Intestinal Bacterial Community Research Articles

Variation in the intestinal bacterial community composition under different water temperature culture conditions in largemouth bass (Micropterus salmoides).

This study aimed to investigate the impact of temperature on the intestinal microbiota of largemouth bass using 16S rRNA gene amplicon sequencing, focusing on the under-explored role of abiotic factors in shaping the gut microbial community. Five water temperature groups (20.0±0.2°C, 25.0±0.2°C, 28.0±0.2°C, 31.0±0.2°C, and 35.0±0.2°C) were established, each with three replicates. Significant variations in intestinal bacterial community composition were observed across these conditions. Elevated temperatures (31.0±0.2°C and 35.0±0.2°C) led to an increase in opportunistic pathogens such as OTU180 Vibrio and OTU2015 Vogesella (P<0.05). Species correlation network analysis showed a shift towards more positive relationships among intestinal microbes at higher temperatures (P<0.05). Ecological process analysis highlighted a greater role of ecological drift in microbial community structure at 31.0±0.2°C and 35.0±0.2°C (P<0.05). The study suggests that higher temperatures may predispose largemouth bass to opportunistic pathogens by altering their intestinal microbiota. Effective water temperature management is crucial for largemouth bass aquaculture to mitigate pathogen risks and maintain a balanced intestinal microbiota. This research provides critical insights into the temperature-microbiota relationship and offers practical recommendations for aquaculture practices.

Alteration of the Intestinal Bacterial Community in Rainbow Trout (Oncorhynchus mykiss): The Role of Animal, Plant, and Microbial Diets

Intestinal bacterial community in rainbow trout (Oncorhynchus mykiss) is increasingly recognized as important for aquaculture and fish health. This review summarizes the current knowledge on how various feed components, including animal- and plant-derived ingredients, as well as other feed additives, influence the gut microbiota of rainbow trout. Studies using 16S rRNA gene profiling and metagenomics demonstrate how dietary changes affect the composition, diversity, and functionality of bacterial communities. The findings suggest that there is no single optimal alternative ingredient for fish feeds, but emphasize that the ratio of natural components plays a more significant role in shaping the intestinal bacterial community of trout. This balance is crucial for maintaining diversity, functionality, and overall fish health, thereby promoting growth and disease resistance, while enhancing aquaculture efficiency. The use of popular animal protein derived from the larva of Hermetia illucens increases the amount of Pseudomonadota, but the chitin they contain can prevent the absorption of nutrients. Thus, the development of optimal feed formulas requires careful selection and balancing of various natural ingredients to sustain a healthy microbiota and overall fish well-being.

Comparative analysis of intestinal flora community composition and diversity of Anas platyrhynchos and Anser fabalis in the Yellow River Delta

Abstract The Yellow River Delta wetland is a habitat for wintering waterfowl, where mallard (Anas platyrhynchos) and tundra bean goose (Anser fabalis) are commonly observed. Although the intestinal flora plays a pivotal role in maintaining host health and promoting nutrient absorption, it remains unclear whether the same overwintering habitat and challenging feeding conditions specifically affect the composition and diversity of intestinal flora in both species. Here, high-throughput sequencing was used to compare the intestinal bacterial communities of mallard and tundra bean goose from the same region. There was no significant difference in alpha diversity and beta diversity between the two species. Firmicutes and Proteobacteria were the two predominant phyla, accounting for more than 50.00% of the total. They enhanced the nutrient absorption and metabolic efficiency during overwintering. Catellicoccus was the most dominant genus in the intestinal flora of tundra bean goose, accounting for 33.91%, whereas Clostridium sensu stricto 1 was the most dominant genus in mallard, accounting for 7.34%. This difference is considered to be related to the feeding habits of these two species. No significant differences in the structure and diversity of intestinal bacterial communities were observed between mallard and tundra bean goose, and the similarity of intestinal flora between them was high. This study deepens our understanding of the intestinal flora of two coexisting species with different dietary preferences in the Yellow River Delta. It also lays the foundation for waterfowl disease prevention in this area, carrying significant scientific and practical implications for biodiversity and ecosystem conservation.

Comparison of distinct gut bacterial communities in different stage of prediapause and nondiapause larvae in Loxostege sticticalis.

