Potential Beneficial Bacteria Research Articles

Melatonin promotes the recovery of apple plants after waterlogging by shaping the structure and function of the rhizosphere microbiome.

The dynamics of the physiological adaptability of plants and the rhizosphere soil environment after waterlogging remain unclear. Here we investigated the mechanisms regulating plant condition and shaping of the rhizosphere microbiome in a pot experiment. In the experiment, we added melatonin to waterlogged plants, which promoted waterlogging relief. The treatment significantly enhanced photosynthesis and the antioxidant capacity of apple plants, and significantly promoted nitrogen (N) utilization efficiency by upregulating genes related to N transport and metabolism. Multiperiod soil microbiome analysis showed the dynamic effects of melatonin on the diversity of the microbial community during waterlogging recovery. Random forest and linear regression analyses were used to screen for potential beneficial bacteria (e.g., Azoarcus, Pseudomonas and Nocardioides) specifically regulated by melatonin and revealed a positive correlation with soil nutrient levels and plant growth. Furthermore, metagenomic analyses revealed the regulatory effects of melatonin on genes involved in N cycling in soil. Melatonin positively contributed to the accumulation of plant dry weight by upregulating the expression of nifD and nifK (N fixation). In summary, melatonin positively regulates physiological functions in plants and the structure and function of the microbial community; it promoted the recovery of apple plants after waterlogging stress.

Temporal patterns of endophytic microbial heterogeneity across distinct ecological compartments within the Panax ginseng root system following deforestation for cultivation.

Alterations in the microbial community significantly impact the yield and quality of ginseng. Yet, the dynamics of microbial community shifts within the root endophytes of ginseng across varying cultivation periods remain inadequately understood. This study zeroes in on the microbial community variations within the xylem (M), phloem (R), and fibrous roots (X) of ginseng during the fourth (F4) and fifth (F5) years of cultivation, aiming to bridge this research gap. We assessed soil physicochemical properties, enzyme activities, and nine individual saponins, complemented by high-throughput sequencing techniques (16S rDNA and ITS) to determine their profiles. The results showed that cultivation years mainly affected the microbial diversity of endophytic bacteria in ginseng fibrous roots compartment: the ASVs number and α-diversity Chao1 index of bacteria and fungi in F5X compartment with higher cultivation years were significantly higher than those in F4X compartment with lower cultivation years. It is speculated that the changes of fibrous roots bacterial groups may be related to the regulation of amino acid metabolic pathway. Such as D-glutamine and D-glutamate metabolism D-glutamine, cysteine and methionine metabolism regulation. The dominant bacteria in ginseng root are Proteobacteria (relative abundance 52.07-80.35%), Cyanobacteria (1.97-42.52%) and Bacteroidota (1.11-5.08%). Firmicutes (1.28-3.76%). There were two dominant phyla: Ascomycota (60.10-93.71%) and Basidiomycota (2.25-30.57%). Endophytic fungi were more closely related to soil physicochemical properties and enzyme activities. AN, TK, OP, SWC and EC were the main driving factors of endophytic flora of ginseng root. Tetracladium decreased with the increase of cultivation years, and the decrease was more significant in phloem (F4R: 33.36%, F5R: 16.48%). The relative abundance of Bradyrhizobium, Agrobacterium and Bacillus in each ecological niche increased with the increase of cultivation years. The relative abundance of Bradyrhizobium and Agrobacterium in F5X increased by 8.35 and 9.29 times, respectively, and Bacillus in F5M increased by 5.57 times. We found a variety of potential beneficial bacteria and pathogen antagonists related to ginseng biomass and saponins, such as Bradyrhizobium, Agrobacterium, Bacillus and Exophiala, which have good potential for practical application and development.

Antibiotic Cocktail Effects on Intestinal Microbial Community, Barrier Function, and Immune Function in Early Broiler Chickens.

