16S rRNA High-throughput Sequencing Research Articles

Alterations of microbiota and metabolites in the feces of calves with diarrhea associated with rotavirus and coronavirus infections.

The changes in the composition of intestinal microbiota and metabolites have been linked to digestive disorders in calves, especially neonatal calf diarrhea. Bovine rotavirus (BRV) and bovine coronavirus (BCoV) are known to be the primary culprits behind neonatal calf diarrhea. In this study, we analyzed changes in the fecal microbiota and metabolites of calves with neonatal diarrhea associated with BRV and BCoV infection using high-throughput 16S rRNA sequencing and metabolomics technology. The microbial diversity in the feces of calves infected with BRV and BCoV with diarrhea decreased significantly, and the composition changed significantly. The significant increase of Fusobacterium and the reductions of some bacteria genera, including Faecalibacterium, Bifidobacterium, Ruminococcus, Subdoligranulum, Parabacteroides, Collinsella, and Olsenella, etc., were closely related to diarrhea associated with BRV and BCoV infection. Metabolites in the feces of BRV and BCoV-infected calves with diarrhea were significantly changed. Phosphatidylcholine [PC; 16:1(9 Z)/16:1(9 Z)], lysophosphatidylethanolamine (LysoPE; 0:0/22:0), lysophosphatidylcholine (LysoPC; P-16:0) and LysoPE (0:0/18:0) were significantly higher in the feces of BRV-infected calves with diarrhea. In contrast, some others, such as desthiobiotin, were significantly lower. BRV infection affects glycerophospholipid metabolism and biotin metabolism in calves. Two differential metabolites were significantly increased, and 67 differential metabolites were significantly reduced in the feces of BCoV-infected calves with diarrhea. Seven significantly reduced metabolites, including deoxythymidylic acid (DTMP), dihydrobiopterin, dihydroneopterin triphosphate, cortexolone, cortisol, pantetheine, and pregnenolone sulfate, were enriched in the folate biosynthesis, pantothenate and CoA biosynthesis, pyrimidine metabolism, and steroid hormone biosynthesis pathway. The decrease in these metabolites was closely associated with increased harmful bacteria and reduced commensal bacteria. The content of short-chain fatty acids (SCFAs) such as acetic acid and propionic acid in the feces of BRV and BCoV-infected calves with diarrhea was lower than that of healthy calves, which was associated with the depletion of SCFAs-producing bacteria such as Parabacteroides, Fournierella, and Collinsella. The present study showed that BRV and BCoV infections changed the composition of the calf fecal microbiota and were associated with changes in fecal metabolites. This study lays the foundation for further revealing the roles of intestinal microbiota in neonatal calf diarrhea associated with BRV and BCoV infection.

Root endophytic bacterial and fungal communities in a natural hot desert are differentially regulated in dry and wet seasons by stochastic processes and functional traits

Dryland ecosystems experience seasonal cycles of severe drought and moderate precipitation. Desert plants may develop symbiotic relationships with root endophytic microbes to survive under the repeated wet and extremely dry conditions. Although community coalescence has been found in many systems, the colonization by functional microbes and its relationship to seasonal transitions in arid regions are not well understood. Here we examined root endophytic microbial taxa, and their traits in relation to their root colonization, during the dry and wet seasons in a hot desert of the southwestern United States. We used high-throughput DNA sequencing of 16S rRNA and internal transcribed spacer gene profiling of five desert shrubs, and analyzed the seasonal change in endophytic microbial lineages. Goodness of fit to the neutral community model in relationship to microbial traits was evaluated. In summer, Actinobacteria and Bacteroidia increased, although this was not genus-specific. For fungi, Glomeraceae selectively increased in summer. In winter, Gram-negative bacterial genera, including those capable of nitrogen fixation and plant growth promotion, increased. Neutral model analysis revealed a strong stochastic influence on endophytic bacteria but a weak effect for fungi, especially in summer. The taxa with higher frequency than that predicted by neutral model shared environmental adaptability and symbiotic traits, whereas the frequency of pathogenic fungi was at or under the predicted value. These results suggest that community assembly of bacteria and fungi is regulated differently. The bacterial community was affected by stochastic and deterministic processes via bacterial response to drought (response trait), beneficial effect on plants (effect trait), and likely stable mutualistic interactions with plants suggested by the frequency of nodule bacteria. For fungi, mycorrhizal fungi were selected by plants in summer. The regulation of beneficial microbes by plants in both dry and wet seasons suggests the presence of plant–soil positive feedback in this natural desert ecosystem.