Symbiotic microorganisms in insects regulate multiple physiological functions, widely participating in nutrient metabolism, immune regulation, and crucial regulatory roles in development. However, little is known about how microbial factors might respond to the preparation of insect diapause. The gut bacterial communities of Loxostege sticticalis larvae induced at different photoperiod of long (LD16:8, nondiapause) and short (LD12:12, prediapause) daylength were compared, by 16S rRNA Illumina MiSeq. A total number of 42 phylum, 78 classes, 191 orders, 286 families, 495 genera, and 424 species were identified in the intestinal bacterial community of L. sticticalis larvae. Alpha diversity and beta diversity analyses revealed significant differences between nondiapause and prediapause larvae. In non-diapause larvae, the dominant intestinal bacteria were Firmicutes and Proteobacteria. In specific, in 3rd and 4th instar larvae, the main intestinal bacteria were Staphylococcus, while in 5th instar, it was JC017. For the prediapause larvae, the dominant phylum in 3rd instar larvae was Firmicutes, with the dominant genus of Staphylococcus, while in 4th and 5th instar larvae was Bacteroidota, with the dominant genus 4th instar was Staphylococcus, and in 5th instar was JC017. KEGG functional prediction analysis revealed that functional bacterial groups involved in metabolism had the highest abundance values. Specifically, the amino acid metabolism of metabolism-related functional genes in the 3rd instar prediapause larvae was significantly lower than that in the 4th and 5th instar prediapause larvae and the non-diapause treatment. However, the carbohydrate metabolism in 3rd instar prediapause larvae was significantly higher than that in 4th and 5th instar prediapause larvae and non-diapause treatments. The dominant bacterial phylum in the prediapause larvae at different stages of L. sticticalis was varied, and there were significant differences in community diversity and richness. These results suggest a complex interaction between the hosts' physiological state and its gut microbiota, indicating that bacterial communities may assist insects in adapting to diapause preparation by regulating their metabolic levels. This study lays the foundation for further understanding the physiological mechanisms by which intestinal microorganisms regulate overwintering dormancy in the L. sticticalis.

Insights into the intestinal microbiota of Exopalaemon annandalei and Exopalaemon carinicauda in the Yangtze River estuary.

The gut microbiota plays a crucial role in food webs, carbon cycling, and related elements. Exopalaemon annandalei and Exopalaemon carinicauda are two important forage species in the Yangtze River estuary with extremely similar living habits and morphological characteristics. Exploring the microorganisms in the guts of these two shrimp species can help us understand the survival status of forage species and gut microbiota in the Yangtze River estuary. Therefore, this study analyzed the similarities and differences in the intestinal flora of E. annandalei and E. carinicauda through high-throughput sequencing of 16S rRNA gene amplicons. The results showed that the dominant bacteria in the intestinal flora of E. annandalei and E. carinicauda at the phylum level were Proteobacteria and Firmicutes, respectively. At the genus level, the intestinal flora had higher concentrations of Psychrobacter, Bacillus, Pseudomonas, Acinetobacter, and Macrococcus. In both shrimp species, the contents of Acinetobacter and Macrococcus were higher in spring than in winter. The most important potential functions of the intestinal microbiota were amino acid metabolism and purine metabolism. Additionally, the functions of metabolism and diseases in the intestinal microbiota of E. annandalei were greatly influenced by the season. Furthermore, the experimental results indicated that a lower ratio of Firmicutes to Bacteroidetes was associated with a larger body weight in shrimp. Overall, this study provides a theoretical reference for understanding the intestinal bacterial community of shrimp in estuaries and the healthy cultivation of E. annandalei and E. carinicauda.