This study investigated the effects of an antibiotic cocktail on intestinal microbial composition, mechanical barrier structure, and immune functions in early broilers. One-day-old healthy male broiler chicks were treated with a broad-spectrum antibiotic cocktail (ABX; neomycin, ampicillin, metronidazole, vancomycin, and kanamycin, 0.5 g/L each) or not in drinking water for 7 and 14 days, respectively. Sequencing of 16S rRNA revealed that ABX treatment significantly reduced relative Firmicutes, unclassified Lachnospiraceae, unclassified Oscillospiraceae, Ruminococcus torques, and unclassified Ruminococcaceae abundance in the cecum and relative Firmicutes, Lactobacillus and Baccillus abundance in the ileum, but significantly increased richness (Chao and ACE indices) and relative Enterococcus abundance in the ileum and cecum along with relatively enriched Bacteroidetes, Proteobacteria, Cyanobacteria, and Enterococcus levels in the ileum following ABX treatment for 14 days. ABX treatment for 14 days also significantly decreased intestinal weight and length, along with villus height (VH) and crypt depth (CD) of the small intestine, and remarkably increased serum LPS, TNF-α, IFN-γ, and IgG levels, as well as intestinal mucosa DAO and MPO activity. Moreover, prolonged use of ABX significantly downregulated occludin, ZO-1, and mucin 2 gene expression, along with goblet cell numbers in the ileum. Additionally, chickens given ABX for 14 days had lower acetic acid, butyric acid, and isobutyric acid content in the cecum than the chickens treated with ABX for 7 days and untreated chickens. Spearman correlation analysis found that those decreased potential beneficial bacteria were positively correlated with gut health-related indices, while those increased potential pathogenic strains were positively correlated with gut inflammation and gut injury-related parameters. Taken together, prolonged ABX application increased antibiotic-resistant species abundance, induced gut microbiota dysbiosis, delayed intestinal morphological development, disrupted intestinal barrier function, and perturbed immune response in early chickens. This study provides a reliable lower-bacteria chicken model for further investigation of the function of certain beneficial bacteria in the gut by fecal microbiota transplantation into germ-free or antibiotic-treated chickens.

Toxicity of three microcystin variants on the histology, physiological and metabolism of hepatopancreas and intestinal microbiota of Litopenaeus vannamei

Microcystins (MCs) are prevalent harmful contaminants within shrimp aquaculture systems, exhibiting a diverse array of variants. Gut microbiota can engage in mutual interactions with the host through the gut-liver axis. In this study, the shrimp Litopenaeus vannamei were subjected to three different variants of MCs (LR, YR, RR) at a concentration of 1 μg/L each, and elucidated the alterations in both intestinal microbiota and hepatopancreas physiological homeostasis. The results showed that all three variants of MCs prompted histological alterations in the hepatopancreas, induced elevated levels of oxidative stress biomarkers (H2O2, T-SOD, and CAT), disturbed the transcription levels of immune-related genes (Crus, ALF, and Lys), along with an increase in apoptotic genes (Casp-3 and P53). Furthermore, the metabolic profiles of the hepatopancreas were perturbed, particularly in amino acid metabolism such as “lysine degradation” and “β-alanine metabolism”; the mTOR and FoxO signaling were also influenced, encompassing alterations in the transcription levels of related genes. Additionally, the alterations were observed in the intestinal microbiota's diversity and composition, particularly potential beneficial bacteria (Alloprevotella, Bacteroides, Collinsella, Faecalibacterium, and Prevotellaceae UCG-001), which exhibited a positive correlation with the metabolite berberine. These findings reveal that the three MCs variants can impact the health of the shrimp by interfering with the homeostasis of intestinal microbial and hepatopancreas physiology.

Defensive alteration of root exudate composition by grafting Prunus sp. onto resistant rootstock contributes to reducing crown gall disease.

Grafting is a traditional and significant strategy to suppress soil-borne diseases, such as the crown gall disease caused by tumorigenic Agrobacterium and Rhizobium. Root exudates and the rhizosphere microbiome play critical roles in controlling crown gall disease, but their roles in suppressing crown gall disease in grafted plants remain unclear. Here, disease-susceptible cherry rootstock 'Gisela 6' and disease-resistant cherry rootstock 'Haiying 1' were grafted onto each other or self-grafted. The effect of their root exudates on the soil microbiome composition and the abundance of pathogenic Agrobacterium were studied. Grafting onto the disease-resistant rootstock helped to reduce the abundance of pathogenic Agrobacterium, accompanied by altering root exudation, enriching potential beneficial bacteria, and changing soil function. Then, the composition of the root exudates from grafted plants was analyzed and the potential compounds responsible for decreasing pathogenic Agrobacterium abundance were identified. Based on quantitative measurement of the concentrations of the compounds and testing the impacts of supplied pure chemicals on abundance and chemotaxis of pathogenic Agrobacterium and potential beneficial bacteria, the decreased valine in root exudates of the plant grafted onto resistant rootstock was found to contribute to decreasing Agrobacterium abundance, enriching some potential beneficial bacteria and suppressing crown gall disease. This study provides insights into the mechanism whereby grafted plants suppress soil-borne disease.

Fucoxanthin Alleviates Dextran Sulfate Sodium-Induced Colitis and Gut Microbiota Dysbiosis in Mice.