A Two-Step Single Plex PCR Method for Evaluating Key Colonic Microbiota Markers in Young Mexicans with Autism Spectrum Disorders: Protocol and Pilot Epidemiological Application.

Many neurological disorders have a distinctive colonic microbiome (CM) signature. Particularly, children with autism spectrum disorders (ASD) exhibit a very dissimilar CM when compared to neurotypical (NT) ones, mostly at the species level. Thus far, knowledge on this matter comes from high-throughput (yet very expensive and time-consuming) analytical platforms, such as massive high-throughput sequencing of bacterial 16S rRNA. Here, pure (260/280 nm, ~1.85) stool DNA samples (200 ng.µL-1) from 48 participants [39 ASD, 9 NT; 3-13 y] were used to amplify four candidate differential CM markers [Bacteroides fragilis (BF), Faecalibacterium prausnitzii (FP), Desulfovibrio vulgaris (DV), Akkermansia muciniphila (AM)], using micro-organism-specific oligonucleotide primers [265 bp (BF), 198 bp (FP), 196 bp (DV), 327 bp (AM)] and a standardized two-step [low (step 1: °Tm-5 °C) to high (stage 2: °Tm-0 °C) astringent annealing] PCR protocol (2S-PCR). The method was sensitive enough to differentiate all CM biomarkers in the studied stool donors [↑ abundance: NT (BF, FP, AM), ASD (DV)], and phylogenetic analysis confirmed the primers' specificity.

Bacterial community profiling associated with pearl culture facilities of Liusha Bay, the largest marine pearl culture base on the western Guangdong coast, South China

A large number of aquaculture facilities produced during the farming process are made of plastics. These plastics can be a distinct habitat for bacteria due to their unique materials. Therefore, this paper focuses on plastic aquaculture facilities and investigates the impact of bacterial accumulation on plastic surfaces. In this study, the high-throughput sequencing of 16S rRNA was conducted to investigate bacterial community profiling associated with the pearl culture facilities (cultured net cages and foam buoys) and surrounding water of Liusha Bay. Alpha diversity analysis showed that the richness and diversity indexes of bacterial communities in pearl culture facilities were higher than those in the aquatic environment. The richness and diversity indexes of bacterial communities were different between cultured net cages and foam buoys. Spatially influenced bacterial communities attached to pearl culture facilities varied between aquaculture areas. Thus, plastic has become a habitat for bacteria, floating in the marine environment and providing a favorable living environment for marine microorganisms and specific preferences for different substrate types. The relative abundance of certain functions on the attached bacterial community of the culture facility was high, which suggested that plastics did not only alter community structure but also influenced bacterial function. In addition, we detected small amounts of pathogenic bacteria, such as Vibrio and Bruegeria, in pearl culture facilities and surrounding seawater, suggesting that plastics can act as vectors for potentially pathogenic bacteria that may have an impact on the development of aquaculture. Our understanding of plastic ecology has been enriched by the discovery of the various microbial assemblages that can occur in aquaculture facilities.

Characterization of the archaeal community in foods: The neglected part of the food microbiota

