16S rDNA High-throughput Sequencing Research Articles

Blended-protein changes body weight gain and intestinal tissue morphology in rats by regulating arachidonic acid metabolism and secondary bile acid biosynthesis induced by gut microbiota.

The impact of dietary nutrients on body growth performance and the composition of gut microbes and metabolites is well-established. In this study, we aimed to determine whether dietary protein can regulate the physiological indexes and changes the intestinal tissue morphology in rats, and if dietary protein was a crucial regulatory factor for the composition, function, and metabolic pathways of the gut microbiota. A total of thirty male Sprague Dawley (SD) rats (inbred strain, weighted 110 ± 10g) were randomly assigned to receive diets containing animal-based protein (whey protein, WP), plant-based protein (soybean protein, SP), or a blended protein (soybean-whey proteins, S-WP) for a duration of 8weeks. To investigate the effects of various protein supplement sources on gut microbiota and metabolites, we performed a high throughput 16S rDNA sequencing association study and fecal metabolomics profiling on the SD rats. Additionally, we performed analyses of growth indexes, serum biochemical indexes, and intestinal morphology. The rats in S-WP and WP group exhibited a significantly higher body weight and digestibility of dietary protein compared to the SP group (P < 0.05). The serum total protein content of rats in the WP and S-WP groups was significantly higher (P < 0.05) than that in SP group, and the SP group exhibited significantly lower (P < 0.05) serum blood glucose levels compared to the other two groups. The morphological data showed the rats in the S-WP group exhibited significantly longer villus height and shallower crypt depth (P < 0.05) than the SP group. The gut microbial diversity of the SP and S-WP groups exhibited a higher level than that of the WP group, and the microbiomes of the WP and S-WP groups are more similar compared to those of the SP group. The Arachidonic acid metabolism pathway is the most significant KEGG pathway when comparing the WP group and the SP group, as well as when comparing the SP group and the S-WP group. The type of dietary proteins exerted a significant impact on the physiological indices of SD rats. Intake of S-WP diet can enhance energy provision, improve the body's digestion and absorption of nutrients, as well as promote intestinal tissue morphology. In addition, dietary protein plays a crucial role in modulating fecal metabolites by regulating the composition of the gut microbiota. Metabolomics analysis revealed that the changes in the levels of arachidonic acid metabolites and secondary bile acid metabolite induced by Clostridium_sensu_stricto_1 and [Eubacterium]_coprostanoligenes_group maybe the primarily causes of intestinal morphological differences.

Function-oriented mechanism discovery of coumarins from Psoralea corylifolia L. in the treatment of ovariectomy-induced osteoporosis based on multi-omics analysis

Ethnopharmacological relevancePsoraleae Fructus (Bu Gu Zhi) is the fruit of Psoralea corylifolia L. (PCL) and has been used for centuries in traditional Chinese medicine formulas to treat osteoporosis (OP). A new drug called "BX" has been developed from PCL, but its mechanism for treating OP is not yet fully understood. Aim of the studyTo explore the mechanism of action of BX in the treatment of ovariectomy-induced OP based function-oriented multi-omics analysis of gut microbiota (GM) and metabolites. Materials and methodsC57BL/6 mice were bilaterally ovariectomized to replicate the OP model. The therapeutic efficacy of BX was evaluated by bone parameters (BMD, BV/TV, Tb.N, Tb.Sp), hematoxylin and eosin (H&E) staining results, and determination of bone formation markers procollagen type Ⅰ amino-terminal peptide (PⅠNP) and bone-specific alkaline phosphatase (BALP). Serum and fecal metabolomics and high-throughput 16S rDNA sequencing were performed to evaluate effects on endogenous metabolites and GM. In addition, an enzyme-based functional correlation algorithm (EBFC) algorithm was used to investigate functional correlations between GM and metabolites. ResultsBX improved OP in OVX mice by increasing BMD, BV/TV, serum PⅠNP, BALP, and improving Tb.N and Tb.Sp. A total of 59 differential metabolites were identified, and 9 metabolic pathways, including arachidonic acid metabolism, glycerophospholipid metabolism, purine metabolism, and tryptophan metabolism, were found to be involved in the progression of OP. EBFC analysis results revealed that the enzymes related to purine and tryptophan metabolism, which are from Lachnospiraceae_NK4A136_group, Blautia, Rs-E47_termite_group, UCG-009, and Clostridia_UCG-014, were identified as the intrinsic link between GM and metabolites. ConclusionsThe regulation of GM and restoration of metabolic disorders may be the mechanisms of action of BX in alleviating OP. This research provides insights into the function-oriented mechanism discovery of traditional Chinese medicine in the treatment of OP.