The purpose of this study was to evaluate the preventive role and underlying mechanisms of fucoxanthin (Fx) on dextran sulfate sodium (DSS)-induced colitis in mice. The present data demonstrated that oral administration of Fx (50 and 200 mg/kg body weight/day) for 36 days significantly alleviated the severity of colitis in DSS-treated mice, as evidenced by attenuating body weight loss, bloody stool, diarrhea, shortened colon length, colonic epithelium distortion, a thin mucus layer, goblet cell depletion, damaged crypts, and extensive infiltration of inflammatory cells in the colonic mucosa. Additionally, Fx notably relieved DSS-induced intestinal epithelial barrier dysfunction via maintaining the tight junction function and preventing excessive apoptosis of colonic epithelial cells. Moreover, Fx effectively diminished colonic inflammation and oxidative stress in DSS-treated mice, and its mechanisms might be due to blunting the activation of NF-κB and NLRP3 inflammasome signaling pathways. Furthermore, Fx also modulates DSS-induced gut microbiota dysbiosis via recovering the richness and diversity of gut microbiota and reshaping the structure of gut microbiota, such as increasing the Firmicutes and Bacteroidota (F/B) ratio and elevating the relative abundance of some potential beneficial bacteria, including Lactobacillaceae and Lachnospiraceae. Overall, Fx might be developed as a promising functional ingredient to prevent colitis and maintain intestinal homeostasis.

Dapagliflozin ameliorates diabetes-induced spermatogenic dysfunction by modulating the adenosine metabolism along the gut microbiota-testis axis

Male infertility is one of the most common complications of diabetes mellitus (DM). Dapagliflozin is widely used to manage the type II DM. This study aimed to assess the dapagliflozin’s effects on the spermatogenesis by administering either dapagliflozin (Dapa) or vehicle (db) to male db/db mice, and using littermate male db/m mice as the control (Con). We further performed the integrative analyses of the cecal shotgun metagenomics, cecal/plasmatic/testicular metabolomics, and testicular proteomics. We found that dapagliflozin treatment significantly alleviated the diabetes-induced spermatogenic dysfunction by improving sperm quality, including the sperm concentration and sperm motility. The overall microbial composition was reshaped in Dapa mice and 13 species (such as Lachnospiraceae bacterium 3–1) were regarded as potential beneficial bacteria. Metabolites exhibited modified profiles, in which adenosine, cAMP, and 2′-deoxyinosine being notably altered in the cecum, plasma, and testis, respectively. Testicular protein expression patterns were similar between the Dapa and Con mice. In vivo results indicated that when compared with db group, dapagliflozin treatment alleviated apoptosis and oxidative stress in testis tissues by down-regulating 2′-deoxyinosine. This was further validated by in vitro experiments using GC-2 cells. Our findings support the potential use of dapagliflozin to prevent the diabetes-induced impaired sperm quality and to treat diabetic male infertility.

Endophytic bacterial communities in ungerminated and germinated seeds of commercial vegetables

Chile is a prominent seed exporter globally, but the seed microbiome of vegetables (46% of seeds) and its role in the early stages of plant growth have remained largely unexplored. Here, we employed DNA metabarcoding analysis to investigate the composition and putative functions of endophytic bacterial communities in ungerminated and germinated seeds of the commercial vegetables Apiaceae (parsley and carrot), Asteraceae (lettuce), Brassicaceae (cabbage and broccoli), and Solanaceae (tomato). Bacterial quantification showed 104 to 108 copies of the 16S rRNA gene per gram of ungerminated and germinated seeds. Alpha diversity analysis (e.g., Chao1, Shannon, and Simpson indices) did not indicate significant differences (Kruskal–Wallis test) between ungerminated and germinated seeds, except for Solanaceae. However, beta diversity (PCoA) analysis showed distinctions (Adonis test) between ungerminated and germinated seeds, except Apiaceae. Pseudomonadota and Bacillota were identified as the dominant and specialist taxa in both ungerminated and germinated seed samples. Chemoheterotrophy and fermentation were predicted as the main microbial functional groups in the endophytic bacterial community. Notably, a considerable number of the 143 isolated endophytic strains displayed plant growth-promoting traits (10 to 64%) and biocontrol activity (74% to 82%) against plant pathogens (Xanthomonas and Pseudomonas). This study revealed the high variability in the abundance, diversity, composition, and functionality of endophytic bacteria between ungerminated and germinated seeds in globally commercialized vegetables. Furthermore, potential beneficial endophytic bacteria contained in their seed microbiomes that may contribute to the microbiome of the early stages, development, growth and progeny of vegetables were found.