Despite the large number of studies conducted on archaea associated with extreme environments, the archaeal community composition in food products is still poorly known. Here, we investigated a new insight into exploring the archaeal community in several food matrices, with a particular focus on determining whether living archaea were present. A total of 71 samples of milk, cheese and its derived brine, honey, hamburger, clam, and trout were analyzed by high-throughput 16S rRNA sequencing. Archaea were detected in all the samples, ranging from 0.62 % of microbial communities in trout to 37.71 % in brine. Methanogens dominated 47.28 % of the archaeal communities, except for brine, which was dominated by halophilic taxa affiliated with the genus Haloquadratum (52.45 %). Clams were found to be a food with high richness and diversity of archaea and were targeted for culturing living archaea under different incubation time and temperature conditions. A subset of 16 communities derived from culture-dependent and culture-independent communities were assessed. Among the homogenates and living archaeal communities, the predominant taxa were distributed in the genera Nitrosopumilus (47.61 %) and Halorussus (78.78 %), respectively. A comparison of the 28 total taxa obtained by culture-dependent and culture-independent methods enabled their categorization into different groups, including detectable (8 out of 28), cultivable (8 out of 28), and detectable-cultivable (12 out of 28) taxa. Furthermore, using the culture method, the majority (14 out of 20) of living taxa grew at lower temperatures of 22 and 4 °C during long-term incubation, and few taxa (2 out of 20) were found at 37 °C during the initial days of incubation. Our results demonstrated the distribution of archaea in all analyzed food matrices, which opens new perspectives to expand our knowledge on archaea in foods and their beneficial and detrimental effects.

Deciphering the mechanism of jujube vinegar on hyperlipoidemia through gut microbiome based on 16S rRNA, BugBase analysis, and the stamp analysis of KEEG.

Growing data indicate that the gut microbiome may contribute to the rising incidence of hyperlipoidemia. Jujube vinegar lowers lipids, protects the liver, and reduces oxidant capacity, however, it is unknown whether this is due to the gut flora. To further research the role of the gut microbiome in treating hyperlipidemia with jujube vinegar, we looked into whether the action of jujube vinegar is related to the regulation of the gut microbiome. Thirty male ICR mice were used. The control group (CON), the high-fat diet (HFD) group, and the vinegar group (VIN) each consisted of ten female ICR mice fed consistently for eight weeks. For each treatment, we kept track of body mass, liver index, blood lipid levels, and oxidative stress state. We also analyzed mouse feces using high-throughput 16srRNA sequencing to examine the relationship between jujube vinegar's hypolipidemic effect and antioxidant activity and how it affects the gut microbiome. Jujube vinegar reduced body weight by 19.92%, serum TC, TG, and LDL-C by 25.09%, 26.83%, and 11.66%, and increased HDL-C by 1.44 times, serum AST and ALT decreased by 26.36% and 34.87% respectively, the blood levels of SOD and GSH-Px increased 1.35-fold and 1.60-fold, respectively. While blood MDA decreased 33.21%, the liver's SOD and GSH-Px increased 1.32-fold and 1.60-fold, respectively, and the liver's MDA decreased 48.96% in HFD mice. The gut microbiome analysis revealed that jujube vinegar increased the intestinal microbial ASV count by 13.46%, and the F/B (Firmicutes/Bacteroidota) ratio by 2.08-fold in high-fat diet mice, and the proportion was significantly inversely correlated with TC, TG, and LDL-C and positively correlated with HDL-C. Biomarker bacteria in the vinegar group included Lactobacillaceae and Lactobacillus, which correlated favorably with HDL-C, SOD, and GSH-Px and negatively with LDL-C, TC, and TG. Jujube vinegar increased the abundance of the Aerobic, Contains Mobile Elements, and Facultative Aerobic by 2.84 times, 1.45 times, and 2.40 times, while decreased the abundance of Potential pathogens by 44.72%, according to the BugBase study. The KEGG analysis showed that jujube vinegar was predominantly reflected in the biological process of gene function and related to signal transduction pathways, including glucagon signaling system, HIF-1 signaling pathway, adipocytokine signaling pathway, amino sugar, and nucleotide sugar metabolism, and so forth. Based on these findings, jujube vinegar may reduce hyperlipoidemia by controlling the gut microbiome and enhancing antioxidant capacity.

The Effects of Shaking Duration on the Abundance and the Community of Aerobic Denitrifying Bacteria in Shrimp Pond Water and Sediment Samples

