Gut microbial subtypes and clinicopathological value for colorectal cancer.

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. CONCLUSION: Gut microbial subtypes provide characteristic gut bacteria and are expected to contribute to the diagnosis of CRC.

Cyclic Oligosaccharide-Induced Modulation of Immunoglobulin A Reactivity to Gut Bacteria Contributes to Alterations in the Bacterial Community Structure.

Immunoglobulin A (IgA) is a major gut antibody that coats commensal gut bacteria and contributes to shaping a stable gut bacterial composition. Although previous studies have shown that cyclic oligosaccharides, including cyclic nigerosyl-1,6-nigerose (CNN) and cyclodextrins (CDs, including αCD, ßCD, and γCD), alter the gut bacterial composition, it remains unclear whether cyclic oligosaccharides modify the IgA coating of gut bacteria, which relates to cyclic oligosaccharide-induced alteration of the gut bacterial composition. To address this issue, mice were maintained for 12 weeks on diets containing CNN, αCD, ßCD, or γCD; the animals' feces were evaluated for their bacterial composition and the IgA coating index (ICI), a measure of the degree of IgA coating of bacteria. We observed that the intake of each cyclic oligosaccharide altered the gut bacterial composition, with changes in the ICI found at both the phylum and genus levels. The ICI for Bacillota, Lachnospiraceae NK4A136 group, UC Lachnospiraceae, and Tuzzerella were significantly and positively correlated with the relative abundance (RA) in total bacteria for these bacteria; in contrast, significant correlations were not seen for other phyla and genera. Our observations suggest that cyclic oligosaccharide-induced modulation of the IgA coating of gut bacteria may partly relate to changes in the community structure of the gut bacteria.

Impact of a Functional Dairy Powder and Its Primary Component on the Growth of Pathogenic and Probiotic Gut Bacteria and Human Coronavirus 229E.

Milk boasts an array of potent bioactive compounds, such as lactoferrin (Lf), immunoglobulins, and functional proteins, all delivering substantial therapeutic benefits. In this study, Immune Powder (a functional dairy formulation) and its primary component called Fractionated Milk Protein (FMP) containing Lf, zinc, and immunoglobulins and formulated by Ausnutria Pty Ltd. were evaluated for their potential broad-spectrum pharmacological activity. In particular, this study investigated the antibacterial (against pathogenic Escherichia coli), prebiotic (promoting Lactobacillus delbrueckii growth), anti-inflammatory (inhibition of NO production in RAW264.7 macrophages), and antiviral (against human coronavirus 229E) effects of the samples. In addition, the impact of simulated gastric digestion on the efficacy of the samples was explored. LCMS-based proteomics was implemented to unveil cellular and molecular mechanisms underlying antiviral activity. The Immune Powder demonstrated antibacterial activity against E. coli (up to 99.74 ± 11.47% inhibition), coupled with prebiotic action (10.84 ± 2.2 viability fold-change), albeit these activities diminished post-digestion (p < 0.01). The Immune Powder effectively mitigated NO production in lipopolysaccharide-stimulated RAW264.7 macrophages, with declining efficacy post-digestion (p < 0.0001). The Immune Powder showed similar antiviral activity before and after digestion (p > 0.05) with up to 3-fold improvement. Likewise, FMP exhibited antibacterial potency pre-digestion at high concentrations (95.56 ± 1.23% inhibition at 125 mg/mL) and post-digestion at lower doses (61.82 ± 5.58% inhibition at 3906.25 µg/mL). FMP also showed enhanced prebiotic activity post-digestion (p < 0.0001), NO inhibition pre-digestion, and significant antiviral activity. The proteomics study suggested that the formulation and its primary component shared similar antiviral mechanisms by inhibiting scavenger receptor binding and extracellular matrix interaction.

Variation and functional profile of gut bacteria in the scarab beetle, Anomala dimidiata, under a cellulose-enriched microenvironment.