Phytochemical composition of Tibetan tea fermented by Eurotium cristatum and its effects on type 1 diabetes mice and gut microbiota

“Golden-flower” Tibetan tea (GTT) is an innovative dark tea fermented via fungus Eurotium cristatum. To study GTT effects on alleviating the symptoms of type 1 diabetes mellitus (T1DM), GTT's extract (GTTE) was prepared. GTTE chemical compositions were analyzed via HPLC, pyrolysis-gas chromatography-mass (Py-GC-MS) spectrometry analysis, and chemistry analyses. GTTE effects on T1DM were explored on T1DM mice model induced by streptozotocin (STZ). GTTE was composed mainly of tea pigment theabrownin (TB) (49.18%), with high percentages of polysaccharide (16.93%), protein (10.15%), polyphenols (13.90%), amino acids (5.89%), caffeine (1.83%), and flavonoids (0.67%). Py-GC-MS results exhibited that GTTE constituted of phenols, lipids, sugars, and proteins. GTTE attenuated T1DM conditions of mice, relieved their liver and pancreatic injury, restored damaged islet cells, decreased oxidative stress by increasing superoxide dismutase (SOD) and catalase (CAT) levels, modulated cytokine expression leading to the decreasing pro-inflammatory cytokines TNF-α and IL-6, increased anti-inflammatory cytokines IL-4 to improve inflammatory responses, and optimized gut microbiota composition and structure based on high-throughput 16S rDNA sequencing, suggesting multi-channel anti-diabetes mechanisms.

Impact of Doxycycline Addition on Activated Sludge Microflora and Microbial Communities

Municipal wastewater treatment plants (WWTPs) are exposed to high concentrations of micropollutants that can impact conventional activated sludge treatment. The consequences of this include failure to meet discharge standards and the disintegration of flocs, leading to poor sludge settleability. This lab-scale study focuses on the influence of doxycycline, an antibiotic widely used against human and animal diseases, on protozoa, metazoa, and bacterial communities under sludge growing conditions. Doxycycline was added to the mixed liquor of a communal WWTP up to 0, 100, 200, and 400 mg of doxycycline L−1 and incubated in batch conditions for 23 days. The regular addition of nutrient and carbon sources was preformed every 2 days to prevent sludge starvation. Sludge growth, conductivity, and settleability were measured and compared to sludge microbial community structure, determined by microscopic observations and high-throughput 16S rDNA sequencing. The high doxycycline concentration negatively impacted settleability and correlated with a decrease in bacterial diversity and floc disintegration. The addition of doxycycline promoted the enrichment of Proteobacteria Brevundimonas sp., Luteibacter anthropi, and the Bacteroidetes Chryseobacterium massoliae. These species are known to be resistant to a wide spectrum of antibiotics, including tetracyclines. A study of a larger scale may be conducted based on this study’ results.

Dominância da comunidade bacteriana em uma lagoa costeira eutrófica induzida por esgoto utilizando sequenciamento de nova geração: observações iniciais

Abstract: This study investigates the presence of bacterial dominance in one of the most studied sewage-driven eutrophic coastal lagoons, the Imboassica Lagoon in Macaé (RJ), Brazil, utilizing high-throughput sequencing of 16S rDNA. Water samples were collected from three sites within the lagoon. Total microbial DNA was extracted, and the V3-V4 region of the 16S rRNA gene was amplified and sequenced on the Illumina MiSeq platform. A total of 744,879 partial 16S rRNA sequences were clustered, revealing the absence of a single bacterial dominance in the sewage-driven eutrophic coastal lagoon. The prominent phyla detected in the lagoon were Cyanobacteria (27.8%), Proteobacteria (23.7%), and Actinobacteria (14.6%). Proteobacteria emerged as the most abundant phylum in the sewage-impacted lagoon site, whereas Cyanobacteria dominated the other two sampling sites. Among families, Synechococcaceae predominated with genus Synechococcus exhibited the highest prevalence. Families of potentially toxic Cyanobacteria represented less than 1% of the total families. The sewage-impacted lagoon section displayed greater bacterial diversity and richness. The dominance of bacterial communities associated with raw sewage, such as members of the Enterobacteriaceae family, was not confirmed, constituting only 0.75% of the families in the most affected site. This study presents the initial analysis of the bacterial community in the Imboassica Lagoon and suggests that dominance in the lagoon responds to the eutrophication and sewage discharge.