Use of black soldier fly (Hermetia illucens) larvae meal in diets for gilthead seabream juveniles: Effects on growth-related gene expression, intermediary metabolism, digestive enzymes, and gut microbiota modulation

A study was conducted to evaluate the effects of dietary inclusion of defatted Hermetia illucens larvae meal (HM) on the expression of growth-related genes, plasma metabolites, activity of intermediary metabolism enzymes, and gut microbiota modulation in gilthead seabream (Sparus aurata) juveniles. Four experimental diets were formulated (43% crude protein, 18% crude lipids) with increasing levels of defatted HM: 0 (HM0), 15 (HM15), 30 (HM30), and 45% (HM45) replacing fishmeal (included at 34% in the control diet) at 0, 22, 60, and 100%, respectively. Fish were fed these diets for 67 days. At the end of the trial, the expression of muscle growth hormone receptors (ghr1 and ghr2), insulin-like growth factors (igf1 and igf2), cathepsins (cts-a and cts-b), and myogenic determination factor 1 (myod1) were not affected, while a downregulation of myogenic determination factor 2 (myod2) and upregulation of myostatin (mstn) was observed with HM inclusion. Plasma metabolites profile was unaffected by diet composition, except for a linear decrease trend in total lipids. A linear increase of liver alanine aminotransferase (ALT) and glutamate dehydrogenase (GDH) activity and a linear decrease of glucose 6-phosphate dehydrogenase (G6PDH), malic enzyme (ME), and (FAS) activity were observed with HM inclusion. The activity of β-hydroxy acyl-CoA dehydrogenase (HOAD) followed a quadratic trend, being higher in fish fed with diet HM15 than in the control. Likewise, amylase, trypsin, and chymotrypsin activity were higher in the posterior intestine of fish fed with diet HM15. Digesta of fish fed the HM-containing diets showed an increase in the number of operational taxonomic units, microbial richness, and diversity. Conversely, a reduction in these indexes was observed in the mucosa. Among the identified bacteria, Firmicutes represented the predominant phyla. The inclusion of HM increased the abundance of Oceanobacillus, Lederbergia, Bacillus, and Corynebacterium in the digesta while Lactobacillus and Caldalkalibacillus abundance was reduced. Overall, total FM replacement with defatted HM had no major effects on plasma metabolites and muscle growth-related genes but induced a few differences in intermediary metabolism and digestive enzymes activity. HM inclusion improved gut digesta microbiota richness and diversity, promoting the growth of potential beneficial bacteria.

Evaluation of the Antimicrobial Activity of Phytochemicals from Tea and Agarwood Leaf Extracts against Isolated Bacteria from Poultry and Curd.

Antibiotic-resistant bacteria are becoming increasingly common, leading to a global health crisis. The effects of abusing antibiotics not only increase pathogenic resistance but also cause various diseases and syndromes. Gut microbiota contains many beneficial roles for health, while antibiotics kill both pathogens and gut microbiota which is considered one of the major side effects of antibiotics. In fact, new antibiotic compounds are needed in this urgent scenario; phytoremediation is the oldest but most effective method, and research on the antibacterial properties of several types of medicinal plants has already been conducted. Tea and agarwood plants are well known for their economic contribution in both beverage and cosmetic production, as well as for their medicinal value. In this study, tea and agarwood leaf extracts were analyzed for their antimicrobial activity against both pathogenic and beneficial bacteria. Fresh tea (Camellia sinensis) leaves were collected in three varieties, namely, BT-6 from Sylhet, BT-7 from Moulvibazar, and BT-8 from Habiganj; also, green tea (nonfermented tea), black tea (fully fermented tea), and agarwood (Aquilaria malaccensis) were collected from Sylhet region of Bangladesh. Unlike commercial antibiotics, which have side effects on probiotics (beneficiary bacteria), leaf extract activities were analyzed to check if they had positive effects on probiotics that can be found in the gastrointestinal tract as well as dairy products. Potential beneficiary bacteria, Lysinibacillus macroides strain SRU-001 (NCBI accession no. MW665108), and pathogenic bacteria, Aeromonas caviae strain YPLS-62 (NCBI accession no. MW666783), were isolated from the small intestine of poultry and curd, respectively. Tea and agarwood leaves (5 g powder/80 mL methanol) with solvents were kept for seven days at room temperature, and extracts were applied for antimicrobial assays by the disc diffusion assay against the isolated bacteria. 50 µL of each leaf extract was examined against 50 µL of each bacterial culture, where gentamicin was a control. After 24 hours of incubation, tea and agarwood leaf extracts showed an 11-15 mm zone of inhibition against pathogenic A. caviae, while only BT-8 showed 7 mm (disc diameter 6 mm) against probiotic L. macroides. However, compared to leaf extracts, gentamicin showed a 27 mm zone of inhibition against both L. macroides strain SRU-001 and A. caviae strain YPLS-62 bacteria. This research clearly indicates that gentamicin kills both pathogenic and beneficiary bacteria, while leaf extracts from tea and agarwood plants contain antimicrobial activity against only pathogenic A. caviae but no effects on probiotic L. macroides. This outcome indicates not only the potential therapeutic values of tea and agarwood leaves as antibiotics over commercial antibiotics but also the chance of having pathogens in curd and potential beneficial bacteria from the poultry small intestine.