The Composition and Function of Intestinal Microbiota Were Altered in Farmed Bullfrog Tadpoles (Aquarana catesbeiana) during Metamorphosis

The bullfrog Aquarana catesbeiana is one of the main farmed frog species in China, with a low overall survival of farmed bullfrogs from hatching to harvest since bullfrog tadpoles are fragile during the metamorphosis period. The intestinal bacterial community can play crucial roles in animal development; however, little is known about the alteration of the gut microbial community of A. catesbeiana during metamorphosis. The present study used 16S rRNA amplicon sequencing to investigate the intestinal bacterial community in A. catesbeiana at four distinct developmental stages. Moreover, we determined the bullfrog’s body morphological parameters and the intestine histology at different developmental stages. The results showed a reduction in the total length and snout–vent length of A. catesbeiana during metamorphosis. The intestinal microbial composition of A. catesbeiana exhibited variation throughout the process of metamorphosis. The terrestrial stage showed shifts in the bacterial composition compared to the aquatic stages, including a reduction in Bacteroidetes and an increase in Firmicutes. Furthermore, the presence of Prevotella, Bifidobacterium, Leucobacter, Corynebacterium, Bulleidia, Dorea, Robinsoniella, and Clostridium in A. catesbeiana metamorphosis appears to be mainly related to the host’s epithelial cells’ height and total body mass. The results indicated that the intestinal microbial composition changed with the bullfrog–tadpole metamorphosis. The genera of Prevotella, Bifidobacterium, Leucobacter, Corynebacterium, Bulleidia, Dorea, Robinsoniella, and Clostridium might be potential probiotics.

Application of PCR-Based Techniques for the Identification of Genetic Fingerprint Diversity of Dominant Bacteria in Fecal Samples of Children with Diarrhea in Vietnam.

In Vietnam, diarrhea, especially persistent diarrhea, is one of the most common diseases in children, while a significant proportion of cases are negative with pathogens; thus, there is an urgent need to understand gut bacterial dysbiosis. In this study, bacteria in the fecal samples of five healthy and ten diarrheal children were separated from other residues, then adopted to extract their metagenomic DNA for evaluating their diversity based on V3 and V6-V8 regions and the 16S rRNA gene by PCR-RFLP and PCR-DGGE. As a result, bacterial metagenomic DNAs with high quality, quantity and diversity were successfully extracted using a GeneJET kit and a chemical protocol. A sequence analysis of 73 representative DNA fragments from gels indicated a remarkable bacterial dysbiosis in all groups of diarrhea. Viral diarrhea was characterized by extremely reduced bacterial diversity with the blossom of Bifidobacterium and Streptococcus. Streptococcus was also the most abundant in persistent diarrhea. Beneficial bacteria that may play a role in the self- rebalance in intestinal bacterial communities, such as Bifidobacterium, Lactobacillus, and Enterococcus, were seen in all diarrheal groups, while Bacteroides and Akkermansia muciniphila were seen in the healthy group but absent in the diarrheal groups. This study provides additional evidence for a relationship between intestinal bacterial dysbiosis and diarrhea in children, emphasizing an increase in Streptococcus.

Effects of Sophora flavescens dietary supplementation on the growth performance, haematological indices, and intestinal bacterial community of Oreochromis niloticus.

Sophora flavescens is considered to be of various medicinal and economic importance. Previous studies have shown that it has antibacterial, antioxidant, and immune-enhancing functions. To explore the full potential of S. flavescens in fish feed development, we investigated the effects of different levels of S. flavescens added to the diet on the growth performance, haematological indices, and the intestinal bacterial community of Nile tilapia (Oreochromis niloticus). The feeding trial lasted for 56 days, and the initial weight of the fish was 40.00 ± 5.00 g. Nile tilapia were randomly divided into six groups: a control group (CN) and five S. flavescens supplementation groups (0.02%, 0.04%, 0.08%, 0.16%, and 0.3% [w/w] of S. flavescens in diet). The growth performance of fish increased first and then decreased with the increase of S. flavescens supplemental level. Compared with other experimental groups, the growth performance of fish supplemented with 0.08% S. flavescens was significantly improved (p < 0.05). Haematological indices exhibited that erythrocyte (RBC), along with leucocyte (WBC) indices, exhibited a secondary trend of increasing and then decreasing with the increase of S. flavescens, reaching the highest level at 0.08% (p < 0.05). However, mean corpuscular volume (MCV), mean corpuscular haemoglobin (MCH), and mean corpuscular haemoglobin concentration (MCHC) exhibited a secondary trend of first decreasing and then increasing with the increase of S. flavescens and reached the lowest value at 0.08% (p < 0.05). Compared with the CN, alkaline phosphatase (AKP) significantly decreased and changed when the additional amount of S. flavescens was 0.04% in each treatment group (p < 0.05). In another way, the gut microbial profiles revealed that Bacteroides dominated the gut communities, and compared with the control group, two uncultured bacteria were suppressed. In addition, when the supplemental level of S. flavescens was more significant than 0.04%, the proliferation of Arcobacter cryaerophilus, Solibacillus silvestris, and Escherichia sp. in the gut of Nile tilapia was promoted. The results revealed that S. flavescens, as an additive to the Nile tilapia diet with levels ranging from 0.04% to 0.08%, can enhance the growth performance and immunity and promote the proliferation of intestinal beneficial bacteria of Nile tilapia.

