Potential Beneficial Bacteria Research Articles

Effects of dietary Bacillus subtilis DSM 32315 supplementation on the growth, immunity and intestinal morphology, microbiota and inflammatory response of juvenile largemouth bass Micropterus salmoides

This study aimed at evaluating the effects of dietary inclusion of Bacillus subtilis DSM 32315 on the growth, immunity, intestinal architecture and gut microbiota of juvenile largemouth bass Micropterus salmoides (LMB). B. subtilis DSM 32315 was supplemented in the diets at the levels of 0 (control, CON), 1.5 (BS1.5, 3 × 106 CFU/g feed) and 3 g/kg (BS3, 6 × 106 CFU/g feed). Each diet was assigned to four replicate tanks of LMB juveniles (initial mean body weight, 8.32 ± 0.06 g) with 20 fish per tank for 9 weeks. The results showed that the growth and feed utilization of LMB were not sensitive to dietary modifications (p > .05). Compared with the CON fish, dietary BS supplementation did not affect the haematological parameters (white and red blood cell counts and haematocrit value) of LMB (p > .05), but the BS1.5 fish performed better than the BS3 fish. Serum innate immunity indicators (lysozyme activity and complement C3 and C4 levels) were improved with dietary BS supplementation at both doses, while higher serum IgM level was only recorded at 1.5 g/kg feed (p < .05). All the sampled fish exhibited intact intestines, but the intestinal architecture (villus height and muscular layer thickness) still benefited from dietary BS inclusion at both doses (p < .05). Although intestinal anti-inflammatory response (mRNA levels of IL-10 and TGF-β1) did not differ between the BS supplemented fish (p > .05), the BS1.5 fish obtained superior pro-inflammatory response (mRNA levels of IL-1β, IL-8, and TNF-α) over the BS3 fish (p < .05). Compared with the CON fish, the abundance of the harmful Plesiomonas shigelloides decreased in the gut microbiota of the BS1.5 fish (p < .05). Despite the BS3 fish obtained higher diversity of gut microbiota, the abundances of potential beneficial (Cetobacterium somerae and Shewanella xiamenensis) and harmful bacteria (Acinetobacter johnsonii and P. shigelloides) increased or decreased simultaneously (p < .05). Taken together, it was concluded that dietary BS DSM 32315 inclusion presented some positive effects on LMB. Although the BS1.5 fish performed better than the BS3 fish, the best supplemental dose need to be further studied.

Improvements of immune genes and intestinal microbiota composition of turbot (Scophthalmus maximus) with dietary oregano oil and probiotics

Plant extract (oregano oil) and probiotics as dietary additives can improve weight gain, feed efficiency and disease resistance in cultured fish. In this research, we evaluated the effects of oregano oil and probiotics (strain Bacillus coagulans G1902) on growth performance, intestinal microbiota and expression of intestinal and splenic immune related genes (IL-1β, TNF-α, MHC-I and IFIH1) of turbots (Scophthalmus maximus) by a 30-day feeding experiment. Three treatment groups including oregano oil supplementation (O) group, probiotic strain B. coagulans supplementation (P) group and common feeding (CK) group were designed, respectively. As a result, turbots showed better growth performance, increased digestion and absorption capacity, and decreased incidence rates of A. salmonicida infection in O and P groups compared with CK group. The expression levels of IL-1β, TNF-α, MHC-I and IFIH1 were significantly up-regulated in O group after 10 days of oregano oil feeding (P < 0.05). We performed 16S rRNA sequencing analysis, identified the differentially abundant taxa, predicted metabolic pathways of intestinal microbiota and constructed the co-abundance networks. The supplementary of oregano oil or probiotics decreased the relative abundances of Listonella and Sphingomonas and increased the relative abundances of several potential beneficial bacteria (such as Akkermansia, Bifidobacteium and Faecalibacterium) (LDA > 2, P < 0.05). The relative abundance of bacterial secretion system decreased in turbots supplemented dietary oregano oil on day 20 and 30, and several pathways related to glycan, lipid and amino acid metabolism upregulated in turbots supplemented dietary probiotics on day 30 (P < 0.05). Oregano oil or B. coagulans may provide health benefits by modulate gut microbiota and impact the immunostimulatory effects of the host. Our findings provide a new perspective to explore the mechanism of growth improvement and immune enhancement by usage of oregano oil or probiotics, and study the application of oregano oil and probiotics as fish feeds in health culture of turbots.

Responses of soil bacterial and fungal communities to the long-term monoculture of grapevine.

