BACKGROUND: Gut bacteria are related to colorectal cancer (CRC) and its clinicopathologic characteristics.
OBJECTIVE: To develop gut bacterial subtypes and explore potential microbial targets for CRC.
METHODS: Stool samples from 914 volunteers (376 CRCs, 363 advanced adenomas, and 175 normal controls) were included for 16S rRNA sequencing. Unsupervised learning was used to generate gut microbial subtypes. Gut bacterial community composition and clustering effects were plotted. Differences of gut bacterial abundance were analyzed. Then, the association of CRC-associated bacteria with subtypes and the association of gut bacteria with clinical information were assessed. The CatBoost models based on gut differential bacteria were constructed to identify the diseases including CRC and advanced adenoma (AA).
RESULTS: Four gut microbial subtypes (A, B, C, D) were finally obtained via unsupervised learning. The characteristic bacteria of each subtype were Escherichia-Shigella in subtype A, Streptococcus in subtype B, Blautia in subtype C, and Bacteroides in subtype D. Clinical information (e.g., free fatty acids and total cholesterol) and CRC pathological information (e.g., tumor depth) varied among gut microbial subtypes. Bacilli, Lactobacillales, etc., were positively correlated with subtype B. Positive correlation of Blautia, Lachnospiraceae, etc., with subtype C and negative correlation of Coriobacteriia, Coriobacteriales, etc., with subtype D were found. Finally, the predictive ability of CatBoost models for CRC identification was improved based on gut microbial subtypes.
CONCLUSIONS: Gut microbial subtypes provide characteristic gut bacteria and are expected to contribute to the diagnosis of CRC.

Gut microbiota is a diverse community of microorganisms that constantly work to protect the gut against pathogens. Salmonella stands out as a notorious foodborne pathogen that interacts with gut microbes, causing an imbalance in the overall composition of microbiota and leading to dysbiosis. This review focuses on the interactions between Salmonella and the key commensal bacteria such as E. coli, Lactobacillus, Clostridium, Akkermansia, and Bacteroides. The review highlights the role of these gut bacteria and their synergy in combating Salmonella through several mechanistic interactions. These include the production of siderophores, which compete with Salmonella for essential iron; the synthesis of short-chain fatty acids (SCFAs), which exert antimicrobial effects and modulate the gut environment; the secretion of bacteriocins, which directly inhibit Salmonella growth; and the modulation of cytokine responses, which influences the host\'s immune reaction to infection. While much research has explored Salmonella, this review aims to better understand how specific gut bacteria engage with the pathogen, revealing distinct defense mechanisms tailored to each species and how their synergy may lead to enhanced protection against Salmonella. Furthermore, the combination of these commensal bacteria could offer promising avenues for bacteria-mediated therapy during Salmonella-induced gut infections in the future.

Osmia excavata is an excellent pollinator in nature and plays a vital role in the conservation of agro-ecosystems and food security. Given the important role of the gut bacterial community in host health and regulation of host growth and development, using 16S rRNA gene sequencing data, the present study explored the composition of the gut bacterial community and its diversity at different life stages (eggs, young larvae, old larvae, young pupae, old pupae, and 1-day-old adults in cocoons) of the solitary bee Osmia excavata. The results showed that the core phyla in the gut of O. excavata at different life stages were Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteriota, and the core genera were Sodalis, Tyzzerella, and Ralstonia. The highest intestinal bacterial diversity was found in the Egg period, and the lowest bacterial alpha diversity was found in the 1-day-old Adult period; the bacterial diversity of O. excavata showed a process of decreasing, as it was growing from the Egg period to the 1-day-old Adult period. Our study found that O. excavata undergoes a significant change in the structure of the gut flora when it grows from the young pupae to old pupae stage, a period of growth that coincides with the process of cocooning and isolation from the external environment after food depletion. This suggests that food and environmental factors are key contributors to the structure of the bacterial community in the gut of solitary bees.

Insects and their gut bacteria form a tight and beneficial relationship, especially in utilization of host nutrients. The red turpentine beetle (RTB), a destructive and invasive pine pest, employs mutualistic microbes to facilitate its invasion success. However, the molecular mechanism underlying the utilization of nutrients remains unknown. In this study, we found that gut bacteria are crucial for the utilization of D-glucose, a main carbon source for RTB development. Downstream assays revealed that gut bacteria-induced gut hypoxia and the secretion of riboflavin are responsible for RTB development by regulating D-glucose transport via the activation of a hypoxia-induced transcription factor 1 (Hif-1α). Further functional investigations confirmed that Hif-1α mediates glucose transport by direct upregulation of two glucose transporters (ST10 and ST27), thereby promoting RTB development. Our findings reveal how gut bacteria regulate the development of RTB, and promote our understanding of the mutualistic relationship of animals and their gut bacteria.