Effects of settleable versus unsettled biofloc removal strategy on aquaculture system performance and microbial community

The management of biofloc quality and quantity is critical in biofloc-based aquaculture systems. This research explores the effects of the selective removal of settleable and unsettled bioflocs on biofloc quality, fish growth, nitrogen transformation and bacterial community dynamics in these systems. Nile tilapia (Oreochromis niloticus) was reared at a density of 2.7 kg/m3 in nine 250-L conical breeding tanks over a 47-day period. Systems where unsettled bioflocs were removed outperformed others, achieving a 26 % higher weight gain in tilapia and maintaining more stable and lower levels of total ammonia (0.45 mg-N/L) and nitrite (0.35 mg-N/L). Additionally, these systems maintained a healthier bacterial environment, evidenced by a 27 % increase in beneficial bacterial populations and a 30 % reduction in harmful bacteria. Conversely, tanks removing settleable bioflocs showed a 19 % higher microbial diversity but experienced fluctuations in nitrogen levels. Notably, the intestinal bacterial community in tilapia from the unsettled biofloc group closely mirrored (87 % similarity) that of their corresponding bioflocs, with significant pathogenic symptoms observed (p < 0.05). These findings suggest the importance of implementing precise biofloc management strategies, highlighting that the selective removal of unsettled bioflocs enhances fish growth and improves overall system health. Future research should explore the mechanistic relationships between settleable and unsettled bioflocs to refine management strategies that bolster sustainability and economic benefits.

Gut microbiome and plasma lipidome analysis reveals a specific impact of Clostridioides difficile infection on intestinal bacterial communities and sterol metabolism.

There is increasing evidence about the influence the changes in microbiota and its metabolism has on numerous diseases and infections such as Clostridioides difficile infection (CDI). The knowledge of these changes at local and systemic levels can help us manage this infection to avoid recurrences and apply the best therapies, such as fecal microbiota transfer (FMT). This study shows a better restoration of the gut in FMT-treated patients than in antibiotic-treated patients, resembling healthy controls and showing increased levels of cholesterol-reducing bacteria. Furthermore, it evidences the CDI impact on plasma lipidome. We observed in CDI patients a global depletion in circulating lipids, particularly cholesteryl esters, and a specific decrease in linoleic acid-containing lipids, an essential fatty acid. Our observations could impact CDI management because the lipid content was only partially recovered after treatment, suggesting that continued nutritional support, aiming to restore healthy lipid levels, could be essential for a full recovery.

Ammonia nitrogen stress induces dysbiosis of the intestinal bacterial community and facilitates the enrichment of pathogenic bacteria in intestines of shrimp

Environmental stress can disrupt the intestinal microbiota of aquatic animals, thereby impacting their health status. In this study, we aimed to elucidate the dynamic changes in the bacterial community within shrimp intestines under short-term ammonia nitrogen stress and investigate the subsequent ecological risks associated with it. Our findings revealed a significant reduction in the Chao1 diversity index within shrimp intestines of the ammonia nitrogen stress group compared to the Control group. Furthermore, distinct disparities in the bacterial community structures were observed between the two groups at 72 h and 120 h post-stress. Additionally, ammonia nitrogen stress significantly altered the abundances of specific bacterial taxa within shrimp intestines. Specifically, the abundance of Bacillus subtilis increased while that of Lactococcus garvieae decreased in the intestine under stress at 72 h. Additionally, Roseivivax jejudonensis exhibited an increase, whereas uncultured_o_Saccharimonadales and Hyphomicrobium sp. showed a decrease at 120 h. Notably, opportunistic pathogens such as Vibrio parahaemolyticus experienced a significant increase at 72 h post-stress, potentially due to a substantial contribution from stochastic processes in shaping the assembly of the intestinal community. Additionally, the intestinal bacterial community of shrimp displayed a noticeable decrease in complexity of bacterial co-association networks under stress conditions. Thus, short-term exposure to ammonia nitrogen disrupts the integrity of shrimp's intestinal community, indicating potential ecological risks within their microhabitat. Confirmatively, we conducted the immersion challenge experiment of V. parahaemolyticus on shrimp post community disturbance under stress, and observed a significantly higher copy numbers of V. parahaemolyticus in host intestines of stressed compared to control shrimp. These findings can provide novel insights into the interactions among ammonia nitrogen stress, intestinal microbiota and host health of aquatic animals, and guide the practices for shrimp healthy culture.