Soil microorganisms are essential for the long-term sustainability of agricultural ecosystems. However, continuous grapevine replanting can disrupt the stability of soil microbial communities. We investigated the bacterial and fungal abundance, diversity, and community composition in rhizosphere soils with continuous grapevine replanting for 5, 6, 7 (Y5, Y6, and Y7; short-term), and 20 (Y20; long-term) years with high-throughput sequencing. Results showed that diversities and abundances of bacterial and fungal communities in Y20 were significantly lower than in other samples. The bacterial and fungal community compositions were markedly affected by the replanting time and planting year. After short-term grapevine replanting, relative abundances of potential beneficial bacteria and harmful fungi in rhizosphere soils were higher compared to long-term planting. Bacterial and fungal communities were significantly correlated with available nitrogen (AN), available phosphorus, available potassium (AK), and pH. AK and AN were the primary soil factors related to the shift of bacterial and fungal communities. Bacterial and fungal co-occurrence patterns were remarkably affected by replanting time, showing that fallow land harbored co-occurrence networks more complex than those in other groups, with the Y20 group showing the lowest complexity. Then, we isolated the dominant fungi in grapevine rhizosphere soil after continuous replanting and verified the harmful effects of three candidate strains through pot experiments. The results showed that 12days post-treating the soil with fungal spore suspensions significantly inhibited grapevine seedlings' growth, whereas Fusarium solani inhibited plant growth. Overall, we showed that F. solani might be a potentially harmful fungus related to grapevine replant diseases. KEY POINTS: • Continuous grapevine planting reduced soil microbe diversities/abundances. • Beneficial bacteria and harmful fungi increased after short-term replanting. • F. solani may be a harmful fungus related to grapevine replant diseases.

Potentials of Microorganisms in Human Health

There are large numbers of powerful species of microorganisms present within our bodies that make up the diverse human microbiomes. Microbiomes, the collective genomes of the microorganisms in a particular environment, support and maintain our health, but they are disturbed in some fashion in case of the presence of some diseases such as autoimmune diseases and cancer. Different food products provide different growth conditions for microorganisms. Microbial growth is also controlled by some factors such as pH, nutrients, moisture content, temperature, relative humidity, and gases. Thus the growth of microorganisms in optimum conditions results in spoilage and degradation of food products resulting in a sour or foul-smelling, in addition to a visible change in color, effervescences on the food surface, etc. Microbial contamination of food can occur at any point in the food production process starting from growth, harvesting, transport, storage, or final preparation. A variety of environmental factors can influence intestinal microbial imbalance, which has a close relationship with human health and disease. There are many numerous potential probiotics or beneficial bacteria that may prevent or treat certain diseases such as Lactobacillus and Bifidobacterium. On the other hand, a few destructive microorganisms play a major role in the development and progression of major human diseases such as infectious diseases, liver diseases, gastrointestinal cancers, metabolic diseases, respiratory diseases, mental or psychological diseases, and autoimmune diseases. With the increased understanding of the relationship between the human microbiome and a variety of diseases, the use of these findings to predict or diagnose diseases has attracted a great deal of attention. Thus, the aim of the present work was to review briefly the role of microorganisms in human health, during the development of autoimmune and tumor diseases. This review article also includes microbiota diversity, colonization, and normalization of perturbed intestinal microbial communities, the safety of gastrointestinal tract, and the beneficial role of probiotics.

Effects of different dietary lipid levels on intestinal mucosal barrier and microbial community of juvenile tiger puffer Takifugu rubripes

A 65-day feeding trial was conducted to investigate the effects of different levels of dietary lipid on intestinal health of tiger puffer. Three experimental diets were formulated, differing in lipid level, that is, 90.3 (control-suitable lipid, C-SL), 130.3 (moderately high lipid, MHL) and 170.3 (extremely high lipid, EHL) g/kg dry matter. The results showed that with increasing dietary lipid levels, the activities of total antioxidant capacity, Na+ K+-ATP, amylase and trypsin were significantly decreased by diets MHL and EHL. Compared with C-SL, the mRNA expression of the intestinal tight junction proteins (Claudin14, Claudin18, junctional adhesion molecule-A) were significantly down-regulated and the serum diamine oxidase enzyme activity was significantly increased in the EHL group. Diet EHL up-regulated the gene expression of the pro-inflammatory cytokines, tumour necrosis factor-α, interferon-2, interleukin (IL)-1β, IL-8 and IL-15, and down-regulated that of anti-inflammatory cytokine transforming growth factor -β. Sequencing of intestinal bacterial 16s rRNA V4 region showed that diet EHL significantly increased the Firmicutes/Bacteroidetes ratio, decreased the alpha diversity of intestinal microbiota and the relative abundance of some potential beneficial bacteria such as Lactobacillus, Sphingomonas and Thermus. These results showed that high level of dietary lipid (170.3 g/kg) had negative effects on function status, mucosal barrier and microbial communities of tiger puffer intestine, indicating that tiger puffer was sensitive to the dietary lipid level.