With the rapid development of intensive aquaculture, the considerable release of nitrogenous organic compounds has become a serious threat to aquatic organisms. Currently, isolating autochthonous aerobic denitrifying bacteria (ADB) from aquaculture environments is essential for the biological elimination of nitrogenous pollutants. In this study, the enrichment of ADB from shrimp pond water and sediment samples was conducted under different shaking durations. The absolute abundance of total bacteria, nosZ-type, and the napA-type ADB was measured using qPCR. High-throughput sequencing of 16S rRNA, nosZ, and napA genes was performed to reveal the community structure of bacteria and ADB, respectively. Our data revealed that absolute abundance and the community structure of the total bacteria, nosZ-type and napA-type ADB, were significantly altered under different shaking durations. Specifically, the order Pseudomonadales, possessing both nosZ and napA genes, was significantly enriched in water and sediment samples under both 12/12 and 24/0 shaking/static cycles. However, in water samples, compared to the 24/0 shaking/static cycles, the 12/12 shaking/static cycles could lead to a higher enrichment rate of aerobic denitrification bacteria indicated by the higher absolute abundance of bacteria and the higher accounting percentage of orders Oceanospirillales and Vibrionales. Moreover, although the order Pseudomonadales notably increased under the 12/12 of shake/static cycle compared to the 24/0 shaking/static cycle, considering the relative higher abundance of ADB in 24/0 shaking/static cycle, the enrichment of ADB in sediment may be efficient with the 24/0 shaking/static cycle.

The Application of Sulfur Influences Microbiome of Soybean Rhizosphere and Nutrient-Mobilizing Bacteria in Andosol.

This study aimed to determine the effect of sulfur (S) application on a root-associated microbial community resulting in a rhizosphere microbiome with better nutrient mobilizing capacity. Soybean plants were cultivated with or without S application, the organic acids secreted from the roots were compared. High-throughput sequencing of 16S rRNA was used to analyze the effect of S on microbial community structure of the soybean rhizosphere. Several plant growth-promoting bacteria (PGPB) isolated from the rhizosphere were identified that can be harnessed for crop productivity. The amount of malic acid secreted from the soybean roots was significantly induced by S application. According to the microbiota analysis, the relative abundance of Polaromonas, identified to have positive association with malic acid, and arylsulfatase-producing Pseudomonas, were increased in S-applied soil. Burkholderia sp. JSA5, obtained from S-applied soil, showed multiple nutrient-mobilizing traits among the isolates. In this study, S application affected the soybean rhizosphere bacterial community structure, suggesting the contribution of changing plant conditions such as in the increase in organic acid secretion. Not only the shift of the microbiota but also isolated strains from S-fertilized soil showed PGPB activity, as well as isolated bacteria that have the potential to be harnessed for crop productivity.

Early life exposure to low-dose perfluorooctane sulfonate disturbs gut barrier homeostasis and increases the risk of intestinal inflammation in offspring

Perfluorooctane sulfonate (PFOS), one of the legacy per- and poly-fluoroalkyl substances (PFAS), is associated with multiple adverse health effects on children. However, much remains to be known about its potential impacts on intestinal immune homeostasis during early life. Our study found that PFOS exposure during pregnancy in rats significantly increased the maternal serum levels of interleukin-6 (IL-6) and zonulin, a gut permeability biomarker, and decreased gene expressions of Tight junction protein 1 (Tjp1) and Claudin-4 (Cldn4), the tight junction proteins, in maternal colons on gestation day 20 (GD20). Being exposed to PFOS during pregnancy and lactation in rats significantly decreased the body weight of pups and increased the offspring's serum levels of IL-6 and tumor necrosis factor-α (TNF-α) on postnatal day 14 (PND14), and induced a disrupted gut tight junction, manifested by decreased expressions of Tjp1 in pup's colons on PND14 and increased pup's serum concentrations of zonulin on PND28. By integrating high-throughput 16S rRNA sequencing and metabolomics, we demonstrated that early-life PFOS exposure altered the diversity and composition of gut microbiota that were correlated with the changed metabolites in serum. The altered blood metabolome was associated with increased proinflammatory cytokines in offspring. These changes and correlations were divergent at each developmental stage, and pathways underlying immune homeostasis imbalance were significantly enriched in the PFOS-exposed gut. Our findings provide new evidence for the developmental toxicity of PFOS and its underlying mechanism and explain in part the epidemiological observation of its immunotoxicity.

In sickness and in health: the dynamics of the fruit bat gut microbiota under a bacterial antigen challenge and its association with the immune response.