Effects of different levels of Citri Sarcodactylis Fructus by-products fermented feed on growth performance, serum biochemical, and intestinal health of cyan-shank partridge birds

This research aimed to investigate the effects of supplements containing fermented feed made from Citri Sarcodactylis Fructus by-products (CSFBP-Fermented feed) on the growth performance, immunological function, and gut health of broilers. 1080 cyan-shank partridge birds aged 47 days were chosen and casually distributed to four groups, each with 6 replicates and 45 birds per replicate. The experimental groups were provided with 1% (group T2), 3% (group T3) and 5% (group T4) of CSFBP-fermented feed in the basic diet, while the control group (group T1) received the basic diet. The findings revealed that supplementation with CSFBP-Fermented feed reduced ADFI and FCR and improved ADG in birds (P < 0.05). MDA levels in the serum of birds fed CSFBP-fermented feed were lower than in the control group (P < 0.05). The CAT activity in the serum of broilers increased after supplementation with 3% CSFBP-Fermented feed (P < 0.05). Supplementing broilers with CSFBP-fermented feed enhanced VH in the ileum, jejunum, and duodenum (P < 0.05). The addition of 3% CSFBP-Fermented feed decreased CD in the jejunum (P < 0.05). The addition of 3% and 5% CSFBP-Fermented feed increased the mRNA expression of ZO-1 and Occludin in the jejunum of broiler chickens and reduced the mRNA expression of IL-6 (P < 0.05). The addition of 3% CSFBP-Fermented feed increased the mRNA expression of Claudin in the jejunum of broiler chickens and reduced IL-1β mRNA expression (P < 0.05). Compared to the control group, all experimental groups exhibited decreased mRNA expression of TNF-α and INF-γ in the jejunal mucosa of the birds (P < 0.05). According to research using high-throughput sequencing of microorganisms' 16S rDNA, and an analysis of α-diversity found that supplementing broilers with 3% CSFBP-Fermented feed decreased the number of bacteria in their cecum (P < 0.05). Bacteroidota was higher in all groups after supplementation with CSFBP-Fermented feed. At the genus level, after addition with 3% CSFBP-Fermented feed, the abundance of Bacteroide and Prevotellaceae_Ga6A1_group were higher than the control group (33.36% vs 29.95%, 4.35% vs 2.94%). The abundance of Rikenellaceae_RC9_gut_group and Fusobacterium were lower than the control group (5.52% vs. 7.17%,0.38% vs. 1.33%). In summary, supplementing the diet with CSFBP-Fermented feed can promote the growth of performance by enhancing intestinal morphology, and barrier function, as well as modulating intestinal inflammatory factors and microbial composition in broilers.

Butyrate protects against MRSA pneumonia via regulating gut-lung microbiota and alveolar macrophage M2 polarization.

Pneumonia caused by methicillin-resistant Staphylococcus aureus (MRSA) continues to carry a high burden in terms of mortality. With the roles of gut microbiota in mediating lung diseases being gradually uncovered, the details of the molecular mechanism of the "gut-lung axis" mediated by beneficial microorganisms and small-molecule metabolites have gradually attracted the attention of researchers. However, further studies are still necessary to determine the efficacy of microbial-based interventions. Our findings indicate that sodium butyrate (NaB) alleviates MRSA-induced pulmonary inflammation by improving gut-lung microbiota and promoting M2 polarization of alveolar macrophages. Therefore, the preventive administration of NaB might be explored as an effective strategy to control MRSA pneumonia.