Exploring Biocontrol Agents From Microbial Keystone Taxa Associated to Suppressive Soil: A New Attempt for a Biocontrol Strategy.

Recent studies have observed differing microbiomes between disease-suppressive and disease-conducive soils. However, it remains unclear whether the microbial keystone taxa in suppressive soil are critical for the suppression of diseases. Bacterial wilt is a common soil-borne disease caused by Ralstonia solanacearum that affects tobacco plants. In this study, two contrasting tobacco fields with bacterial wilt disease incidences of 0% (disease suppressive) and 100% (disease conducive) were observed. Through amplicon sequencing, as expected, a high abundance of Ralstonia was found in the disease-conducive soil, while large amounts of potential beneficial bacteria were found in the disease-suppressive soil. In the fungal community, an abundance of the Fusarium genus, which contains species that cause Fusarium wilt, showed a positive correlation (p < 0.001) with the abundance of Ralstonia. Network analysis revealed that the healthy plants had more complex bacterial networks than the diseased plants. A total of 9 and 13 bacterial keystone taxa were identified from the disease-suppressive soil and healthy root, respectively. Accumulated abundance of these bacterial keystones showed a negative correlation (p < 0.001) with the abundance of Ralstonia. To complement network analysis, culturable strains were isolated, and three species belonging to Pseudomonas showed high 16S rRNA gene similarity (98.4–100%) with keystone taxa. These strains displayed strong inhibition on pathogens and reduced the incidence of bacterial wilt disease in greenhouse condition. This study highlighted the importance of keystone species in the protection of crops against pathogen infection and proposed an approach to obtain beneficial bacteria through identifying keystone species, avoiding large-scale bacterial isolation and cultivation.

Community Structure of Protease-Producing Bacteria Cultivated From Aquaculture Systems: Potential Impact of a Tropical Environment

Protease-producing bacteria play vital roles in degrading organic matter of aquaculture system, while the knowledge of diversity and bacterial community structure of protease-producing bacteria is limited in this system, especially in the tropical region. Herein, 1,179 cultivable protease-producing bacterial strains that belonged to Actinobacteria, Firmicutes, and Proteobacteria were isolated from tropical aquaculture systems, of which the most abundant genus was Bacillus, followed by Vibrio. The diversity and relative abundance of protease-producing bacteria in sediment were generally higher than those in water. Twenty-one genera from sediment and 16 genera from water were identified, of which Bacillus dominated by Bacillus hwajinpoensis in both and Vibrio dominated by Vibrio owensii in water were the dominant genera. The unique genera in sediment or water accounted for tiny percentage may play important roles in the stability of community structure. Eighty V. owensii isolates were clustered into four clusters (ET-1–ET-4) at 58% of similarity by ERIC-PCR (enterobacterial repetitive intergenic consensus-polymerase chain reaction), which was identified as a novel branch of V. owensii. Additionally, V. owensii strains belonged to ET-3 and ET-4 were detected in most aquaculture ponds without outbreak of epidemics, indicating that these protease-producing bacteria may be used as potential beneficial bacteria for wastewater purification. Environmental variables played important roles in shaping protease-producing bacterial diversity and community structure in aquaculture systems. In sediment, dissolved oxygen (DO), chemical oxygen demand (COD), and salinity as the main factors positively affected the distributions of dominant genus (Vibrio) and unique genera (Planococcus and Psychrobacter), whereas temperature negatively affected that of Bacillus (except B. hwajinpoensis). In water, Alteromonas as unique genus and Photobacterium were negatively affected by NO3−-N and NO2−-N, respectively, whereas pH as the main factor positively affected the distribution of Photobacterium. These findings will lay a foundation for the development of protease-producing bacterial agents for wastewater purification and the construction of an environment-friendly tropical aquaculture model.