The effects of kelp powder and fucoidan on the intestinal digestive capacity, immune response, and bacterial community structure composition of large yellow croakers (Larimichthys crocea)

Feed terrestrial components can induce intestinal stress in fish, affecting their overall health and growth. Recent studies suggest that seaweed products may improve fish intestinal health. In this experiment, three types of feed were prepared: a basic diet (C group), a diet with 0.2 % fucoidan (F group), and a diet with 3 % kelp powder (K group). These diets were fed to large yellow croaker (Larimichthys crocea) over an 8-week period. Each feed was randomly assigned to three seawater cages (4.0 m × 4.0 m × 5.0 m) containing 700 fish per cage. The study assessed changes in growth and intestinal health, including intestinal tissue morphology, digestive enzyme activities, expression of immune-related genes, and bacterial community structure. Results showed that incorporating seaweed products into the diet improved the growth and quality traits of large yellow croakers and significantly enhanced their intestinal digestive capacity (P < 0.05). Specifically, the 0.2 % fucoidan diet significantly increased the intestinal villus length and the activities of digestive enzymes such as trypsin, lipase, and α-amylase (P < 0.05). The 3 % kelp powder diet significantly enhanced the intestinal crypt depth and the activities of trypsin and lipase (P < 0.05). Both seaweed additives significantly enhanced intestinal health by mitigating inflammatory factors. Notably, the control group's biomarkers indicated a high presence of potential pathogenic bacteria, such as Streptococcus, Pseudomonas, Enterococcus, Herbaspirillum, Neisseria, Haemophilus, and Stenotrophomonas. After the addition of seaweed additives, these bacteria were no longer the indicator bacteria, while the abundance of beneficial bacteria like Ligilactobacillus and Lactobacillus increased. Significant reductions in the expression of inflammatory factors (e.g., il-6, tnf-α, ifn-γ in the fucoidan group and il-8 in the kelp powder group) further supported these findings. Our findings suggested that both seaweed additives helped balance intestinal microbial communities and reduce bacterial antigen load. Considering the effects, costs, manufacturing, and nutrition, adding 3 % kelp powder to the feed of large yellow croaker might be preferable. This study substantiated the beneficial effects of seaweed on the aquaculture of large yellow croaker, particularly in improving intestinal health. These findings advocated for its wider and more scientifically validated use in fish farming practices.

Gut Microbiota Mediate Plutella xylostella Susceptibility to Bt Cry1Ac Protoxin and Exopolysaccharides.

Exopolysaccharides (EPSs) are carbohydrate polymers that are synthesized and secreted into the extracellular during the growth of microorganisms. Bacillus thuringiensis (Bt) is a type of entomopathogenic bacterium, that produces various insecticidal proteins and EPSs. In our previous study, the EPSs produced by Bt strains were first found to enhance the toxicity of insecticidal crystal proteins against Plutella xylostella. However, the response of the intestinal bacterial communities of P. xylostella under the action of EPSs is still unelucidated. In this study, 16S rRNA amplicon sequencing was used to characterize the intestinal bacterial communities in P. xylostella treated with EPSs alone, Cry1Ac protoxin alone, and both the Cry1Ac protoxin and EPSs. Compared with the control group, alpha diversity indices, the Chao1 and ACE indices were significantly altered after treatment with EPSs alone, and no significant difference was observed between the groups treated with Cry1Ac protoxin alone and Cry1Ac protoxin + EPSs. However, compared with the gut bacterial community feeding on Cry1Ac protoxin alone, the relative abundance of 31 genera was significantly changed in the group treated with Cry1Ac protoxin and EPSs. The intestinal bacteria, through the oral of Cry1Ac protoxin and EPSs, significantly enhanced the toxicity of the Cry1Ac protoxin towards the axenic P. xylostella. In addition, the relative abundance of the 16S rRNA gene in the chloroplasts of Brassica campestris decreased after adding EPSs. Taken together, these results show the vital contribution of the gut microbiota to the Bt strain-killing activity, providing new insights into the mechanism of the synergistic insecticidal activity of Bt proteins and EPSs.