This study utilized cultivable methods and 16 S amplicon sequencing to compare taxonomic profiles and functional potential of gut bacteria in the scarab beetle, Anomola dimidiata, under cellulose-enriched conditions. Eight culturable cellulolytic gut bacteria were isolated from the midgut and hindgut of the scarab larvae, respectively. 16 S amplicon sequencing evinced that the most represented taxonomic profiles at phylum level in the fermentation chamber and midgut were Bacillota (71.62 and 56.76%), Pseudomonadota (22.66 and 36.89%) and Bacteroidota (2.7 and 2.81%). Bacillota (56.74 and 91.39%) were significantly enriched in the midgut with the addition of cellulose. In contrast, Bacillota and Psedomonadota were significantly enriched in the fermentation chamber. Carbohydrate metabolism was up-regulated in the midgut, while nitrogen and phosphorus metabolism were up-regulated in the fermentation chamber, suggesting these symbionts' possible metabolic roles to the host. An analysis of total cellulases as well as amplicon sequence variants indicated that the gut bacteria belonging to Acinetobacter, Bacillus, Brucella, Brevibacillus, Enterobacter, Lysinibacillus and Paenibacillus are involved in nutrition provisioning. These results have provided additional insights into the gut bacteria associated with cellulose digestion in A. dimidiata and created a platform for bioprospecting novel isolates to produce biomolecules for biotechnological use, besides identifying eco-friendly targets for its management.

Exploration of Protease Resources in the Gut of Omnivorous Gryllotalpa orientalis (Orthoptera: Gryllotalpidae).

An insect's gut microbiome is an essential "organ" in their life cycle, playing a crucial role by aiding food digestion and nutrient absorption. This study employed both culture-independent and culture-dependent methods to explore the protease resources present in the gut of the omnivorous insect Gryllotalpa orientalis. The findings revealed that the gut extract of G. orientalis contained a diverse array of proteases, including cysteine proteases, pepsin, serine proteases, and trypsin, as well as some unidentified proteases. Furthermore, the protease gene htpX, derived from gut bacterium Priestia megaterium DX-3, has been cloned and recombinantly expressed. The recombinant DX-3-htpX protease exhibited a 61.9-fold increase in fermentation level compared to the DX-3 protease. This protease was characterized as a neutral, heat-resistant metalloprotease with an M48 peptidase domain, and it was observed that the binding of Ca2+ to the recombinant protease resulted in the formation of the largest active pocket. This study provides technical support for further development and utilization of functional protein resources in insect gut.

Effects of mycotoxin-producing fungi on the fitness and gut bacterial community of the soil springtail Folsomia candida.

Mycotoxin-producing fungi are widespread and their adverse effects on mammals have been investigated; however, their impacts on soil invertebrates are not fully understood. Folsomia candida is a model soil arthropod that represents an important part of the soil invertebrate community. This study investigated the consequences of F. candida grazing on mycotoxin-producing fungi Fusarium verticillioides, F. graminearum, Aspergillus ochraceus, and A. nidulans. Consuming mycotoxin-producing fungi affected the body size and reproductive ability of F. candida, and altered the gut bacterial composition, with decreased Proteobacteria and increased Actinobacteria (Microbacterium) abundances. Notably, the abundance of foodborne fungi can be detected. Furthermore, certain bacteria isolated from F. candida's gut inhibited the growth of corresponding mycotoxin-producing fungi. The gut bacteria that inhibited mycotoxin-producing fungi growth in Aspergillus groups were also associated with poor fitness parameters and larger disruption in gut microbiota. Importantly, switching back to yeast diets reversed both the fitness parameters and gut bacterial composition. Together, our study demonstrated that grazing of mycotoxin-producing fungi by F. candida resulted in reduced physiological parameters and disturbed the gut bacterial community, and those changes can be restored by switching back to yeast diets, which indicates a strong resilience of springtails to mycotoxin-producing fungi. IMPORTANCE: Mycotoxin-producing fungi are widespread in nature and raise concerns for human and livestock health. Although they share the same ecosystem, interactions between mycotoxin-producing fungi and soil arthropods are not well understood. In this study, we report an unexpected finding that the soil arthropod Folsomia candida is rather tolerant to these mycotoxin-producing fungi. F. candida can survive solely on mycotoxin-producing fungi as a food source with reduced physiological parameters. Moreover, the gut microbial community is disturbed by mycotoxin-producing fungi, and some of the bacteria isolated from F. candida's gut can inhibit the growth of corresponding fungi. Notably, the altered physiological parameters and gut microbiota are restored when a normal diet is reintroduced, suggesting F. candida's resilience to mycotoxin-producing fungi. These findings clarify the impact of toxin-producing diets on F. candida, shedding light on how organisms can build resilience to environmental stimuli.

Gegen Qinlian decoction alleviates depression-like behavior by modulating the gut microenvironment in CUMS rats.