Shifts in the coral microbiome in response to in situ experimental deoxygenation.

Marine hypoxia is a threat for corals but has remained understudied in tropical regions where coral reefs are abundant. Though microbial symbioses can alleviate the effects of ecological stress, we do not yet understand the taxonomic or functional response of the coral microbiome to hypoxia. In this study, we experimentally lowered oxygen levels around Siderastrea siderea and Agaricia lamarcki colonies in situ to observe changes in the coral microbiome in response to deoxygenation. Our results show that hypoxia triggers a stochastic change of the microbiome overall, with some bacterial families changing deterministically after just 48 hours of exposure. These families represent an increase in anaerobic and opportunistic taxa in the microbiomes of both coral species. Thus, marine deoxygenation destabilizes the coral microbiome and increases bacterial opportunism. This work provides novel and fundamental knowledge of the microbial response in coral during hypoxia and may provide insight into holobiont function during stress.

Natural Magnolol ameliorates coccidiosis infected with Eimeria tenella by affecting antioxidant, anti-inflammatory, and gut microbiota of chicks

Magnolol, a natural extract from magnolia officinalis, has received growing interest in its bioactive properties such as antioxidant, anti-inflammatory, and antibacterial activities. Nevertheless, there is little research on Magnolol in the treatment of parasitic infections currently. Eimeria tenella (E. tenella) infection causes damage to epithelial cells and cecal mucosa, resulting in increased intestinal permeability, which is pretty detrimental to the balance of the intestinal microenvironment. However, at present, in the treatment of chicken coccidiosis, the abuse of antibiotics is quite serious, which has brought losses and harms to the chicken farming industry that cannot be ignored. In this study, based on the excellent antioxidant and anti-inflammatory properties of Magnolol, we proved that it does have a desirable therapeutic potential on chicks infected with E. tenella. Actually, the results showed that the clinical symptoms of the chicks infected with E. tenella were relieved and their growth performance was restored by Magnolol treatment. Furthermore, Magnolol improved the antioxidant and anti-inflammatory properties of chicks. Meanwhile, the Magnolol reversed the imbalance of the intestinal microbiota of sick chicks, which recovered the diversity, promoted the potential beneficial bacteria, and inhabited the potential pathogenic bacteria. Overall, Magnolol may be an alternative to chemical drugs that are effective in treating E. tenella infections.

Biocontrol of tomato bacterial wilt by a combination of Bacillus subtilis GSJB-1210 and ningnanmycin

Bacillus subtilis GSJB-1210 with strong antagonism against Ralstonia solanacearum was combined with different bactericides to investigate its ability to mitigate tomato bacterial wilt. The control activity of six bactericides and GSJB-1210 against tomato bacterial wilt was determined via the bacteriostasis assay, and the concentration for 50% of maximal effect (EC50) value was calculated. The compatibility of the bactericide and GSJB-1210 was determined by ultraviolet spectrophotometry, and the compound scheme was determined by the Horsfall method. The EC50 of ningnanmycin was 3.66 mg/L and it had good biocompatibility with the GSJB-1210 strain. When ningnanmycin (3.66 mg/L) was combined with GSJB-1210 (1.0 × 108 CFU/mL) at a volume ratio of 4:6, the mitigation effect on tomato bacterial wilt reached 77.02%, which was significantly higher than that of the individual agents. To determine the impact of GSJB-1210 on the tomato rhizosphere microbial communities, the V3-V4 regions of 16S rRNA were amplified. The α- and β-diversity of tomato rhizosphere bacteria were increased and the relative abundance of potential beneficial bacteria at genus level (Pseudomonas and Burkholderia) was improved. Ningnanmycin can be combined with B. subtilis GSJB-1210 to control bacterial wilt, with a significant synergistic effect. Mixed application can reduce the required amount of chemical pesticides by half. This combination can be used as a novel biocontrol agent to attain sustainability in disease management due to its intense antibacterial activity and ability to transform the microbial community structure toward a healthy state.