Genistein alleviates dextran sulfate sodium-induced colitis in mice through modulation of intestinal microbiota and macrophage polarization.

Ulcerative colitis (UC) is a colonic immune system disorder, manifested with long duration and easy relapse. Genistein has been reported to possess various biological activities. However, it remains unclear whether genistein can ameliorate UC by modulating the homeostasis of the intestinal bacterial community. The dextran sodium sulfate (DSS)-induced UC mice were administrated with genistein (20mg/kg/day) or genistein (40mg/kg/day) for ten days. The general physical condition of the mice was monitored. After sacrifice, the changes in colon length and colonic pathological morphology were observed. The expression of intestinal barrier proteins, inflammatory cytokines, and macrophage markers in the colon was detected. The composition and metabolic products of the intestinal microbiota were analyzed. Genistein treatment visibly improved body weight change and disease activity index in DSS-induced mice. Genistein treatment ameliorated colonic pathological alterations and promoted the expression of mucin-2 and tight junction proteins. Genistein administration inhibited myeloperoxidase activity and colonic inflammatory cytokines. Furthermore, genistein administration improved the structure of the intestinal microbial community, promoted the production of short-chain fatty acids, and modulated macrophage polarization. These results revealed that genistein mediated macrophage polarization balance by improving intestinal microbiota and its metabolites, thereby alleviating DSS-induced colitis.

Xylooligosaccharides alleviate the carbohydrate-enriched diet-induced intestinal barrier dysfunction in carp Megalobrama amblycephala by promoting intestinal development, immunity and gut microbiota

To date, although the high-carbohydrate (HC) feed has been extensively adopted in the aquaculture industry, its effects on the intestinal function and development of aquatic animals still remain unclear. In addition, the corresponding nutritional intervention is still barely reported. This study aimed to evaluate the influence of xylooligosaccharides (XOS) on the intestinal health of Megalobrama amblycephala subjected to a HC feeding. Fish (average weight: 44.55 ± 0.15 g) were randomly offered 3 diets, including a control one (29 % carbohydrate), a HC one (41 % carbohydrate), and a XOS supplemented one (HC + 1.0 % XOS, HCX) respectively for 12 weeks. The HC feeding caused morphological abnormalities of intestine, an increased intestinal permeability, and the intestinal immunosuppression, all of which were markedly reversed by XOS administration. In addition, compared with the HC group, HCX feeding remarkably promoted the intestinal activities of digestive and brush border enzymes, and the expressions of cell proliferation-related proteins (Wnt10b and Cyclin D1). The 16s rDNA sequencing also revealed that XOS administration increased the abundance of beneficial bacteria, and decreased that of pathogenic ones. In conclusion, dietary supplementation of XOS improved the intestinal histomorphology, barrier function, cell proliferation and bacterial communities of carbohydrate-overloaded fish Megalobrama amblycephala.

Remodeling of intestinal bacterial community and metabolome of Dezhou donkey induced by corn silage