A comparison of digestive strategies for fishes with different feeding habits: Digestive enzyme activities, intestinal morphology, and gut microbiota.

Fish feeding habit determines the digestive tract structure and intestinal microflora. However, the relationship between feeding habit, digestive intestinal morphology, and microbial diversity of omnivorous, herbivorous, plankton feeder, and carnivorous fish from the same environment has not been compared. This study compared the digestive enzyme activities, intestinal morphology, and intestinal microflora of omnivorous (Carassius auratus), herbivorous (Ctenopharyngodon idellus), carnivorous (Siniperca chuatsi), and plankton feeder (Schizothorax grahami) fishes and predicted the potential functions of specific microflora on different nutrients. Twelve intestine samples were collected from each of the four fishes from Dianchi Lake. The composition and diversity of microbial communities were determined by using high-throughput sequencing of 16S rDNA. The results showed that the carnivorous fish (S. chuatsi) had higher trypsin and pancrelipase activities in the hepatopancreas and enteropeptidase in the intestine, but lower amylase activities in the intestine. The carnivorous fish intestine had more microvilli branches and complex structures than other fish species in the order carnivorous > herbivorous > plankton feeder > omnivorous. The intestinal microflora diversity was higher in the omnivorous fish and followed the order omnivorous > herbivorous > plankton feeder > carnivorous. Acinetobacter species and Bacteroides species were the most dominant flora in the carnivorous and herbivorous fishes, respectively. Acinetobacter species and Pseudomonas species might help the host to digest protein, while Bacteroidetes species may help the host to digest cellulose. Taken together, feeding habit determines the digestive enzyme activities, intestinal tissue morphology, and differential colonization of fish intestinal flora. The knowledge obtained is useful in feed formulation and feeding practices for the studied fish species.

Maslinic acid alleviates LPS-induced mice mastitis by inhibiting inflammatory response, maintaining the integrity of the blood-milk barrier and regulating intestinal flora.

Mastitis occurs frequently in breastfeeding women and not only affects the women's health but also hinders breastfeeding. Maslinic acid is a type of pentacyclic triterpenoid widely found in olives that has good anti-inflammatory activity. This study aims to discuss the protective function of maslinic acid against mastitis and its underlying mechanism. For this, mice models of mastitis were established using lipopolysaccharide (LPS). The results revealed that maslinic acid reduced the pathological lesions in the mammary gland. In addition, it reduced the generation of pro-inflammatory factors and enzymes (IL-6, IL-1β, TNF-α, iNOS, and COX2) in both mice mammary tissue and mammary epithelial cells. The high-throughput 16S rDNA sequencing of intestinal flora showed that in mice with mastitis, maslinic acid treatment altered β-diversity and regulated microbial structure by increasing the abundance of probiotics such as Enterobacteriaceae and downregulating harmful bacteria such as Streptococcaceae. In addition, maslinic acid protected the blood-milk barrier by maintaining tight-junction protein expression. Furthermore, maslinic acid downregulated mammary inflammation by inhibiting the activation of NLRP3 inflammasome, AKT/NF-κB, and MAPK signaling pathways. Thus, in a mice model of LPS-induced mastitis, maslinic acid can inhibit the inflammatory response, protect the blood-milk barrier, and regulate the constitution of intestinal flora.

Dynamics of microbial communities associated with flavor formation during sour juice fermentation and the milk fan drying process

Milk fan is an acid-curd cheese with strong national characteristics (a traditional dairy product of the Bai nationality with a shape like a piece of paper) and a long history in Yunnan province, China. In our previous study, we characterized the microbial community diversity of milk fan, but the succession of microorganisms associated with flavor formation in milk fan is still unknown. Therefore, we examined the predominant microorganisms and their correlations with the formation of flavor in the fermentation of sour juice and drying of milk fan by gas chromatography mass spectrometry, high-throughput 16S rDNA sequencing, intergenic spacer sequencing and metatranscriptome analysis. We found that the relative abundances of Lactobacillus and Issatchenkia initially decreased and then increased with time during the fermentation of sour juice. However, the relative abundances of Acetobacter, Leuconostoc, Lactococcus, Geotrichum, and Dipodascus initially increased and then decreased. During the drying step, the relative abundances of Lactobacillus and Issatchenkia continuously increased and became the dominant microorganisms in the milk fan. The metatranscriptomes generated from the milk fan showed that "carbohydrate metabolism," "translation," and "signal transduction" were the main metabolic functions of the microbial communities. Rhodotorula and Yarrowia contained more differentially expressed genes than other genera, which indicated they may be associated with the production of the characteristic flavor. Furthermore, a Pearson correlation analysis showed that Lactococcus, Rhodotorula, Candida, Cutaneotrichosporon, and Yarrowia were significantly positively correlated with more aroma-active compounds, mainly ethyl acetate, 2-heptanone, isovaleraldehyde, butyric acid, nonanal, and hexanal. In conclusion, these findings contribute to a better understanding of the flavor production mechanism during the production of milk fan.