A comparative study on effects of dietary three strains of lactic acid bacteria on the growth performance, immune responses, disease resistance and intestinal microbiota of Pacific white shrimp, Penaeus vannamei

The present study evaluated the growth performance, immune responses, disease resistance and intestinal microbiota in Penaeus vannamei fed diets supplemented with three strains of lactic acid bacteria (LAB). The basal diet (control, CO) supplemented with Lactobacillus plantarum W2 (LA), Pediococcus acidilactici Nj (PE), Enterococcus faecium LYB (EN) and florfenicol (FL), respectively, formed three LAB diets (1 × 1010 cfu kg−1) and a florfenicol diet (15 mg kg−1, positive control), were fed to shrimp for 42 days. Results indicated that specific growth rate, feed efficiency rate, and disease resistance of shrimp against Vibrio parahaemolyticus in the treatment groups were significantly improved versus the control (P < 0.05). Compared with the control, acid phosphatase, alkaline phosphatase, phenonoloxidase, total nitric oxide synthase, peroxidase, superoxide dismutase activities, total antioxidant capacity, and lysozyme content in the serum and the relative expression levels of SOD, LZM, proPO, LGBP, HSP70, Imd, Toll, Relish, TOR, 4E-BP, eIF4E1α and eIF4E2 genes in the hepatopancreas of LAB groups were enhanced to various extents. Intestinal microbiota analysis showed that the LA and EN groups significantly improved microbial diversity and richness, and LAB groups significantly altered intestinal microbial structure of shrimp. At the phylum level, the Verrucomicrobiota in the LA and PE groups, the Firmicutes in the EN group, and the Actinobacteriota in the PE and EN groups were enriched. Moreover, the CO group increased the proportion of potential pathogens (Vibrionaceae and Flavobacteriaceae). The potential pathogen (Vibrio) was reduced, and potential beneficial bacteria (Tenacibaculum, Ruegeria and Bdellovibrio) were enriched in response to dietary three strains of LAB. When the intestinal microbiota homeostasis of shrimp is considered, L. plantarum and E. faecium showed better effects than P. acidilactici. However, due to the concerns on the possible potential risks of E. faecium strains to human health, L. plantarum W2 is more suitable for application in aquaculture than E. faecium LYB. Considering collectively the above, Lactobacillus plantarum W2 could be applied as better probiotic to improve the growth performance, non-specific immunity, disease resistance and promote intestinal health of P. vannamei.

Evaluation of the effects of dietary mycotoxin-degrading adsorbent on juvenile turbot (Scophthalmus maximus L.) fed aflatoxin B1-contaminated diets

This eight-week feeding trial was conducted to investigate whether adding yeast cell wall extract mixed with bacteria producing mycotoxin-degrading enzymes (YEMDE) to an aflatoxin B1 (AFB1)-contaminated diet affects the growth performance, liver health, antioxidant status, and intestinal microbiota status of juvenile turbot. A total of 480 fish were divided into four groups (three replicate tanks each group): basal diet (Control); Control diet supplemented with 100 μg/kg AFB1 (AFB1); and AFB1 supplemented with 500 mg/kg or 1000 mg/kg YEMDE (AFY500 and AFY1000, respectively). The results showed that a minor variation in growth performance was observed among all groups (P > 0.05). Compared to the Control diet, the AFB1 diet significantly deceased the activities of triglyceride and catalase in the serum (P < 0.05); Compared to the Control diet, the AFB1 diet significantly increased the gene expression of cyp3a and apoptosis-related genes (p53, Bax, caspase3, caspase7 and caspase9) (P < 0.05), reduced the expression of catalase in the liver (P < 0.05); In addition, the AFB1 diet negatively changed the communities of intestinal microbiota and down-regulated the abundance of some potential probiotics Bifidobacterium and Stenotrophomonas (P < 0.05). However, both the AFY500 and AFY1000 diets markedly recovered the antioxidant capacity, inhibited the apoptosis of hepatocytes, and improved the communities of intestinal microbiota (P < 0.05). More positive effects were observed in the AFY1000 group. Compared to the AFB1 diet, the AFY1000 diet markedly increased the abundance of some potential beneficial bacteria in the intestine, such as Faecalibacterium and Lachnoanaerobaculum (P < 0.05). In conclusion, dietary YEMDE can effectively reduce the harmful impacts caused by AFB1 on turbot, and in particular, it had beneficial effects on the communities of intestinal microbiota. It is promising to use YEMDE to control AFB1 contamination in fish feeds.