Physiological and metagenomic strategies uncover the rhizosphere bacterial microbiome succession underlying three common environmental stresses in cassava

The most common environmental pollutants such as cadmium (Cd), glyphosate and tetracycline have led to profoundly adverse impacts on plant productivity. However, how tropical crops such as cassava sense these pollutants via roots and how rhizosphere microbiome interacts with the host and pollutants remain largely unknown. In this study, we found these stresses significantly inhibited plant growth and triggered cell damage in a dosage-dependent manner, and the toxic effect on redox homeostasis was correlated with antioxidant metabolism. Using metagenomics technique, we found the rhizosphere microbiomes dynamically altered as the dose of these stresses increased. We also identified stressor-associated metagenome-assembled genomes and microbial metabolic pathways as well as mobile genetic elements in the rhizosphere microbiomes. Next, a co-occurrence network of both physiological and microbiome features was constructed to explore how these pollutants derived oxidative damage through the microbiome succession. Notably, phyllosphere transplantation of Agrobacterium tumefaciens or Pseudomonas stutzeri can significantly alleviate the negative effects of stresses on cassava growth and redox homeostasis. Collectively, this study demonstrated the dynamics of rhizosphere bacterial microbiome of cassava under three common environmental stresses, and A. tumefaciens and P. stutzeri could be developed as potential beneficial bacteria to alleviate Cd, glyphosate and tetracycline-triggered damage to cassava.

The secondary bacterial infection caused by WSSV outbreaks impacts shrimp Marsupenaeus japonicus’ growth as well as its intestinal microbiota’s composition and function

Intestinal microbiota homeostasis is a complex ecosystem and is essential for promoting aquatic animals’ growth. Invading pathogens can cause dynamical composition and structure change in the hosts’ microbiota due to this affecting their functions. WSSV is one of the most common and dangerous shrimp pathogens, which leads to white spot disease with too high mortality. A few studies on shrimp intestinal microbiota mainly focused on the changes during acute infection stage. Marsupenaeus japonicus is one of the most cultured shrimp with a decent ability to cope with environmental changes. In the current research, using M. japonicus as a model, we compared the differences of intestinal microbiota between healthy shrimp and the shrimp that survived through the WSSV outbreak. Our study showed that compared to the healthy M. japonicus, the WSSV outbreak disrupted intestinal microbiota structure in the survived shrimp: There was less potential beneficial bacteria and more harmful bacteria. Furthermore, the diversity and total abundance of intestinal microbiota in WSSV-survived shrimp increased significantly. On top of that, a metagenomic analysis by PICRUSt suggested that the changed intestinal microbiota could help the host to combat the secondary bacterial infections caused by WSSV outbreaks by regulating cell growth and death, reducing cell motility, improving energy metabolism, and increasing intestinal enzyme activities regardless the smaller sizes of WSSV-survived shrimp. This could be a result of excessive energy consumption and reduced nutrient-absorbing intestinal microbiota. Our study indicated that shrimp intestinal microbiota plays a fundamental role in combating against secondary infections and regulating the hosts’ growth post WSSV outbreaks. The eventual goal is to development of more efficient diagnostics and therapeutic strategies.

Gastrointestinal microbiota imbalance is triggered by the enrichment of Vibrio in subadult Litopenaeus vannamei with acute hepatopancreatic necrosis disease

The common shrimp disease, acute hepatopancreatic necrosis disease (AHPND), has caused extensive damage to the shrimp farming industry due to its rapid spread and high mortality rates. However, the alterations in gastrointestinal microbiota (GM) ecosystem in subadult shrimps (Litopenaeus vannamei) with AHPND occurrence are still unclear. This study identified AHPND according to clinical symptoms and the existence of the toxin gene pirAVP, analyzed the microbiome dynamics of healthy and diseased subadult shrimps, and built an ecological model for quantitative evaluation of the GM imbalance. The results showed that the GM community diversity in diseased shrimps was significantly lower than that in healthy ones. The structural composition, dysbiosis-related indices, and assembly processes of the GM community were also evidently changed in diseased shrimps. The different operational taxonomic units (OTUs) in GM of diseased shrimps were mainly composed of Vibrio spp. with a relative abundance >90%, the majority of these were neutrally distributed in the neutral model of AHPND occurrence. Of 39 biomarkers for predicting AHPND occurrence, nine belonging to Vibrio were overrepresented in diseased shrimps, whereas biomarkers such as Rhodobacteraceae OTU3427, Candiadatus aysiosphaera OTU1041, KD4-96 OTU4963, and Rhodobacter OTU3366 were enhanced in healthy shrimps. Functional prediction showed that the gene abundances of the NOD receptor signaling pathway (p = .04), Vibrio infection (p < .01), and Vibrio pathogenic cycle function (p < .01) were significantly increased in diseased compared with healthy shrimps. Disturbed GM was closely correlated with infectious diseases and pirA gene. In contrast, stable GM was maintained by multiple bacterial taxa, which may be benefit for shrimp health through regulating immune system and environmental adaptation. These results indicated that GM imbalance caused by AHPND with the characteristics of expanded variation of GM diversity, increased dysbiosis-related indices, higher abundance of potential pathogens, and lager loss of potential beneficial bacteria or ecological functions, might further accelerate the progression of AHPND outbreaks. This study may provide a basis for understanding the etiology of AHPND from a microecological perspective in subadult shrimp.