Fecal metabonomics combined with 16S rDNA sequencing to analyze the changes of gut microbiota in rats fed with different protein source diets.

When blended, animal and plant proteins can complement each other in terms of amino acid composition and release time. In this study, we investigated whether the blended protein diet has a better feeding effect than the single protein diet, and to reveal the differences in growth and intestinal microbiota composition caused by the blended protein diet. Forty Sprague Dawley (SD) rats received diets with different protein sources, including casein (C), whey protein (WP), black soybean protein (BSP), and black soybean-whey blended protein (BS-WP), for eight weeks. To investigate the effects of blended protein supplement on gut microbiota and metabolites, we performed a high throughput 16S rDNA sequencing and fecal metabolomics profiling. In addition, we determined growth and serum biochemical indices, and conducted intestinal morphology analyses. Compared to those in the BSP and WP groups, the daily body weight gain and feed conversion efficiency increased in the BS-WP group. Serum biochemical indices indicated that the protein utilization efficiency of the WP and BS-WP groups was relatively high, and the BS-WP blended protein diet improved the protein adoption rate. The BS-WP blended protein diet also improved intestinal tissue morphology and promoted intestinal villi development compared to the single protein diets. Furthermore, dietary protein altered the composition of gut microbiota, the gut microbial diversity of rats fed with the BS-WP diet was significantly (P < 0.05) higher than that of the other groups. The difference in dietary protein corresponded with an alteration of fecal amino acids and their metabolites, and tryptophan and tyrosine metabolism were the key mechanisms leading to the changes in fecal microbial composition. Dietary protein sources played an important role in the growth and development of rats by influencing intestinal metabolism and microbial composition. The BS-WP blended protein diet was more conducive to nutrient absorption than the single protein diet. Furthermore, blended protein increased the diversity of intestinal microbes and aided the establishment of intestinal barrier function.

Ganjiang Huangqin Huanglian Renshen Decoction improves insulin sensitivity by regulating intestinal flora in rats with Type 2 diabetes mellitus

Purpose: To study the effect of Ganjiang Huangqin Huanglian Renshen Decoction (GHHRD) on intestinal microflora and insulin resistance (IR) in type 2 diabetes mellitus (T2DM) rats. &#x0D; Methods: Streptozotocin (STZ) injection was used to establish a rat model of T2DM. The T2DM rats were divided into 5 groups: control, T2DM, T2DM + low-dose traditional Chinese medicine (TCM), T2DM + high-dose TCM, and T2DM + metformin groups. Total DNA kit was used for extraction of total DNA from fecal microorganisms from the T2DM model rats. High-throughput 16S rDNA sequencing was carried out to identify the intestinal flora of T2DM model rats. Fasting plasma glucose (FPG) and fasting serum insulin (FINS) levels were determined by a biochemical analyzer. &#x0D; Results: The 16S rDNA sequencing analysis showed that after GHHRD treatment, the levels of Ruminococcus, Prevotellaceae, Escherichia-Shigella and Bacteroidota in the intestinal tract of T2DM model rats exhibited significant changes. Furthermore, GHHRD decreased the Homeostasis Model Assessment-Insulin Resistance (HOMA-IR) index and IR in T2DM model rats. &#x0D; Conclusion: GHHRD mitigates IR in T2DM model rats through alterations in the intestinal flora of the rats. This provides a theoretical basis for the potential use of GHHRD in the clinical management of T2DM.