Probiotics Mediate Intestinal Microbiome and Microbiota-Derived Metabolites Regulating the Growth and Immunity of Rainbow Trout (Oncorhynchus mykiss).

Emerging evidence confirms using probiotics in promoting growth and immunity of farmed fish. However, the molecular mechanisms underlying the host-microbiome interactions mediated by probiotics are not fully understood. In this study, we used rainbow trout (Oncorhynchus mykiss) as a model to investigate the internal mechanisms of host-microbiome interactions influenced by two probiotic bacteria, Bacillus velezensis and Lactobacillus sakei. We carried out experiments, including intestinal histology, serum physiology, and transcriptome and combined intestinal microbiome and metabolite profiling. Our results showed that both probiotics had a positive effect on growth, immunity, serum enzyme activity, the gut microbiome, and resistance to Aeromonas salmonicida in rainbow trout. Moreover, the intestinal microbial structure was reshaped with increased relative abundance of potential beneficial bacteria, such as Ruminococcus, Lachnospiraceae ucg-004, Leptotrichia, Bacillus coagulans, Porphyromonadaceae, Anaerococcus, and Photobacterium in the B. velezensis group and Paenibacillaceae and Eubacterium hallii in the L. sakei group. Metabolomic profiling and transcriptome analysis revealed upregulated metabolites as biomarkers, i.e., sucrose and l-malic acid in the B. velezensis group, and N-acetyl-l-phenylalanine, N-acetylneuraminic acid, and hydroxyproline in the L. sakei group. Additionally, a multiomics combined analysis illustrated significant positive correlations between the relative abundance of microflora, metabolites, and gene expression associated with immunity and growth. This study highlights the significant role of probiotics as effectors of intestinal microbial activity and shows that different probiotics can have a species-specific effect on the physiological regulation of the host. These findings contribute to a better understanding of the complex host-microbiome interactions in rainbow trout and may have implications for the use of probiotics in aquaculture. IMPORTANCE Probiotics are kinds of beneficial live microbes that impart beneficial effects on the host. Recent studies have proven that when given supplementation with probiotics, farmed fish showed improved disease prevention and growth promotion. However, the underlying metabolic functions regarding their involvement in regulating growth phenotypes, nutrient utilization, and immune response are not yet well understood in the aquaculture field. Given the active interactions between the gut microbiota and fish immune and growth performance, we conducted the supplementation experiments with the probiotics Bacillus velezensis and Lactobacillus sakei. The results showed that probiotics mediated intestinal microbiome- and microbiota-derived metabolites regulating the growth and immunity of fish, and different probiotics participated in the species-specific physiological regulation of the host. This study contributed to a better understanding of the functional interactions associated with host health and gut microbiota species.

Oral Administration of Bovine Milk-Derived Extracellular Vesicles Attenuates Cartilage Degeneration via Modulating Gut Microbiota in DMM-Induced Mice.

Osteoarthritis (OA) is the most common joint disease primarily characterized by cartilage degeneration. Milk-derived extracellular vesicles (mEVs) were reported to inhibit catabolic and inflammatory processes in the cartilage of OA patients. However, the current therapies target the advanced symptoms of OA, and it is significant to develop a novel strategy to inhibit the processes driving OA pathology. In this study, we investigated the therapeutic potential of mEVs in alleviating OA in vivo. The results revealed that mEVs ameliorated cartilage degeneration by increasing hyaline cartilage thickness, decreasing histological Osteoarthritis Research Society International (OARSI) scores, enhancing matrix synthesis, and reducing the expression of cartilage destructive enzymes in the destabilization of medial meniscus (DMM) mice. In addition, the disturbed gut microbiota in DMM mice was partially improved upon treatment with mEVs. It was observed that the pro-inflammatory bacteria (Proteobacteria) were reduced and the potential beneficial bacteria (Firmicutes, Ruminococcaceae, Akkermansiaceae) were increased. mEVs could alleviate the progression of OA by restoring matrix homeostasis and reshaping the gut microbiota. These findings suggested that mEVs might be a potential therapeutic dietary supplement for the treatment of OA.

Phenyl lactic acid alleviates Helicobacter pylori infection in C57BL/6 mice.