Water extract of shepherd's purse prevents high-fructose induced-liver injury by regulating glucolipid metabolism and gut microbiota

Shepherd’s purse as a wild vegetable is getting more and more attention on health benefits. Water extract of shepherd’s purse (WESP) was prepared and analyzed for the chemical constituents. The mice were fed high-fructose (HF) diet and treated with WESP at 50, 100 and 200 mg/kg·bw for 8 weeks. The HF-fed mice receiving WESP exhibited the inhibitions against abnormal weight gain, hepatic fat accumulation and lipid metabolic by down-regulating FAS and ACC expressions. WESP also significantly alleviated hyperglycemia, oxidative stress, and inflammatory response by regulating of NF-κB pathway. Moreover, WESP dose-dependently increased the acetic, propionic, and butyric acids levels in HF-fed mice. Furthermore, WESP significantly alleviated the HF-induced gut dysbiosis by reducing the ratio of Firmicutes to Bacteroidetes and increasing the abundance of potential beneficial bacteria. Our findings indicate that WESP may be an effective dietary supplement for preventing the liver damage.

Potential role of\xa0intestinal microflora\xa0in disease progression among patients with different stages of Hepatitis B

BackgroundIncreasing evidence demonstrate that the gut microbiota is involved in the pathogenesis of liver diseases, and faecal microbiota transplantation is considered to be a promising new treatment option. However, there are no reports on the intestinal flora of asymptomatic HBV carriers using next-generation sequencing. This study intends to investigate the potential role of the intestinal microflora in predicting the progression of Hepatitis B patients in different non-cancerous stages.ResultsA total of 266 patients with different stages of Hepatitis B and 31 healthy controls were included in this study. Some of the subjects (217 cases) underwent 16S rRNA gene sequencing. Compared with the control group (CK), the α diversity of patients in Group A (HBV carrier) slightly increased, while that of patients in the other three groups decreased. Each group of patients, especially those in Group C (cirrhosis) and Group D (acute-on-chronic liver failure), could be separated from the CK using weighted UniFrac PCoA and ANOSIM. LEfSe revealed that 40 taxa belonging to three phyla had an LDA larger than 4. In addition to the comparison between Group B (chronic Hepatitis B) and Group C, the specific flora and potential taxonomic function were also identified. Different microbial communities were found to be highly correlated with clinical indicators and the Child-Pugh scores. Changes in the microbial community were highly related to the alternations of host metabolism, which in turn, was related to the development of Hepatitis B. Our analysis identified a total of 47 strains with potential biomarker functions at all levels except for the phylum level.ConclusionsFaecal microbiota transplantation of some potential beneficial bacteria can change with the occurrence of disease, and HBV carriers might be the most suitable donors.

Yellow Mealworm Inclusion in Diets for Heavy-Size Broiler Chickens: Implications for Intestinal Microbiota and Mucin Dynamics

Simple SummaryNowadays, the maximization of chicken productivity cannot be achieved without considering their gut health, which is a complex, multifactorial concept that takes into account several intestinal features (such as the microbiota and the mucin dynamics). The gut health of broilers may be influenced by both intrinsic (i.e., age, sex, breed) and extrinsic (i.e., diet, environment) factors, thus, in turn, influencing the growth performance of the birds. Dietary insect meal inclusion has already been reported to exert positive effects on cecal microbiota and small intestinal mucin composition in female and male light-size broiler chickens (35–40 days of age), in particular when used at low inclusion levels (i.e., 5%). However, since male heavy-size broilers (50–60 days of age) represents a relevant market class in Italy, we herein evaluated the effects of yellow mealworm (Tenebrio molitor, TM) utilization on their gut health. The findings herein obtained interestingly suggested that the administration of insect meal for a longer period could potentially lead to a negative modulation of the cecal microbiota of the birds, thus suggesting a preferable utilization of yellow mealworm in the light-size production cycles. In the present trial, 160 heavy-size male broiler chickens were allocated to 4 dietary treatments (control feed [C] and 5, 10 and 15% TM meal inclusion, respectively, with 5 replicate pens/treatment and 8 birds/pen) to evaluate the influence of TM meal on intestinal microbiota and mucin composition. The broiler chickens fed TM-based diets showed higher beta diversity of their cecal microbiota in comparison with the C birds (p < 0.001). A significant decrease of the relative abundance of Firmicutes phylum and lower Firmicutes:Bacteroidetes ratios (False Discovery Rate [FDR] < 0.05) were also identified in TM15 broiler chickens when compared to the C group. Furthermore, the TM birds showed decreased relative abundance of Clostridium, Coprococcus, L-Ruminococcus and Ruminococcus genera (FDR < 0.05). In relation to the gut mucin composition, higher mucin staining intensity was detected in the intestinal crypts of TM5 birds in comparison with the other TM groups (p < 0.05). In conclusion, dietary TM meal inclusion negatively influenced the cecal microbiota of heavy-size broiler chickens in terms of partial alteration of the physiological microbial population and reduction of the potential beneficial bacteria (with slightly more pronounced effects when testing the 10–15% inclusion levels).

