ovariectomy. EGCG modulated the diversity of gut microbiota in OVX group at the phylum and the genus levels. Our results suggested that the composition of gut microbiota and anxiety in OVX rats were simultaneously affected by EGCG, and therefore, the two conditions might be strongly related, yet the deeper mechanistic links need further exploration.

Dietary Recombinant Phycoerythrin Modulates the Gut Microbiota of H22 Tumor-Bearing Mice.

Normal intestinal flora is widely involved in many functions of the host: nutritional metabolism; maintenance of intestinal microecological balance; regulation of intestinal endocrine function and nerve signal transduction; promotion of intestinal immune system development and maturation; inhibition of pathogenic bacteria growth and colonization, reduction of its invasion to intestinal mucosa, and so on. In recent years, more and more studies have shown that intestinal flora is closely related to the occurrence, development, and treatment of various tumors. It is indicated that recombinant phycoerythrin (RPE) has significant anti-tumor and immunomodulatory effects. However, little is known about the mechanism of the effect of oral (or intragastric) administration of RPE on gut microbiota in tumor-bearing animals. In this study, using high-throughput 16S rDNA sequencing, we examined the response of gut microbiota in H22-bearing mice to dietary RPE supplementation. The results showed that the abundance of beneficial bacteria in the mice intestinal flora decreased and that of the detrimental flora increased after inoculation with tumor cells (H22); following treatment with dietary RPE, the abundance of beneficial bacteria in the intestinal flora significantly increased and that of detrimental bacteria decreased. In this study, for the first time, it was demonstrated that dietary RPE could modulate the gut microbiota of the H22 bearing mice by increasing the abundance of beneficial bacteria and decreasing that of detrimental bacteria among intestinal bacteria, providing evidence for the mechanism by which bioactive proteins affect intestinal nutrition and disease resistance in animals.