Interactions between the gut microbiome (GM) and the immune system influence host health and fitness. However, few studies have investigated this link and GM dynamics during disease in wild species. Bats (Mammalia: Chiroptera) have an exceptional ability to cope with intracellular pathogens and a unique GM adapted to powered flight. Yet, the contribution of the GM to bat health, especially immunity, or how it is affected by disease, remains unknown. Here, we examined the dynamics of the Egyptian fruit bats' (Rousettus aegyptiacus) GM during health and disease. We provoked an inflammatory response in bats using lipopolysaccharides (LPS), an endotoxin of Gram-negative bacteria. We then measured the inflammatory marker haptoglobin, a major acute phase protein in bats, and analyzed the GM (anal swabs) of control and challenged bats using high-throughput 16S rRNA sequencing, before the challenge, 24h and 48h post challenge. We revealed that the antigen challenge causes a shift in the composition of the bat GM (e.g., Weissella, Escherichia, Streptococcus). This shift was significantly correlated with haptoglobin concentration, but more strongly with sampling time. Eleven bacterial sequences were correlated with haptoglobin concentration and nine were found to be potential predictors of the strength of the immune response, and implicit of infection severity, notably Weissella and Escherichia. The bat GM showed high resilience, regaining the colony's group GM composition rapidly, as bats resumed foraging and social activities. Our results demonstrate a tight link between bat immune response and changes in their GM, and emphasize the importance of integrating microbial ecology in ecoimmunological studies of wild species. The resilience of the GM may provide this species with an adaptive advantage to cope with infections and maintain colony health.

Lactobacillus acidophilus Fermented Dandelion Improves Hyperuricemia and Regulates Gut Microbiota

Foodborne prevention and treatment of hyperuricemia (HUA) has received widespread attention. Lactic acid bacteria (LAB) can improve intestinal function, while traditional medicine dandelion has the functions of detoxification and detumescence. Whether LAB fermented dandelion has any effects on HUA and the underlying mechanism is not clear. To address these questions, Lactobacillus acidophilus was selected or maximal xanthine oxidase activity. The effect of Lactobacillus acidophilus fermented dandelion (LAFD) on uric acid metabolism was evaluated by the HUA mouse model. Expression levels of UA, BUN, CRE, XOD, and inflammatory factors in serum were detected. Paraffin sections and staining were used to observe the kidney and small intestine, and mRNA expression of GLUT9, URAT1, OAT1, and ABCG2 related to uric acid metabolism were investigated. Furthermore, the intestinal flora was studied by contents of the cecum and high throughput 16S rRNA sequencing. The results showed that LAFD had a significant inhibitory effect on XOD in vitro (p < 0.01). LAFD could reduce the levels of UA, BUN, CRE, XOD, IL-1 β, IL-6, and TNF- α in serum (p < 0.05), thus inhibiting inflammatory reaction, and reducing UA by decreasing the mRNA expression of GLUT9, URAT1 in kidney and increasing the mRNA expression of OAT1 and ABCG2 in kidney and small intestine (p < 0.05). In addition, the 16S rRNA gene sequencing analysis demonstrated that LAFD treatment can help restore the imbalance of the intestinal microbial ecosystem and reverse the changes in Bacterodietes/Firmicutes, Muribaculaceae, Lachnospiraceae in mice with HUA. It is suggested that the mechanism of LAFD in treating HUA may be related to the regulation of the mRNA expressions of GLUT9, URAT1, OAT1, and ABCG2 in the kidney and small intestine, as well as the regulation of intestinal flora, which provides the experimental basis for the development of new plant fermented products.

Succession of Bacteria Attached to Microplastics After Transferring from a Mariculture Area to a Seagrass Meadow.

Microplastics have been recognized as a novel niche for bacteria. However, studies have characterized the plastisphere microbial community in situ without exploring the microbial changes after transferring to other ecosystems. Here we focus on bacterial succession on typical microplastics (polypropylene and expanded polystyrene) and natural substrates (wood) after transferring from mariculture area to seagrass meadows system. Using high-throughput sequencing of 16S rRNA, we found that alpha diversity significantly reduced after transferring and microplastics especially PP had significant separations on PCoA plots at different succession stages. The abundance and metabolic pathways of potential pathogen-associated microorganisms are significantly decreased. The relative abundance of xenobiotics biodegradation pathways was significantly lower and of energy metabolism pathways was significantly higher by comparing before and after transferring. Main environmental factors affecting microbial communities changed from nutrient characteristics to basic physicochemical properties after transferring. The succession times of the microbial communities of the three materials were different.