BACKGROUND: More than 90% of colorectal cancer (CRC) arises from advanced adenomas (AA) and gut microbes are closely associated with the initiation and progression of both AA and CRC.
OBJECTIVE: To analyze the characteristic microbes in AA.
METHODS: Fecal samples were collected from 92 AA and 184 negative control (NC). Illumina HiSeq X sequencing platform was used for high-throughput sequencing of microbial populations. The sequencing results were annotated and compared with NCBI RefSeq database to find the microbial characteristics of AA. R-vegan package was used to analyze α diversity and β diversity. α diversity included box diagram, and β diversity included Principal Component Analysis (PCA), principal co-ordinates analysis (PCoA), and non-metric multidimensional scaling (NMDS). The AA risk prediction models were constructed based on six kinds of machine learning algorithms. In addition, unsupervised clustering methods were used to classify bacteria and viruses. Finally, the characteristics of bacteria and viruses in different subtypes were analyzed.
RESULTS: The abundance of Prevotella sp900557255, Alistipes putredinis, and Megamonas funiformis were higher in AA, while the abundance of Lilyvirus, Felixounavirus, and Drulisvirus were also higher in AA. The Catboost based model for predicting the risk of AA has the highest accuracy (bacteria test set: 87.27%; virus test set: 83.33%). In addition, 4 subtypes (B1V1, B1V2, B2V1, and B2V2) were distinguished based on the abundance of gut bacteria and enteroviruses (EVs). Escherichia coli D, Prevotella sp900557255, CAG-180 sp000432435, Phocaeicola plebeiuA, Teseptimavirus, Svunavirus, Felixounavirus, and Jiaodavirus are the characteristic bacteria and viruses of 4 subtypes. The results of Catboost model indicated that the accuracy of prediction improved after incorporating subtypes. The accuracy of discovery sets was 100%, 96.34%, 100%, and 98.46% in 4 subtypes, respectively.
CONCLUSIONS: Prevotella sp900557255 and Felixounavirus have high value in early warning of AA. As promising non-invasive biomarkers, gut microbes can become potential diagnostic targets for AA, and the accuracy of predicting AA can be improved by typing.

BACKGROUND: Propionate is a food preservative and platform chemical, but no biological process competes with current petrochemical production routes yet. Although propionate production has been described for gut bacteria of the class Bacteroidia, which also carry great capacity for the degradation of plant polymers, knowledge on propionate yields and productivities across species is scarce. This study aims to compare propionate production from glucose within Bacteroidia and characterize good propionate producers among this group.
RESULTS: We collected published information on propionate producing Bacteroidia, and selected ten species to be further examined. These species were grown under defined conditions to compare their product formation. While propionate, acetate, succinate, lactate and formate were produced, the product ratios varied greatly among the species. The two species with highest propionate yield, B. propionicifaciens (0.39 gpro/ggluc) and B. graminisolvens (0.25 gpro/ggluc), were further examined. Product formation and growth behavior differed significantly during CO2-limited growth and in resting cells experiments, as only B. graminisolvens depended on external-added NaHCO3, while their genome sequences only revealed few differences in the major catabolic pathways. Carbon mass and electron balances in experiments with resting cells were closed under the assumption that the oxidative pentose pathway was utilized for glucose oxidation next to glycolysis in B. graminisolvens. Finally, during pH-controlled fed-batch cultivation B. propionicifaciens and B. graminisolvens grew up to cell densities (OD600) of 8.1 and 9.8, and produced 119 mM and 33 mM of propionate from 130 and 105 mM glucose, respectively. A significant production of other acids, particularly lactate (25 mM), was observed in B. graminisolvens only.
CONCLUSIONS: We obtained the first broad overview and comparison of propionate production in Bacteroidia strains. A closer look at two species with comparably high propionate yields, showed significant differences in their physiology. Further studies may reveal the molecular basis for high propionate yields in Bacteroidia, paving the road towards their biotechnological application for conversion of biomass-derived sugars to propionate.