Changes in the gut microbiome of patients with type a aortic dissection.

To investigate the characteristic changes in the gut microbiota of patients with type A aortic dissection (AAD) and provide a theoretical basis for future microbiome-oriented interventional studies. High-throughput 16S rDNA sequencing was performed on the stool samples of patients with and without (healthy control subjects) AAD. Using alpha and beta diversity analysis, we compared the gut microbiota composition of 20 patients with AAD and 20 healthy controls matched for gender, age, BMI, and geographical region. The accuracy of AAD prediction by differential microbiome was calculated using the random forest machine learning model. Targeted measurement of the plasma concentration of short-chain fatty acids (SCFAs), which are the main metabolites of the gut microbiome, was performed using gas chromatography-mass spectrometry (GC-MS). Spearman's correlation analysis was conducted to determine the relationships of gut microbiome and SCFAs with the clinical characteristics of subjects. The differences in gut microbiota alpha diversity between patients with AAD and the healthy controls were not statistically significant (Shannon index: p = 0.19; Chao1: p = 0.4); however, the microbiota composition (beta diversity) was significantly different between the two groups (Anosim, p = 0.001). Bacteroidota was enriched at the phylum level, and the SCFA-producing genera Prevotella, Porphyromonas, Lachnospiraceae, and Ruminococcus and inflammation-related genera Fenollaria and Sutterella were enriched at the genus level in the AAD group compared with those in the control group. The random forest model could predict AAD from gut microbiota composition with an accuracy of 87.5% and the area-under-curve (AUC) of the receiver operating characteristic curve was 0.833. The SCFA content of patients with AAD was higher than that of the control group, with the difference being statistically significant (p < 0.05). The different microflora and SCFAs were positively correlated with inflammatory cytokines. To the best of our knowledge, this is the first demonstration of the presence of significant differences in the gut microbiome of patients with AAD and healthy controls. The differential microbiome exhibited high predictive potential toward AAD and was positively correlated with inflammatory cytokines. Our results will assist in the development of preventive and therapeutic treatment methods for patients with AAD.

Optimizing the Use of Solid-Phase Reversible Immobilization Beads for High-Throughput Full-Length 16S rDNA Sequencing Library Construction

Objective: Solid-phase reversible immobilization (SPRI) beads are widely used for high-throughput sequencing library construction to purify and recover nucleic acids. This research was aimed at investigating the effects of SPRI bead ratio, incubation time, and elution time on nucleic acid recovery during full-length 16S rDNA high-throughput sequencing library construction. Methods: The effects of different SPRI bead ratios, incubation times, and elution times were compared for three different initial sample amounts. An L9(33) orthogonal experiment was designed to determine the optimal combination of these factors. Results: The incubation time of three factors including SPRI beads ratio, incubation time, and elution time had a statistically significant effect on the recovery rate for the initial sample amount of 1500 ng and 3000 ng. The orthogonal experiment results indicated that incubation time had the greatest impact among the three factors. Conclusion: Incubation time significantly influences recovery rate in full-length 16S rDNA high-throughput sequencing library construction. The use of 0.8× SPRI beads, 15 minutes of incubation, and 10 minutes of elution resulted in the highest recovery rate. SPRI beads offer a viable method for recovering full-length 16S rDNA amplicons.

Efficacy and Mechanism of Quercetin in the Treatment of Experimental Colitis Using Network Pharmacology Analysis.

Quercetin, a flavonoid that is present in vegetables and fruits, has been found to have anti-inflammatory effects. However, the mechanism by which it inhibits colitis is uncertain. This study aimed to explore the effect and pharmacological mechanism of quercetin on dextran sodium sulfate (DSS)-induced ulcerative colitis (UC). Mice were given a 4% (w/v) DSS solution to drink for 7 days, followed by regular water for the following 5 days. Pharmacological mechanisms were predicted by network pharmacology. High-throughput 16S rDNA sequencing was performed to detect changes in the intestinal microbiota composition. Enzyme-linked immunosorbent assay and western blotting were performed to examine the anti-inflammatory role of quercetin in the colon. Quercetin attenuated DSS-induced body weight loss, colon length shortening, and pathological damage to the colon. Quercetin administration modulated the composition of the intestinal microbiota in DSS-induced mice and inhibited the growth of harmful bacteria. Network pharmacology revealed that quercetin target genes were enriched in inflammatory and neoplastic processes. Quercetin dramatically inhibited the expression of phosphorylated protein kinase B (AKT) and phosphatidylinositol 3-kinase (PI3K). Quercetin has a role in the treatment of UC, with pharmacological mechanisms that involve regulation of the intestinal microbiota, re-establishment of healthy microbiomes that favor mucosal healing, and the inhibition of PI3K/AKT signaling.