Multicompartmental traumatic injury induces sex-specific alterations in the gut microbiome.

Previous preclinical studies have demonstrated an altered gut microbiome after traumatic injury; however, the impact of sex on dysbiosis remains unknown. We hypothesized that the "pathobiome" phenotype induced by multicompartmental injuries and chronic stress is host sex specific with unique microbiome signatures. Male and proestrus female Sprague-Dawley rats (n = 8/group) aged 9 weeks to 11 weeks were subjected to either multicompartmental injury (PT) (lung contusion, hemorrhagic shock, cecectomy, bifemoral pseudofractures), PT plus 2 hours daily chronic restraint stress (PT/CS) or naive controls. Fecal microbiome was measured on Days 0 and 2 using high-throughput 16S rRNA sequencing and Quantitative Insights Into Microbial Ecology bioinformatics analyses. Microbial alpha-diversity was assessed using Chao1 (number of different unique species) and Shannon (species richness and evenness) indices. Beta-diversity was assessed using principle coordinate analysis. Intestinal permeability was evaluated by plasma occludin and lipopolysaccharide binding protein. Histologic evaluation of ileum and colon tissues was scored for injury by a blinded pathologist. Analyses were performed in GraphPad and R, with significance defined as p < 0.05 between males versus females. At baseline, females had significantly elevated alpha-diversity (Chao1, Shannon indices) compared with males ( p < 0.05) which was no longer present 2 days postinjury in PT and PT/CS. Beta-diversity also differed significantly between males and females after PT ( p = 0.01). At Day 2, the microbial composition in PT/CS females was dominated by Bifidobacterium , whereas PT males demonstrated elevated levels of Roseburia ( p < 0.01). The PT/CS males had significantly elevated ileum injury scores compared with females ( p = 0.0002). Plasma occludin was higher in PT males compared with females ( p = 0.004); plasma lipopolysaccharide binding protein was elevated in PT/CS males ( p = 0.03). Multicompartmental trauma induces significant alterations in microbiome diversity and taxa, but these signatures differ by host sex. These findings suggest that sex is an important biological variable that may influence outcomes after severe trauma and critical illness.

Effect of tea polysaccharides on faecal microbiota and their short-chain fatty acid metabolic products

To explore the effect of tea polysaccharides on the gut microbiota and their short-chain fatty acid (SCFA) metabolic products, we used the faecal microbiota to simulate the gut microbiota in vitro, and cultured them to obtain a preculture solution. Ultrapure water, tea polysaccharides, and glucose were added to the precultured solution for anaerobic fermentation. Samples of each group were harvested at 0, 6, 12, and 24th hour during fermentation to test the contents of the SCFAs. In addition, high-throughput 16S rRNA sequencing was performed to analyse the microbiota in the fermentation medium. Results showed that the faecal microbiota used tea polysaccharides to generate SCFAs. When compared with the fermentation group with the addition of ultrapure water, the group with the addition of tea polysaccharides increased the relative abundance of Firmicutes, and decreased the relative abundance of Bacteroidetes at the phylum level. The relative abundances of Butyricimonas, Roseburia, Eubacterium rectale group, Ruminococcus 1, Lachnospira, and Parasutterella increased significantly at the genus level. Based on the LEfSe analysis of key microbiota at the genus level, significant differences between the groups were observed. It was clear that tea polysaccharides selectively enriched the microbiota to produce SCFAs, and the correlation between the SCFAs and faecal microbiota was confirmed.