Corn silage can usually improve the growth performance and the meat quality of ruminants, and subsequently increase the economic benefits of farming. However, little is known about the effects of corn silage on donkeys. This experiment investigated the effects of corn silage on the weight gain, gut microbiota and metabolites of Dezhou donkeys. A total of 24 Dezhou donkeys, sourced from the same farm and exhibiting similar age and average body weight, were utilized in this experiment. The donkeys were allocated into two groups: a control group receiving a basic diet and a test group receiving a basic diet supplemented with 30% corn silage. Each group comprised 12 donkeys, evenly distributed by sex (6 males and 6 females). The experiment lasted for 100 days. Results showed that dietary supplementation with corn silage significantly (P < 0.05) improved the weight gain of Dezhou donkeys at the end of the experiment. And the supplementation of corn silage in the diet significantly altered the bacterial community composition and metabolome in the feces of the donkeys. Notably, the relative abundance ratio of Bacteroidetes to Firmicutes was 0.76 in the control group compared to 0.96 in the test group. Furthermore, members of the Bacteroidetes and Firmicutes phyla were associated with differentiated metabolites enriched in the arachidonic acid metabolism and pentose and glucuronate interconversion pathways, both of which have been reported to be related to animal growth. Specifically, Bacteroidia exhibited statistically (P < 0.05) positive correlations with 15S-HpETE, while Bacilli demonstrated statistically (P < 0.05) negative correlations with D-Xylulose. The findings of this study can advance our mechanistic understanding of the remodeling of intestinal microbiota and metabolome induced by corn silage, as well as their relationships with the growth performance of Dezhou donkeys, which in turn favor the improvement in nutrition of Dezhou donkeys.

Cultivation of earthworms and analysis of associated bacterial communities during earthworms’ growth using two types of agricultural wastes

Earthworm cultivation can effectively promote the resource utilization of agricultural waste. The efficient utilization of agricultural waste by earthworms mainly depends on the microbial communities in the guts. This study used silkworm excrement and cow manure as substrates for earthworm cultivation and investigated the associated bacterial communities during earthworms’ growth. The survival rate of earthworms remained above 89% after 21 days of feeding with the two substrates. Proteobacteria, Actinobacteria, and Firmicutes constituted the predominant bacterial communities in earthworm growth, accounting for over 81% of the relative abundance in both guts and vermicompost. The bacteria richness and diversity in the foregut and midgut of earthworm were lower than those in the hindgut. The prediction function of intestinal bacterial communities of earthworms cultured with two substrates mainly involved biosynthesis, decomposition and energy production.

The Potential Implications of Sex-Specific Differences in the Intestinal Bacteria of the Overwintering Wolf Spider Pardosa astrigera (Araneae: Lycosidae).

Gut microbiota can promote the resistance of host arthropods to low-temperature stress. Female Pardosa astrigera have a lower anti-freeze compound level and weaker resistance to cold temperatures than the males in winter, which implies that their intestinal bacteria may be different during overwintering. This study primarily compared the intestinal bacterial communities between the two sexes of P. astrigera in a temperate region using 16S rRNA gene sequencing. Our findings indicated that the Chao1 and Shannon indices of intestinal bacteria in females were significantly higher than those in males, while the Simpson index in females was significantly lower than that in males. The male intestinal bacterial community was characterized by Proteobacteria and Actinobacteriota at the phylum level and by Pseudomonas and Rhodococcus at the genus level, with total relative abundances of 89.58% and 85.22%, respectively, which were also significantly higher than those in females, whose total relative abundances were 47.49% and 43.68%, respectively. In contrast, the total relative abundances of Bacteroidota and Firmicutes were significantly lower in males (4.26% and 4.75%, respectively) than in females (26.25% and 22.31%, respectively). Noteworthy divergences in bacterial communities were also found through an LEfSe analysis between females and males. Additionally, the results of the PICRUSt2 analysis showed that six out of eleven level-2 pathways related to key metabolic functions were significantly (or marginally significantly) higher in females than males, and five other level-2 pathways were significantly (or marginally significantly) lower in females than males. Our results imply that significant gender differences exist in intestinal bacterial communities of overwintering P. astrigera. We suggest that Pseudomonas versuta (belonging to Proteobacteria) and Rhodococcus erythropolis (belonging to Actinobacteriota) may have the potential to play key roles in overwintering P. astrigera.

