Discovery of potential genes contributing to the biosynthesis of short-chain fatty acids and lactate in gut microbiota from systematic investigation in E. coli

Zhao, Chunhua; Dong, Hongjun; Zhang, Yanping; Li, Yin

doi:10.1038/s41522-019-0092-7

Cited by 50 publications

(42 citation statements)

References 49 publications

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“…3a). Of 21 candidate genes, shown to be important in SCFA synthesis in previous studies [27][28][29] , the abundance of five genes were significantly different across groups (Supplementary Table 3). Importantly, pyruvate carboxylase (pycA), responsible for the production of oxaloacetate from pyruvate was overexpressed in NAFLD-HCC compared to NAFLD-cirrhosis and non-NAFLD control (P = 0.004) ( Fig.…”

Section: Resultsmentioning

confidence: 91%

Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma

et al. 2021

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The gut microbiota is reported to modulate the immune response in hepatocellular carcinoma (HCC). Here, we employ metagenomic and metabolomic studies to characterise gut microbiota in patients with non-alcoholic fatty liver disease (NAFLD) related cirrhosis, with or without HCC, and evaluate its effect on the peripheral immune response in an ex vivo model. We find that dysbiosis characterises the microbiota of patients with NAFLD-cirrhosis, with compositional and functional shifts occurring with HCC development. Gene function of the microbiota in NAFLD-HCC supports short chain fatty acid production, and this is confirmed by metabolomic studies. Ex vivo studies show that bacterial extracts from the NAFLD-HCC microbiota, but not from the control groups, elicit a T cell immunosuppressive phenotype, characterised by expansion of regulatory T cells and attenuation of CD8 + T cells. Our study suggest that the gut microbiota in NAFLD-HCC is characterised by a distinctive microbiome/metabolomic profile, and can modulate the peripheral immune response.

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Section: Resultsmentioning

confidence: 91%

Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma

et al. 2021

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“…Endoglucanase and endo-1,4-betaxylanase contribute greatly to breaking down fiber content. MgsA is related to LA generation by LA bacteria during second-stage fermentation (12). These three genes belong to carbohydrate metabolism pathways.…”

Section: Resultsmentioning

confidence: 99%

Dynamics of the Physicochemical Characteristics, Microbiota, and Metabolic Functions of Soybean Meal and Corn Mixed Substrates during Two-Stage Solid-State Fermentation

Wang

Shi

et al. 2020

mSystems

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Substantial annual economic loss in livestock production is caused by antinutritional factors in soybean meal and corn mixed substrates, which can be degraded by microbial fermentation. Although considerable efforts have been made to explain the effects of fermentation on soybean meal and corn-based feed, the dynamics of the physicochemical characteristics, microbiota, and metabolic functions of soybean meal and corn mixed substrates during solid-state fermentation remain unclear. Here, multiple physicochemical analyses combined with high-throughput sequencing were performed to reveal the dynamic changes that occur during a novel two-stage solid-state fermentation process. Generally, inoculated bacteria rapidly proliferated in the initial 12-h aerobic fermentation (P = 0.002). Notably, most nutritional changes occurred during 12 to 24 h compared to 0 to 12 h. Second-stage anaerobic fermentation increased the bacterial abundance and lactic acid content (P < 0.00). Bacillus spp., Enterococcus spp., and Pseudomonas spp. were predominantly involved in the maturation of the fermented mixed substrates (P < 0.05). Additionally, the available phosphorus exhibited the greatest interaction with the microbial community structure. Cellular processes and environmental information processing might be the main metabolic processes of the microbiota during this fermentation. An in vivo model further evaluated the growth-promoting effects of the fermented products. These results characterized the dynamic changes that occur during two-stage solid-state fermentation and provided potential references for additional interventions to further improve the effectiveness and efficiency of solid-state fermentation of feed. IMPORTANCE Solid-state fermentation (SSF) plays pivotal roles not only in human food but also farm animal diets. Soybean meal (SBM) and corn account for approximately 70% of the global feed consumption. However, the nutritional value of conventional SBM and corn mixed substrates (MS) is limited by antinutritional factors, causing substantial economic loss in livestock production. Although emerging studies have reported that SSF can improve the nutritional value of SBM-based substrates, the dynamic changes in the physicochemical features, microbiota, and metabolic functions of MS during SSF remain poorly understood, limiting further investigation. To provide insights into the dynamics of the physicochemical characteristics and the complex microbiome during the two-stage SSF of MS, multiple physicochemical analyses combined with high-throughput sequencing were applied here. These novel insights shed light on the complex changes that occur in the nutrition and microbiome during two-stage SSF of MS and are of great value for industrial feed-based practices and metabolomic research on SSF ecosystems.

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“…63,64 Megamonas species are important propionate and acetate producers. 65,66 Thus, based on these results, a greater emphasis on Megamonas, and its potential impact on gastrointestinal health, may be justified in the future.…”

Section: Discussionmentioning

confidence: 99%

Dysbiosis in a canine model of human fistulizing Crohn’s disease

et al. 2020

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Crohn's disease (CD) is a chronic immune-mediated inflammatory condition caused by the loss of mucosal tolerance toward the commensal microbiota. On average, 29.5% and 42.7% CD patients experience perianal complications at 10 and 20 y after diagnosis, respectively. Perianal CD (pCD) result in high disease burden, diminished quality of life, and elevated health-care costs. Overall pCD are predictors of poor long-term outcomes. Animal models of gut inflammation have failed to fully recapitulate the human manifestations of fistulizing CD. Here, we evaluated dogs with spontaneous canine anal furunculosis (CAF), a disease with clinical similarities to pCD, as a surrogate model for understanding the microbial contribution of human pCD pathophysiology. By comparing the gut microbiomes between dogs suffering from CAF (CAF dogs) and healthy dogs, we show CAF-dog microbiomes are either very dissimilar (dysbiotic) or similar (healthy-like), yet unique, to healthy dog's microbiomes. Compared to healthy or healthy-like CAF microbiomes, dysbiotic CAF microbiomes showed an increased abundance of Bacteroides vulgatus and Escherichia coli and a decreased abundance of Megamonas species and Prevotella copri. Our results mirror what have been reported in previous microbiome studies of patients with CD; particularly, CAF dogs exhibited two distinct microbiome composition: dysbiotic and healthy-like, with determinant bacterial taxa such as E. coli and P. copri that overlap what it has been found on their human counterpart. Thus, our results support the use of CAF dogs as a surrogate model to advance our understanding of microbial dynamics in pCD.

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Discovery of potential genes contributing to the biosynthesis of short-chain fatty acids and lactate in gut microbiota from systematic investigation in E. coli

Cited by 50 publications

References 49 publications

Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma

Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma

Dynamics of the Physicochemical Characteristics, Microbiota, and Metabolic Functions of Soybean Meal and Corn Mixed Substrates during Two-Stage Solid-State Fermentation

Dysbiosis in a canine model of human fistulizing Crohn’s disease

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