Effect of tea polysaccharides on faecal microbiota and their short-chain fatty acid metabolic products

To explore the effect of tea polysaccharides on the gut microbiota and their short-chain fatty acid (SCFA) metabolic products, we used the faecal microbiota to simulate the gut microbiota in vitro, and cultured them to obtain a preculture solution. Ultrapure water, tea polysaccharides, and glucose were added to the precultured solution for anaerobic fermentation. Samples of each group were harvested at 0, 6, 12, and 24th hour during fermentation to test the contents of the SCFAs. In addition, high-throughput 16S rRNA sequencing was performed to analyse the microbiota in the fermentation medium. Results showed that the faecal microbiota used tea polysaccharides to generate SCFAs. When compared with the fermentation group with the addition of ultrapure water, the group with the addition of tea polysaccharides increased the relative abundance of Firmicutes, and decreased the relative abundance of Bacteroidetes at the phylum level. The relative abundances of Butyricimonas, Roseburia, Eubacterium rectale group, Ruminococcus 1, Lachnospira, and Parasutterella increased significantly at the genus level. Based on the LEfSe analysis of key microbiota at the genus level, significant differences between the groups were observed. It was clear that tea polysaccharides selectively enriched the microbiota to produce SCFAs, and the correlation between the SCFAs and faecal microbiota was confirmed.

The Effect of Schizochytrium sp. on Growth, Fatty Acid Profile and Gut Microbiota of Silver Pomfret (Pampus argenteus)

Schizochytrium sp. is a kind of heterotrophic protist, rich in docosahexaenoic acid (DHA). To study the application value of Schizochytrium sp. in fish diet, a 20-day feeding experiment was initiated to evaluate its effect on growth, fatty acid contents, and the gut microbiota of the important economic fish, silver pomfret. In this study, the diets of the treatment group were added with 2% Schizochytrium sp. The fish in the treatment group gained more weight and had a higher growth rate than the control group. The levels of DHA, eicosapentaenoic acid, and polyunsaturated fatty acids in the edible tissue of fish were highly increased in the treatment group after 20 days. After feeding Schizochytrium sp., high-throughput 16S rRNA sequencing showed that the Proteobacteria, Firmicutes and Bacteroidetes were the phyla with the highest abundance, and at the genus and species level, we observed an increased abundance of probiotics. The results indicated that ingestion of Schizochytrium sp. could change the dominant microbiota population, which might lead to accelerated growth and improved unsaturated fatty acid content and fish health. This study provides a reference for Schizochytrium sp. supplementation in fish diets and could aid in the industrialization of silver pomfret.

Does diet or macronutrients intake drive the structure and function of gut microbiota?

Shift of ingestive behavior is an important strategy for animals to adapt to change of the environment. We knew that shifts in animal dietary habits lead to changes in the structure of the gut microbiota, but we are not sure about if changes in the composition and function of the gut microbiota respond to changes in the nutrient intake or food items. To investigate how animal feeding strategies affect nutrient intakes and thus alter the composition and digestion function of gut microbiota, we selected a group of wild primate group for the study. We quantified their diet and macronutrients intake in four seasons of a year, and instant fecal samples were analyzed by high-throughput sequencing of 16S rRNA and metagenomics. These results demonstrated that the main reason that causes seasonal shifts of gut microbiota is the macronutrient variation induced by seasonal dietary differences. Gut microbes can help to compensate for insufficient macronutrients intake of the host through microbial metabolic functions. This study contributes to a deeper understanding of the causes of seasonal variation in host-microbial variation in wild primates.

Linking Soil Bacterial Communities to Soil Aggregates after Afforestation in a Karst Rocky Desertification Region

Afforestation influences soil aggregates and the soil microenvironment, and it also affects soil bacterial communities. However, the interactions between soil aggregation, soil properties, and the bacterial community that occur following afforestation are still unclear and are rarely studied in karst ecosystems. Soil samples were collected from cropland, for reference, and from natural secondary forests and managed forests in a karst rocky desertification region of Southwest China. Soil aggregates were isolated using the wet-sieving method, and the soil bacterial community composition was determined using high-throughput 16S rRNA sequencing. Afforestation promoted significant macro-aggregation (p &lt; 0.05) and increased the soil organic carbon (38%), nitrogen (35.4%), exchangeable Ca (78.6%), and soil water contents (4.1%) but decreased the pH and bulk density. The changes in these soil aggregates and soil properties had marked effects on the abundance and composition of the bacterial community. Variation-partitioning analysis showed that, together, the soil aggregates and soil characteristics explained 23.4% of the variation in the bacterial community, and their interaction formed the largest contribution (14.6%). Overall, our findings suggest that both natural and managed afforestation may shift soil bacterial communities by promoting significant macro-aggregation and altering soil properties.