Hydrocarbons removal and microbial community succession in petroleum-contaminated soil under hydrogen peroxide treatment.

Chemical oxidation as a pretreatment step coupled with bioremediation for petroleum-contaminated soil may pose serious impacts on indigenous microorganisms and the available nutrients. Petroleum-contaminated soil were treated by hydrogen peroxide (H2O2) at initial concentrations of 105mM (HH), 21mM (HL), and 105mM in three equal amounts (HT) without adding any external catalyst. The contents of total petroleum hydrocarbons (TPH) and dissolved nutrients (total organic compounds, nitrogen, and phosphate), and the indigenous bacteria community succession (analyzed by high-throughput sequencing of 16S rDNA) were investigated over 50days. Compared to the control treatment without H2O2 addition, H2O2 treatments for the petroleum-contaminated soil significantly promoted the TPH removal especially in the first 4days and impacted the contents of dissolved nutrients. Both of chemical oxidation and nutrients contributed to microbial community structure changes in alpha diversity. Although the soil microbial community structure had undergone significant changes after different chemical oxidation pretreatments, Firmicutes, Proteobacteria, Gemmatimonadetes, and Actinobacteria were the main bacterial phyla. Compared with adding H2O2 at one time, H2O2 added in stepwise was beneficial to indigenous bacterial diversity recovery and TPH removal. H2O2 oxidation treatments showed a great influence on the microbial community structures in the start-up stage, while recovery time rather than the oxidation treatments presented greater effects on the composition of the microbial community structure with the incubation time extended. Therefore, adding H2O2 as pretreatment for petroleum-contaminated soil showed little effect on the structure of soil indigenous microbial community from a long-term scale, and was conducive to the continuous removal of TPH by indigenous microorganisms.

Antibiotic-induced alternations in gut microflora are associated with the suppression of immune-related pathways in grass carp (Ctenopharyngodon idellus).

Gut microbiota play a vital role in fish health homeostasis. Antibiotics are known to alter microbial community composition and diversity; however, the substantial effects of antibiotics upon the gut microbiome with respect to immune-related pathways in healthy fish remain unclear. Accordingly, here we explored the impact of two antibiotics on the intestinal health, immune response, microbiome dynamics, and transcriptome profiles of grass carp. A two-week feeding trial was carried out in which the basal diet was complemented with enrofloxacin (10 mg/kg) or florfenicol (10 mg/kg). The results showed that: (1) Enrofloxacin and florfenicol both induced intestinal oxidative stress and reduced the digestive enzyme activity of grass carp. (2) High-throughput sequencing of 16S rDNA revealed that enrofloxacin but not the florfenicol treatment influenced gut microbiota diversity in grass carp by shifting α/β-diversity with more abundant pathogens detected. (3) Transcriptome profiling demonstrated that florfenicol down-regulated the immune-related pathways of grass carp, and the network analysis revealed that IgA was negatively correlated with certain pathogens, such as Shewanella and Aeromonas. (4) Antibiotic-induced alternations of gut core microbes were revealed via immune-related transcripts, as were lower mRNA expression levels of mucosal-related genes. (5) Apoptosis and histopathological changes were detected in the enrofloxacin- and florfenicol-treated groups compared with the control group. Overall, administering antibiotics will promote oxidative stress, cause intestinal flora dysbiosis, inhibit the mucosal immune system, and induce apoptosis in grass carp.