BACKGROUND: Gegen Qinlian Decoction (GQD) is a classical traditional Chinese medicine (TCM) formula primarily utilized for treating gut disorders. GQD showed therapeutic effects on several diseases in clinical and animal studies by targeting gut microbes. Our recent studies also found that GQD efficiently alleviated anxiety in methamphetamine-withdrawn mice via regulating gut microbiome and metabolism. Given that various studies have indicated the link between the gut microbiome and the development of depression, here we endeavor to explore whether GQD can manage depression disorders by targeting the gut microbiome. METHODS AND MATERIALS: The depression-like model was induced in rats through chronic unpredictable mild stress (CUMS) and the depression levels were determined using the sucrose preference test (SPT). To address the depression-like behavior in rats, oral administration of GQD was employed. The colon microbiome and metabolite patterns were determined by 16s rRNA sequencing and untargeted metabolomics, respectively. RESULTS: We found 6 weeks of CUMS can induce depression-like behavior in rats and 4 weeks of GQD treatment can significantly alleviate the depression-like behavior. GQD treatment can also ameliorate the histological lesions in the colon of CUMS rats. Then, CUMS increased the abundance of gut microbes, while GQD treatment can restore it to a lower level. We further discovered that the abundances of 19 bacteria at the genus level were changed with CUMS treatment, among which the abundances of Ruminococcus, Lachnoclostridium, Pygmaiobacter, Bacteroides, Pseudomonas, and Pseudomonas Family_XIII_AD3011_group were stored by GQD treatment. Besides, we identified the levels of 36 colon metabolites were changed with CUMS treatment, among which the levels of Fasciculic acid B, Spermine, Fludrocortisone acetate, alpha-Ketoglutaric acid, 2-Oxoglutaric acid, N'-(benzoyloxy)-2-(2,2-dichlorocyclopropyl) ethanimidamide, N6-Succinyl Adenosine Oleanolic acid, KQH, Ergosta-5,7,9(11),22-Tetraen-3-beta-Ol, Gentisic acid, 4-Hydroxyretinoic Acid, FAHFA (3:0/16:0), Leucine-enkephalin and N-lactoyl-phenylalanine can be restored by GQD treatment. CONCLUSION: Our findings provide evidence supporting the therapeutic efficacy of GQD in alleviating depression-like behavior in CUMS rats, potentially being targeted on colon bacteria (especially the abundance of Ruminococcus and Bacteroides) and metabolites (especially the level of Oleanolic acid).

Co-Culture of Gut Bacteria and Metabolite Extraction Using Fast Vacuum Filtration and Centrifugation.

This protocol describes a robust method for the extraction of intra and extracellular metabolites of gut bacterial mono and co-cultures. In recent years, the co-culture techniques employed in the field of microbiology have demonstrated significant importance in regard to understanding cell-cell interactions, cross-feeding, and the metabolic interactions between different bacteria, fungi, and microbial consortia which enable the mimicking of complex co-habitant conditions. This protocol highlights a robust reproducible physiologically relevant culture and extraction protocol for the co-culture of gut bacterium. The novel extraction steps are conducted without using quenching and cell disruption through bead-cell methods, freeze-thaw cycles, and sonication, which tend to affect the physical and biochemical properties of intracellular metabolites and secretome. The extraction procedure of inoculated bacterial co-cultures and monocultures use fast vacuum filtration and centrifugation. The extraction methodology is fast, effective, and robust, requiring 4 h to complete.

Isolation and Identification of Human Gut Bacteria Capable of Converting Curcumin to Its Hydrogenated Metabolites.

Curcumin is widely recognized for its health benefits, though the role of gut microbiota in its metabolic transformation was not well studied. In this study, bacterial strains capable of metabolizing curcumin were isolated from human stool samples. Using 16S rRNA and whole-genome sequencing, two novel strains (Clostridium butyricum UMA_cur1 and Escherichia coli UMA_cur2) were identified. In addition, the metabolic products were analyzed using liquid chromatography-mass spectrometry. These strains efficiently converted curcumin into dihydro-curcumin (DHC) and tetrahydro-curcumin (THC). Notably, E. coli UMA_cur2 also produced hexahydro-curcumin (HHC) and octahydro-curcumin (OHC), marking the first identification of a strain capable of such transformations. The absence of the YncB gene (typically involved in curcumin conversion) in C. butyricum UMA_cur1 suggests an alternative metabolic pathway. Curcumin metabolism begins during the stationary growth phase, indicating that it is not crucial for primary growth functions. Furthermore, E. coli UMA_cur2 produced these metabolites sequentially, starting with DHC and THC and progressing to HHC and OHC. These findings identified two novel strains that can metabolize curcumin to hydrogenated metabolites, which enhance our understanding of the interaction between curcumin and gut microbiota.