Unraveling the microbial succession during the natural fermentation of grass carp and their correlation with volatile flavor formation

Complex microbial communities contribute significantly to the flavor formation of traditional fermented fish products. However, the relationship between microorganisms and flavor formation in traditional fermented grass carp products is still unclear. In this study, the diversity and succession of microbial communities and the variation of volatile compounds during natural fermentation of grass carp were analyzed using high-throughput sequencing of 16S rRNA and headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS), respectively. The core functional microorganism and key volatile compounds were identified, and their potential relationship was revealed using a correlation network model analysis. The microbial community analysis result showed that the microbial diversity during natural fermentation of grass carp decreased markedly with increasing fermentation time, and Lactiplantibacillus, Staphylococcus, and Enterobacter were the dominant genera in naturally fermented grass carp. HS-SPME-GC-MS analysis result showed that 45 volatile compounds were identified from fermented samples, among which 13 compounds (e.g., hexanal, heptanal, nonanal, decanal, 3-octanone, 3-methyl-1-butanol, 1-hexanol, 1-heptanol, 1-octen-3-ol, 1-octanol, ethyl acetate, 3-methyl-1-butanol acetate, and 2-methoxy-4-vinylphenol) were identified as the key volatile compounds. Additionally, the correlation network model analysis result revealed that Lactiplantibacillus showed significantly positive correlations with most of the key volatile compounds, making an important contribution to the formation of volatile flavor in naturally fermented grass carp. This study may lead to an understanding of the role of core functional microorganisms in the formation of volatile flavor during the natural fermentation of grass carp and provide some theoretical guidance for the industrial production of high-quality fermented grass carp products.

Fermented Chinese Herbal Medicine Promoted Growth Performance, Intestinal Health, and Regulated Bacterial Microbiota of Weaned Piglets.

To investigate the effects of fermented Chinese herbal medicine on growth performance, diarrhea rate, nutrient digestibility, and intestinal health of weaned piglets, and to provide the theoretical basis for applying fermented Chinese herbal medicines to weaned piglet production, a total of 162 weaned and castrated piglets at 25 days of age (Duroc × Landrace × Yorkshire, half male and half female) with an initial body weight of 7.77 ± 0.03 kg were randomly divided into the following three groups according to the principle of similar body weight: basal diet (CON) group, basal diet + 3 kg/t fermented Chinese herbal medicine (LFHM) group, and basal diet + 5 g/kg fermented Chinese herbal medicine (HFHM) group. Each group underwent six replicates and there were nine piglets in each replicate. The experiment lasted 24 days, i.e., 3 days for preliminary feeding, and 21 days for the experiment. From Day 1 of the experiment, the piglets were observed and recorded for diarrhea each day. As compared with the CON group, the results indicated: Following the addition of fermented Chinese herbal medicine, the piglets in the LFHM and HFHM groups increased final weight (FW); average daily feed intake (ADFI); average daily gain (ADG) (p < 0.01); apparent digestibility of crude protein (CP) (p < 0.05); as well as chymotrypsin, α-amylase, and lipase activities (p < 0.01). In addition, α-amylase activity in the LFHM group was higher than that in the HFHM group (p < 0.05); chymotrypsin activity in the LFHM group was lower than that in the HFHM group (p < 0.05); as compared with the CON group, the LFHM and the HFHM increased villus height (VH) and crypt depth (CD) in piglet jejunum; isovaleric acid concentration with the HFHM was higher than those with the CON and the LFHM (p < 0.05), but butyrate concentration with the HFFM was lower than those with the CON and the LFHM (p < 0.05). The high-throughput 16S rRNA sequencing of intestinal microbiota results showed that the LFHM and the HFHM affected the microbial α diversity index in weaned piglet colon (p < 0.01). In conclusion, fermented Chinese herbs can improve the growth performance of weaned piglets by promoting the secretion of intestinal digestive enzymes, changing intestinal microbial diversity, regulating the contents of intestinal short chain fatty acids (SCFAs), promoting intestinal health, and improving nutrients digestibility.