Helicobacter pylori is a gastric pathogen that colonizes approximately 50% of the world's population. Infection with H. pylori causes chronic inflammation and significantly increases the risk of developing duodenal and gastric ulcer disease and gastric cancer. In the present study, we found that phenyl lactic acid (PLA) derived from Lactobacillus plantarum ZJ316 (L. plantarum ZJ316) can directly inhibit the growth and urease activity of H. pylori in vitro with a minimum inhibitory concentration (MIC) of 2.5 mg mL-1. Moreover, PLA also caused a dramatic morphological transformation from a spiral to a coccoid form in H. pylori. In this work, we also analyzed the beneficial effects of PLA in mice. The results showed that PLA administration ameliorated H. pylori-induced gastric mucosal damage and significantly decreased lymphocyte infiltration and inflammatory cytokines, including interleukin-1β (IL-1β), interleukin 6 (IL-6), and interferon-γ (IFN-γ) by 59.93%, 63.95%, and 48.05%, respectively, but elevated the interleukin-10 (IL-10) and glutathione (GSH) levels. Furthermore, PLA administration improved microbiota diversity with increased Bacteroidetes abundance and decreased Proteobacteria abundance by 46.39% and 24.05%, respectively. PLA also significantly reduced the abundance of H. pylori but increased the relative abundances of potential beneficial bacteria, such as Faecalibacterium, Bifidobacterium, and Lactobacillus. These results demonstrated that PLA can ameliorate H. pylori-induced inflammation and support beneficial gut bacteria, providing a new perspective against H. pylori infection.

Leymus chinensis resists degraded soil stress by modulating root exudate components to attract beneficial microorganisms.

Phytoremediation is an effective means to improve degraded soil nutrients and soil structure. Here, we investigated the remediation effects of Leymus chinensis on the physicochemical properties and structure of degraded soil after 3 years of cultivation and explored the bacterial and fungal drivers in root exudates by metabolomics and high-throughput sequencing. The results showed that root exudates increased soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP) and soil aggregates, and organic acids in root exudates reduced pH and activated insoluble nutrients into forms that are available to plants, such as available nitrogen (NH4 +-N), nitrate nitrogen (NO3 --N), and available phosphorus (AP). The cultivation of L. chinensis restored the diversity and richness of soil microorganisms and recruited potential beneficial bacteria and fungi to resist degraded soil stress, and L. chinensis also regulated the abundances of organic acids, amino acids and fatty acids in root exudates to remediate degraded soils. Spearman correlation analysis indicated that glutaric acid, 3-hydroxybutyric acid and 4-methylcatechol in root exudates attracted Haliangium, Nitrospira and Mortierella to the rhizosphere and dispersed the relative abundance of the harmful microorganisms Fusicolla and Fusarium. Our results demonstrate that L. chinensis enhances soil fertility, improves soil structure, promotes microbial diversity and abundance, and recruits potentially beneficial microorganisms by modulating root exudate components.

Intercropping with Achyranthes bidentata alleviates Rehmannia glutinosa consecutive monoculture problem by reestablishing rhizosphere microenvironment.

The consecutive monoculture of Rehmannia glutinosa leads to a serious decrease in its production and quality. Previous studies have demonstrated that intercropping altered species diversity and rhizosphere microbial diversity. However, it remained unknown whether the impaired growth of monocultured plants could be restored by enhanced belowground interspecific interactions. In the present research, a continuous cropping facilitator Achyranthes bidentata was intercropped with R. glutinosa under pot conditions, and three different types of root barrier treatments were set, including that complete belowground interaction (N), partial belowground interaction (S), and no belowground interspecies interaction (M), with the aims to investigate belowground interaction and the underlying mechanism of alleviated replanting disease of R. glutinosa by intercropping with A. bidentata. The results showed that the land equivalent ratio (LER) of the two years was 1.17, and the system productivity index (SPI) increased by 16.92 % under S treatment, whereas no significant difference was found in N and M regimes. In the rhizosphere soil, intercropping systems had significantly increased the contents of sugars and malic acid in the soil of R. glutinosa, together with the content of organic matter and the invertase and urease activities. Meanwhile, intercropping increased the community diversity of fungi and bacteria, and the relative abundance of potential beneficial bacteria, such as Bacillus, Nitrospira, and Sphingomonas, despite the pathogenic Fusarium oxysporum was still the dominant genus in the rhizospheric soil of R. glutinosa under various treatments. The results of antagonism experiments and exogenous addition of specific bacteria showed that Bacillus spp. isolated from rhizosphere soil had a significant antagonistic effect on the pathogen of R. glutinosa. Taken together, our study indicated that the R. glutinosa//A. bidentata intercropping systems alleviate the consecutive monoculture problem of R. glutinosa by recruiting beneficial bacteria. The studies we have conducted have a positive effect on sustainable agricultural development.