Microbiome analysis reveals microecological advantages of emerging ditchless rice-crayfish co-culture mode

Ditchless rice-crayfish co-culture is an emerging model of rice-crayfish farming that circumvents the potential hazards of digging ditches in traditional rice-crayfish farming. However, due to the complex interactions among crayfish, ambient microbiota, and environmental variables, it is necessary to assess the differences in bacterial structure between ditchless and traditional rice-crayfish culture. In this study, the crayfish culture area in the Sichuan basin was selected as the study area, and the bacterial communities of two rice-crayfish culture systems were compared by high-throughput sequencing of 16S rDNA. The results showed that the ditchless system had lower water depth, higher dissolved oxygen, lower total ammonia nitrogen and lower morbidity. There are intuitive differences in the composition of environmental bacterial communities due to environmental changes, even if they are similar in composition at the phylum level. Microbiota in sediments from ditchless systems appear to produce less ammonia nitrogen. The abundance of the pathogens colonizing the intestine of ditchless crayfish was lower than ditched one, and the composition was similar to water. Ditch-farmed crayfish appear to be more susceptible to environmental microbes and have a more fragile intestinal structure. Water depth and dissolved oxygen are the main environmental factors that determine the distribution of microbiota. This study is the first to investigate the bacterial ecology of a ditchless rice- crayfish farming system. The results show that the ditchless rice-crayfish culture model has a more superior bacterial system than the traditional rice-crayfish culture.

A Correlation Between Pericarpium Citri Reticulatae Volatile Components and the Change of the Coexisting Microbial Population Structure Caused by Environmental Factors During Aging.

Pericarpium Citri Reticulatae (PCR) is a natural citrus by-product with beneficial health and nutritive properties that is used widely in food and is an ingredient in traditional Chinese medicine. PCR improves gradually with aging. However, the present research has not yet revealed the reasons for this. Some data prove the important role of microorganisms in the quality of tobacco and fermented tea with the time of the aging of these foods. Our studies further proved that the coexisting Aspergillus niger plays an important role in the change of flavonoids and volatile oil in PCR during this process. Therefore, we put forward that longer storage is better for PCR and is highly correlated with the change of the coexisting microbial population structure caused by environmental factors. Samples of PCR aged in Beijing, Sichuan, Guangdong, and Yunnan were collected at different time points. Using GC/MS and high throughput 16S rDNA and ITS sequencing techniques, massive changes in volatile profile and microbial communities were observed during aging. Spearman correlation analysis indicated that Exobasidium, Xeromyces, Pseudocercospora, Russula, Aspergillus, Herbaspirillum, Sphingomonas, and Streptococcus, which are the dominant microbial genera in Sichuan and Guangdong showed strong connections with volatile components of chemical markers. It was preliminarily verified that the changes of volatile components for PCR are highly correlated with the change of the coexisting microbial population structure caused by environmental factors, providing a new idea for the research on the aging mechanism of PCR and key influencing factors of aging quality.

Using 16S rDNA Sequencing Technology to Preliminarily Analyze Intestinal Flora in Children with Mycoplasma pneumoniae Pneumonia

ObjectiveWe investigated changes in the intestinal flora of children with Mycoplasma pneumoniae pneumonia (MPP). MethodsBetween September 2019 and November 2019, stool samples from 14 children with MPP from The Fourth Hospital of Baotou city, Inner Mongolia Autonomous Region, were collected and divided into general treatment (AF) and probiotic (AFY) groups, according to the treatment of “combined Bifidobacterium, Lactobacillus, Enterococcus, and Bacillus cereus tablets live”. High-throughput 16S rDNA sequencing was used to identify intestinal flora. ResultsIntestinal flora abundance and diversity in children with MPP were decreased. Both Shannon and Simpson indices were lower in the AF group when compared with healthy controls (P < 0.05). When compared with healthy controls, the proportion of Enterorhabdus was lower in the AF group, while the proportion of Lachnoclostridium was higher (P < 0.05). The proportion of Bifidobacteria and Akkermansia was lower in the AFY group but Enterococcus, Lachnoclostridium, Roseburia, and Erysipelatoclostridium proportions were higher. The proportion of Escherichia coli–Shigella in the AFY group after treatment was decreased (P < 0.05). ConclusionsThe intestinal flora of children with MPP is disturbed, manifested as decreased abundance and diversity, and decreased Bifidobacteria. Our probiotic mixture partly improved intestinal flora disorders.