Effects of Bacillus amyloliquefaciens and Bacillus pumilus on Rumen and Intestine Morphology and Microbiota in Weanling Jintang Black Goat.

Simple SummarySelecting Bacillus amyloliquefaciens and Bacillus pumilus in the present work, antibiotic substitutes were found for weaned black goat health and growth. This study indicated that Bacillus amyloliquefaciens fsznc-06 and Bacillus pumilus fsznc-09 improved the development of rumen and small intestine in weanling Jintang black goats. They also regulated microbial communities by increasing the richness of beneficial bacteria, but decreasing that of pathogenic bacteria in rumen and caecum for nutrient metabolism and promoting healthy conditions.The importance of Bacillus as feed additives in animals’ production is well recognized. Bacillus amyloliquefaciens and Bacillus pumilus are involved in promoting animal growth performance and immunological indicators. However, their precise roles in the modulation of microbiota and immune response in goat rumen and intestines have not been investigated. The aim of the current work was to evaluate the impacts of Bacillus amyloliquefaciens fsznc-06 and Bacillus pumilus fsznc-09 in the development of rumen and small intestinal and microbial communities in rumen and caecum of weanling Jintang black goats. Morphological alterations of rumen and small intestine (duodenum, jejunum, and ileum) were evaluated by histochemical staining, and ruminal contents and cecal feces were analyzed by 16S rRNA sequencing in an Illumina NovaSeq platform. Morphological analysis showed that feeding weanling goats with Bacillus amyloliquefaciens fsznc-06 or Bacillus pumilus fsznc-09 enhanced ruminal papilla and small intestinal villus growth. In addition, 16S rRNA sequencing analysis indicated that microbial richness and diversity (Shannon, Simpson, Chao1, and ACE) and the relative richness of multiple or potential beneficial bacteria were higher in weaned black goats fed on Bacillus amyloliquefaciens fsznc-06 or Bacillus pumilus fsznc-09, but that of multiple or potentially pathogenic bacteria were lower, as compared with the control group. Tax4Fun analysis predicting the functional profiling of microbial communities showed that microbial communities in rumen or caecum were highly influential on metabolism and organism systems after feeding weanling goats with Bacillus amyloliquefaciens fsznc-06 or Bacillus pumilus fsznc-09. It was suggested that Bacillus amyloliquefaciens fsznc-06 and Bacillus pumilus fsznc-09 might be an auspicious antibiotic alternative to improve black goat growth and health by changing rumen and gut microbiota positively.

Microbiota in the Rhizosphere and Seed of Rice From China, With Reference to Their Transmission and Biogeography.

Seeds play key roles in the acquisition of plant pioneer microbiota, including the transmission of microbes from parent plants to offspring. However, the issues about seed microbial communities are mostly unknown, especially for their potential origins and the factors influencing the structure and composition. In this study, samples of rice seed and rhizosphere were collected from northeast and central-south China in two harvest years and analyzed using a metabarcoding approach targeting 16S rRNA gene region. A higher level of vertical transmission (from parent seed microbiota to offspring) was revealed, as compared to the acquisition from the rhizosphere (25.5 vs 10.7%). The core microbiota of the rice seeds consisted of a smaller proportion of OTUs (3.59%) than that of the rice rhizosphere (7.54%). Among the core microbiota, species in Arthrobacter, Bacillus, Blastococcus, Curtobacterium, Pseudomonas, and Ramlibacter have been reported as potential pathogens and/or beneficial bacteria for plants. Both the seed and the rhizosphere of rice showed distance-decay of similarity in microbial communities. Seed moisture and winter mean annual temperature (WMAT) had significant impacts on seed microbiota, while WMAT, total carbon, available potassium, available phosphorus, aluminum, pH, and total nitrogen significantly determined the rhizosphere microbiota. Multiple functional pathways were found to be enriched in the seed or the rhizosphere microbiota, which, to some extent, explained the potential adaptation of bacterial communities to respective living habitats. The results presented here elucidate the composition and possible sources of rice seed microbiota, which is crucial for the health and productivity management in sustainable agriculture.