Synergistic impacts of antibiotics and heavy metals on Hermetia illucens: Unveiling dynamics in larval gut bacterial communities and microbial metabolites

Hermetia illucens larvae showcases remarkable bioremediation capabilities for both antibiotics and heavy metal contaminants. However, the distinctions in larval intestinal microbiota arising from the single and combined effects of antibiotics and heavy metals remain poorly elucidated. In this study, we delved into the details of larval intestinal bacterial communities and microbial metabolites when exposed to single and combined contaminants of oxytetracycline (OTC) and hexavalent chromium (Cr(VI)). After conversion, single contaminant-spiked substrate showed 75.5% of OTC degradation and 95.2% of Cr(VI) reductiuon, while combined contaminant-spiked substrate exhibited 71.3% of OTC degradation and 93.4% of Cr(VI) reductiuon. Single and combined effects led to differences in intestinal bacterial communities, mainly reflected in the genera of Enterococcus, Pseudogracilibacillus, Gracilibacillus, Wohlfahrtiimonas, Sporosarcina, Lysinibacillus, and Myroide. Moreover, these effects also induced differences across various categories of microbial metabolites, which categorized into amino acid and its metabolites, benzene and substituted derivatives, carbohydrates and its metabolites, heterocyclic compounds, hormones and hormone-related compounds, nucleotide and its metabolites, and organic acid and its derivatives. In particular, the differences induced OTC was greater than that of Cr(VI), and combined effects increased the complexity of microbial metabolism compared to that of single contaminant. Correlation analysis indicated that the bacterial genera, Preudogracilibacillus, Enterococcus, Sporosarcina, Lysinibacillus, Wohlfahrtiimonas, Ignatzschineria, and Fusobacterium exhibited significant correlation with significant differential metabolites, these might be used as indicators for the resistance and bioremediation of OTC and Cr(VI) contaminants. These findings are conducive to further understanding that the metabolism of intestinal microbiota determines the resistance of Hermetia illucens to antibiotics and heavy metals.

A shared group of bacterial taxa in the duodenal microbiota of undernourished Pakistani children with environmental enteric dysfunction.

Environmental enteric dysfunction (EED) is a subclinical syndrome of altered small intestinal function postulated to be an important contributor to childhood undernutrition. The role of small intestinal bacterial communities in the pathophysiology of EED is poorly defined due to a paucity of studies where there has been a direct collection of small intestinal samples from undernourished children. Sixty-three members of a Pakistani cohort identified as being acutely malnourished between 3 and 6 months of age and whose wasting (weight-for-length Z-score [WLZ]) failed to improve after a 2-month nutritional intervention underwent esophagogastroduodenoscopy (EGD). Paired duodenal luminal aspirates and duodenal mucosal biopsies were obtained from 43 children. Duodenal microbiota composition was characterized by sequencing bacterial 16S rRNA gene amplicons. Levels of bacterial taxa (amplicon sequence variants [ASVs]) were referenced to anthropometric indices, histopathologic severity in biopsies, expression of selected genes in the duodenal mucosa, and fecal levels of an immunoinflammatory biomarker (lipocalin-2). A "core" group of eight bacterial ASVs was present in the duodenal samples of 69% of participants. Streptococcus anginosus was the most prevalent, followed by Streptococcus sp., Gemella haemolysans, Streptococcus australis, Granulicatella elegans, Granulicatella adiacens, and Abiotrophia defectiva. At the time of EGD, none of the core taxa were significantly correlated with WLZ. Statistically significant correlations were documented between the abundances of Granulicatella elegans and Granulicatella adiacens and the expression of duodenal mucosal genes involved in immune responses (dual oxidase maturation factor 2, serum amyloid A, and granzyme H). These results suggest that a potential role for members of the oral microbiota in pathogenesis, notably Streptococcus, Gemella, and Granulicatella species, warrants further investigation.IMPORTANCEUndernutrition among women and children is a pressing global health problem. Environmental enteric dysfunction (EED) is a disease of the small intestine (SI) associated with impaired gut mucosal barrier function and reduced capacity for nutrient absorption. The cause of EED is ill-defined. One emerging hypothesis is that alterations in the SI microbiota contribute to EED. We performed a culture-independent analysis of the SI microbiota of a cohort of Pakistani children with undernutrition who had failed a standard nutritional intervention, underwent upper gastrointestinal tract endoscopy, and had histologic evidence of EED in their duodenal mucosal biopsies. The results revealed a shared group of bacterial taxa in their duodenums whose absolute abundances were correlated with levels of the expression of genes in the duodenal mucosa that are involved in inflammatory responses. A number of these bacterial taxa are more typically found in the oral microbiota, a finding that has potential physiologic and therapeutic implications.