Exploring the effects of seasonal variation on the gut microbiota of cold-water fish plays an important role in understanding the relationship between seasonal variation and cold-water fish. Gut samples of cold-water fish and environmental samples were collected during summer and winter from the lower reaches of the Yalong River. The results of the 16S rRNA sequencing showed that significant differences were identified in the composition and diversity of gut bacteria of cold-water fish. Co-occurrence network complexity of the gut bacteria of cold-water fish was higher in summer compared to winter (Sum: nodes: 256; edges: 20,450; Win: nodes: 580; edges: 16,725). Furthermore, from summer to winter, the contribution of sediment bacteria (Sum: 5.3%; Win: 23.7%) decreased in the gut bacteria of cold-water fish, while the contribution of water bacteria (Sum: 0%; Win: 27.7%) increased. The normalized stochastic ratio (NST) and infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP) showed that deterministic processes played a more important role than stochastic processes in the microbial assembly mechanism of gut bacteria of cold-water fish. From summer to winter, the contribution of deterministic processes to gut bacteria community assembly mechanisms decreased, while the contribution of stochastic processes increased. Overall, these results demonstrated that seasonal variation influenced the gut bacteria of cold-water fish and served as a potential reference for future research to understand the adaptation of fish to varying environments.

This study investigated the effects of white meat, such as chicken, intake combined with resistance training on muscle mass and strength in the elderly women, and whether the underlying mechanism involves changes in the gut microbiota. Ninety-three volunteers (age 59-79 years) were randomly allocated to sedentary control with placebo (Sed + PL) or chicken meat (Sed + HP) and resistance training with placebo (RT + PL) or chicken meat (RT + HP). Resistance training sessions were performed 3 d/week for 12 weeks using leg extensions and curls. Boiled chicken meat (110 g, containing 22.5 g protein) was ingested 3 d/week for 12 weeks. Maximal muscle strength and whole-body lean mass increased significantly in the RT + PL group compared to the Sed + HP group, and the RT + HP group showed a significantly greater increase than the Sed + HP and RT + PL groups. Additionally, the gut microbiota composition did not change before or after the interventions in any of the four groups. Moreover, the individual comparison of gut bacteria using false discovery rate-based statistical analysis showed no alterations before or after the interventions in the four groups. Resistance training combined with chicken meat intake may effective have increased muscle mass and strength without drastically modifying the gut microbiota composition in elderly women.

UNASSIGNED: The alpha-glucosidase inhibitor acarbose is approved for the treatment of type 2 diabetes (T2D). It acts in the lumen of the gut by reducing intestinal hydrolysis and absorption of ingested carbohydrates. This reduces postprandial blood glucose concentration and increases the content of carbohydrates in the distal parts of the intestine potentially influencing gut microbiome (GM) composition and possibly impacting the gut microbiome (GM) dysbiosis associated with T2D. Here, we investigated the effect of acarbose on GM composition in patients with T2D.
UNASSIGNED: Faecal samples were collected in a previously conducted randomised, placebo-controlled, double-blind, crossover study in which 15 individuals with metformin-treated T2D (age 57-85 years, HbA1c 40-74 mmol/mol, BMI 23.6-34.6 kg/m2) were subjected to two 14-day treatment periods with acarbose and placebo, respectively, separated by a 6-week wash-out period. Faecal samples were collected before and by the end of each treatment period. The GM profiles were evaluated by 16S rRNA gene amplicon sequencing.
UNASSIGNED: The GM profiles after the treatment periods with acarbose or placebo remained unaffected (P > 0.7) when compared with the GM profiles before treatment. This applied to the analysis of within-sample diversity (α-diversity) and between-sample bacterial composition diversity (β-diversity). Additionally, no dominant bacterial species differentiated the treatment groups, and only minor increases in the relative abundances of Klebsiella spp. and Escherichia coli (P < 0.05) were observed after acarbose treatment.
UNASSIGNED: In patients with metformin-treated T2D, 14 days of treatment with acarbose showed only minor effects on GM as seen in increased relative abundances of Klebsiella spp. and Escherichia coli.

Candida albicans: (C. albicans) is a prevalent opportunistic pathogen that can cause severe mucosal and systemic fungal infections, leading to high morbidity and mortality rates. Traditional chemical drug treatments for C. albicans infection have limitations, including the potential for the development of drug resistance. Essential oils, which are secondary metabolites extracted from plants, have gained significant attention due to their antibacterial activity and intestinal regulatory effects. It makes them an ideal focus for eco-friendly antifungal research. This review was aimed to comprehensively evaluate the research progress, mechanisms, and clinical application prospects of essential oils in treating C. albicans infections through their antibacterial and intestinal regulatory effects. We delve into how essential oils exert antibacterial effects against C. albicans infections through these effects and provide a comprehensive analysis of related experimental studies and clinical trials. Additionally, we offer insights into the future application prospects of essential oils in antifungal therapy, aiming to provide new ideas and methods for the development of safer and more effective antifungal drugs. Through a systematic literature review and data analysis, we hope to provide insights supporting the application of essential oils in antifungal therapy while also contributing to the research and development of natural medicines. In the face of increasingly severe fungal infections, essential oils might emerge as a potent method in our arsenal, aiding in the effective protection of human and animal health.