Ursolic acid reverses liver fibrosis by inhibiting interactive NOX4/ROS and RhoA/ROCK1 signalling pathways.

Liver fibrosis is the reversible deposition of extracellular matrix (ECM) and scar formation after liver damage by various stimuli. The interaction between NOX4/ROS and RhoA/ROCK1 in liver fibrosis is not yet clear. Ursolic acid (UA) is a traditional Chinese medicine with anti-fibrotic effects, but the molecular mechanism underlying these effects is still unclear. We investigated the interaction between NOX4/ROS and RhoA/ROCK1 during liver fibrosis and whether these molecules are targets for the anti-fibrotic effects of UA. First, we confirmed that UA reversed CCl4-induced liver fibrosis. In the NOX4 intervention and RhoA intervention groups, related experimental analyses confirmed the decrease in CCl4-induced liver fibrosis. Next, we determined that the expression of NOX4 and RhoA/ROCK1 was decreased in UA-treated liver fibrotic mice. Furthermore, RhoA/ROCK1 expression was decreased in the NOX4 intervention group, but there was no significant change in the expression of NOX4 in the RhoA intervention group. Finally, we found that liver fibrotic mice showed a decline in their microbiota diversity and abundance, a change in their microbiota composition, and a reduction in the number of potential beneficial bacteria. However, in UA-treated liver fibrotic mice, the microbiota dysbiosis was ameliorated. In conclusion, the NOX4/ROS and RhoA/ROCK1 signalling pathways are closely linked to the development of liver fibrosis. UA can reverse liver fibrosis by inhibiting the NOX4/ROS and RhoA/ROCK1 signalling pathways, which may interact with each other.

Effects of Carbon/Nitrogen Ratio on Growth, Intestinal Microbiota and Metabolome of Shrimp (Litopenaeus vannamei).

Increasing the C/N ratio of input feed has been reported as a practical approach for improving water quality and enhancing shrimp growth through changing the bacterial community of rearing water. However, little is known about the effects of different C/N ratios of feed input on the intestinal microbiota and metabolome of shrimp. In the present study, the effects of three different C/N ratio levels (CN6, CN10, and CN15) maintained by adding sucrose on the growth, intestinal microbiota and metabolome of Litopenaeus vannamei, and bioflocs formation were investigated after 17 days of feeding. The results indicated that higher C/N ratio (10 and 15), especially CN15, of feed input significantly enhance the length and weight of shrimp individuals accompanied by a significant accumulation of bioflocs, compared to that of CN6. The increase of C/N ratio input decreased the α-diversity of the intestinal microbiota and changed the microbial community structure through increasing the relative abundance of Actinobacteria, Rhodobacteraceae (mainly consist of Roseobacter and Paracoccus groups), Alteromonadaceae, and inhibiting the growth of Cyanobacteria, certain Rhodobacteraceae, Mycoplasmataceae and Vibrio. The change of microbial community caused by increasing C/N ratio input was closely associated with various bioactive metabolites of flavonoids, benzenoids, prenol lipids, and indole derivatives, which are benefit for shrimp growth either as an antimicrobial agent or as a nutrient component. Overall, this study demonstrated that manipulating high C/N ratio of feed input helps to the growth of shrimp through increasing the relative abundance of potential beneficial bacteria and the accumulation of various bioactive metabolites to suppress the growth of detrimental bacteria.

The effect of Lactobacillus plantarum administration on the intestinal microbiota of whiteleg shrimp Penaeus vannamei