Composition and Diversity of Gut Bacterial Community in Different Life Stages of Osmia excavata Alfken (Hymenoptera: Megachilidae).

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.

A Comprehensive Review Exploring the Protective Role of Specific Commensal Gut Bacteria against Salmonella.

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.

Gut microbiome and antibiotic resistance genes in plateau model animal (Ochotona curzoniae) exhibit a relative stability under cold stress.

Antibiotic resistance genes (ARGs) carried by gut pathogens may pose a threat to the host and ecological environment. However, few studies focus on the effects of cold stress on intestinal bacteria and ARGs in plateau animals. Here, we used 16S rRNA gene sequencing and gene chip technique to explore the difference of gut microbes and ARGs in plateau pika under 4 °C and 25 °C. The results showed that tetracycline and aminoglycoside resistance genes were the dominant ARGs in pika intestine. Seven kinds of high-risk ARGs (aadA-01, aadA-02, ermB, floR, mphA-01, mphA-02, tetM-02) existed in pika's intestine, and cold had no significant effect on the composition and structure of pika's intestinal ARGs. The dominant phyla in pika intestine were Bacteroidetes and Firmicutes. Cold influenced 0.47 % of pika intestinal bacteria in OTU level, while most other bacteria had no significant change. The diversity and community assembly of intestinal bacteria in pika remained relatively stable under cold conditions, while low temperature decreased gut microbial network complexity. In addition, low temperature led to the enrichment of glycine biosynthesis and metabolism-related pathways. Moreover, the correlation analysis showed that eight opportunistic pathogens (such as Clostridium, Staphylococcus, Streptococcus, etc.) detected in pika intestine might be potential hosts of ARGs.

Gut bacteria are essential for development of an invasive bark beetle by regulating glucose transport.

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.

Plasma proteins, circulating metabolites mediate causal inference studies on the effect of gut bacteria on the risk of osteoporosis development.

BACKGROUND: The role of gut bacteria in preventing and delaying osteoporosis has been studied. However, the causal relationship between gut bacteria, plasma proteins, circulating metabolites and osteoporosis (OP) risk has not been fully revealed. MATERIALS AND METHODS: In this study, a two-sample Mendelian randomization study (MR) approach was used to assess the causal associations between gut bacteria, plasma proteins and circulating metabolites, and osteoporosis risk using Genome Wide Association Study (GWAS) data from gut bacteria(n=8208), plasma proteins(n=2263), circulating metabolites (n=123), and osteoporosis (3203 cases and 16380452 controls). Inverse-variance weighted (IVW) was used as the main analytical method to estimate the MR causal effect and to perform directional sensitivity analysis of causality. Finally, the mediating effect values for the influence of gut flora on OP pathogenesis through circulating metabolites were calculated by univariate MR analysis, and multivariate MR analysis. Next, we evaluated the effect of Phosphatidylcholine on the osteogenic function of bone marrow mesenchymal stem cells (BMSCs) through relevant experiments, including Edu detection of cell proliferation, alkaline phosphatase (ALP) staining, Alizarin red staining to evaluate osteogenic function, qPCR and WB detection of osteogenic differentiation related gene expression. RESULTS: A total of 9 gut microbial taxa, 15 plasma proteins and eight circulating metabolites were analysed for significant causal associations with the development of OP. Significant causal effects of 7 on gut bacteria, plasma proteins and circulating metabolites were analysed by univariate MR analysis and these results were used as exposure factors for subsequent multivariate MR. Multivariate MR analyses yielded a significant effect of circulating metabolites Phosphatidylcholine and other cholines on OP (P<0.05). Further mediation effect analysis showed that the mediation effect of Bifidobacteriaceae affecting OP through the circulating metabolite Phosphatidylcholine and other cholines was -0.0224, with a 95 % confidence interval for the mediation effect that did not include 0, and the complete mediation effect was significant. Phosphatidylcholine can promote BMSCs proliferation and osteogenesis. CONCLUSION: Our study demonstrated significant causal associations of gut bacteria, plasma proteins and circulating metabolites on OP, and that Bifidobacteriaceae affect OP through the circulating metabolites Phosphatidylcholine and other cholines. Phosphatidylcholine affects the osteogenic ability of BMSCs. Further exploration of potential microbiota-associated mechanisms of bone metabolism may offer new avenues for osteoporosis prevention and treatment of osteoporosis.

The cultivable gut bacteria Enterococcus mundtii promotes early-instar larval growth of Conogethes punctiferalis via enhancing digestive enzyme activity.

BACKGROUND: Gut bacteria are crucial in influencing insect development and even phenotypic plasticity. The yellow peach moth Conogethes punctiferalis, as a significant borer pest, has been the subject of limited reports regarding the structural and diversification changes in its gut microbiota during feeding, and their potential impacts on the growth and development of the host insects. RESULTS: This study, employing 16S rRNA sequencing, demonstrates distinct shifts in the larvae gut microbiome of C. punctiferalis between different feeding stages, highlighting a pronounced diversity in the early-instar with Enterococcus as a predominant genus in laboratory populations. Through in vitro cultivation and sequencing, three bacterial strains - Micrococcus sp., Brevibacterium sp. and Enterococcus mundtii - were isolated and characterized. Bioassays revealed that E. mundtii-infused corn significantly boosts early-instar larval growth, enhancing both body length and weight. Quantitative PCR and spectrophotometry confirmed a higher abundance of E. mundtii in younger larvae, correlating with increased digestive enzyme activity and total protein levels. CONCLUSION: This study reveals the heightened gut microbiota diversity in early instars of C. punctiferalis larvae, highlighting that Enterococcus represent a predominant bacteria in laboratory populations. In vitro cultivation and bioassays unequivocally demonstrate the significant role of the cultivable gut bacteria E. mundtii in promoting the growth of early-instar larva. These findings provide a solid theoretical foundation for advancing the comprehension of the intricate interactions between gut microbiota and insect hosts, as well as for the development of eco-friendly pest control technologies based on targeted manipulation of insect gut microbial communities. © 2024 Society of Chemical Industry.

Fecal virome transplantation: A promising strategy for the treatment of metabolic diseases.

Metabolic diseases are a group of disorders caused by metabolic abnormalities, including obesity, diabetes, non-alcoholic fatty liver disease, and more. Increasing research indicates that, beyond inherent metabolic irregularities, the onset and progression of metabolic diseases are closely linked to alterations in the gut microbiota, particularly gut bacteria. Additionally, fecal microbiota transplantation (FMT) has demonstrated effectiveness in clinically treating metabolic diseases, notably diabetes. Recent attention has also focused on the role of gut viruses in disease onset. This review first introduces the characteristics and influencing factors of gut viruses, then summarizes their potential mechanisms in disease development, highlighting their impact on gut bacteria and regulation of host immunity. We also compare FMT, fecal filtrate transplantation (FFT), washed microbiota transplantation (WMT), and fecal virome transplantation (FVT). Finally, we review the current understanding of gut viruses in metabolic diseases and the application of FVT in treating these conditions. In conclusion, FVT may provide a novel and promising treatment approach for metabolic diseases, warranting further validation through basic and clinical research.

Modulation of Human Gut Microbiota In Vitro by Inulin-Type Fructan from Codonopsis pilosula Roots.

Inulin-type fructan (ITF) defined as a polydisperse carbohydrate consisting mainly of ß-(2-1) fructosyl-fructose links exerts potential prebiotics properties by selectively stimulating the growth of Bifidobacterium and Lactobacillus. This study reported the modulation of human gut microbiota in vitro by ITF from Codonopsis pilosula roots using 16S ribosomal RNA gene sequencing. The microbiota community structure analysis at genus levels showed that 50 mg/mL ITF significantly stimulated the growth of Prevotella and Faecalibacterium. LEfSe analysis showed that ITF at 25 and 50 mg/mL primarily increased the relative abundance of genera Parabacteroides and Alistipes (LDA Score > 4), and genera Prevotella and Faecalibacterium (LDA Score > 4) as well as Acidaminococcus, Megasphaera, Bifidobacterium and Megamonas (LDA Score > 3.5), respectively. Meanwhile, ITF at 25 and 50 mg/mL exhibited the effects of lowering pH values of samples after 24 h fermentation (p < 0.05). The results indicated that ITF likely has potential in stimulating the growth of Prevotella and Faecalibacterium as well as Bifidobacterium of human gut microbiota.

Deterministic processes dominate microbial assembly mechanisms in the gut microbiota of cold-water fish between summer and winter.

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.

Gut microbes on the risk of advanced adenomas.

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 ß diversity. α diversity included box diagram, and ß 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. CONCLUSION: 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.

Propionate production by Bacteroidia gut bacteria and its dependence on substrate concentrations differs among species.

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.