Along with the intensification of culture systems to meet the increasing global demands, there is an elevated risk of disease outbreak and substantial loss for shrimp farmers. Probiotics, e.g., Lactobacillus plantarum, are among the most promising feed supplements for controlling or treating microbial diseases in shrimp aquaculture. The maintenance of live and viable probiotic bacterial culture during storage is, however, quite challenging. This study investigated the paraprobiotic potential of L. plantarum on whiteleg shrimp (Penaeus vannamei), specifically on the intestinal microbiota. Four different experimental diet preparations of L. plantarum (fermentation supernatant (FS), live bacteria (LB), dead bacteria (DB), and cell-free extract (CE)) were used in the 15-day feeding trial. Subsequently, 16S rDNA gene sequencing technology was applied to analyze and characterize the whiteleg shrimp intestinal microbiota. Results showed that Proteobacteria was the most prevalent phylum in whiteleg shrimp gut microbiota, independent of the diet. Other phyla, including Bacteroidetes, Verrucomicrobia, Tenericutes, and Euryarchaeota were also recorded and independent of the diet. The microbiota of the whiteleg shrimp fed with the L. plantarum CE diet showed the highest abundance of Acidobacteria, with a 70-fold increase compared to that of the animals on the control diet. The abundance of Verrucomicrobia was the highest in the whiteleg shrimp fed with L. plantarum DB diet. Moreover, the abundance of Cyanobacteria, Crenarcheota, and Euryarchaeota in the microbiota of animals fed with L. plantarum FS diet were more than 10-fold higher, compared to that of the whiteleg shrimp fed with the control diet. An increased number of the potential beneficial bacteria from the genera Demequina, Rubritalea, Tenacibaculum, Marinicella and Phaeobacter versus a significantly decreased amount of the potential pathogenic genus Synechococcus were encountered in the microbiota of the CE diet-fed animals. There were 382 operational taxonomic units (OTUs) shared among all gut samples. The microbiota of the shrimps on the CE diet had the most unique OTUs, followed by those included in the FS and DB diet groups. These results demonstrated that P. vannamei fed with L. plantarum CE and FS diets had a significantly altered gastrointestinal microbiota. In conclusion, L. plantarum CE and FS diets have the potential to be used as paraprobiotics, due to the capacity to positively modulate the gastrointestinal microbiota in P. vannamei.

Enrichment of potentially beneficial bacteria from the consistent microbial community confers canker resistance on tomato

The soil microbiota interacts with plants closely and exerts strong influences on plant health and productivity. However, the relationship between the microbiota and the bacterial canker of tomato that is caused by Clavibacter michiganensis subsp. michiganensis (Cmm) is still unclear. In order to establish causal relationship between the microbiota and plant phenotypes, the microbial communities of 49 tomato samples (including 15 cultivars) with different canker symptoms collected from the greenhouse in Gansu province, China were investigated via 16S ribosomal RNA sequencing. Roots exhibited a strong filter effect in the process of root colonization by microorganisms according to the α-diversity and the separation patterns of the microbiota in bulk soil, rhizosphere and endosphere. In addition, the gradually decreased cluster extent from bulk soil to endosphere indicating the selective effect of tomato on microbiota. Although the composition of the microbiota is similar, the potential beneficial bacteria and functions (e.g. antibiotics production, pollution degradation, nutrition acquisition) enriched in the rhizosphere and endosphere of healthy samples compared to those in the diseased ones. Furthermore, more robust networks occurred in the rhizosphere and endosphere of healthy samples compared to the diseased ones. Our research provided substantial evidence that although the plant genotype is the dominant factor of phenotype, the rhizosphere and endosphere microbiota, as part of phytobiomes or holobiont, could contribute to the host's phenotype. This causal relationship between microbiota and host phenotypes could guide us in rationally designing novel synthetic communities (SynComs) for tomato canker biocontrol in the near future.

PSII-24 Towards a better understanding of the gut microbiome functions in the swine production: extensive cultivation of the swine gut microbiome from different growth stages

Abstract Substantial progress has been made in the culture-omics of the human gut microbiota. However, little is known about the culture-omics of the swine gut microbiota, despite recent reports of their significant roles in swine health and production. To fill this knowledge gap in research, we tested 52 bacterial cultivation methods with different media and gas combinations. Fresh fecal samples (0.2g/sample) were collected from three pigs at the end of four growth stages: lactation, nursery, growing and finishing and were mixed with a stomacher in 20 mL saline. Aliquots of 50 uL microbial suspensions were then spread onto different media plates and incubated under aerobic and anaerobic conditions at 37C for up to 5 days. An additional aliquot of each sample was subjected to direct DNA extraction as a positive control. Bacterial colonies from each plate were collected and DNA was extracted from these samples using the Powersoil DNA isolation kit and sequenced with an Illumina Miseq sequencer targeting the V4 region of the 16S rRNA gene. Sequences were analyzed with the Deblur algorithm in the QIIME2 package. A total of 378, 482, 565, and 555 bacterial features were observed from microbial solutions at the end of lactation, nursery, growing and finishing. Our culturing methods recovered 415, 675, 808, and 823 features correspondingly, representing 45.2%, 54.8%, 53.3%, and 56.4% of total features observed in microbial solutions. The top ten most easily cultured genus were Escherichia, Streptococcus, Lactobacillus, Megasphaera, Acidaminococcus, Bacillus, Mitsuokella, Enterococcus and Prevotella. Non-parametric permutational multivariate analysis of variance shows that the main factors driving the swine culture-omics included medium, age and oxygen condition. This study identifies the cultivable bacteria from fecal samples collected at different growth stages of pigs and provides a guidance to cultivate potential beneficial or pathogenic bacteria of interests and validate their functions in swine production.