Comparison of enzymatic activities and proteomic profiles of Butyrivibrio fibrisolvens grown on different carbon sources

Sechovcová, Hana; Kulhavá, Lucie; Fliegerová, K.; Trundová, Mária; Morais, Daniel; Mrázek, Jakub; Kopečný, J.

doi:10.1186/s12953-019-0150-3

Cited by 10 publications

(5 citation statements)

References 62 publications

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“…Our results only capture the initial rapid surface level decomposition phase; these findings cannot be extrapolated throughout the salt marsh sedimentary column where the majority of the carbon stock persists. Further exploration of the microbial communities at depth is required to elucidate the functional taxa and the mechanisms they employ to degrade the lignin-enriched carbohydrate complexes that progressively accumulate and contribute to the extensive pool of sequestered carbon as substrate composition is known to modulate the mechanisms employed [ 99 ].…”

Section: Discussionmentioning

confidence: 99%

Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh

et al. 2021

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Background Salt marshes are major natural repositories of sequestered organic carbon with high burial rates of organic matter, produced by highly productive native flora. Accumulated carbon predominantly exists as lignocellulose which is metabolised by communities of functionally diverse microbes. However, the organisms that orchestrate this process and the enzymatic mechanisms employed that regulate the accumulation, composition and permanence of this carbon stock are not yet known. We applied meta-exo-proteome proteomics and 16S rRNA gene profiling to study lignocellulose decomposition in situ within the surface level sediments of a natural established UK salt marsh. Results Our studies revealed a community dominated by Gammaproteobacteria, Bacteroidetes and Deltaproteobacteria that drive lignocellulose degradation in the salt marsh. We identify 42 families of lignocellulolytic bacteria of which the most active secretors of carbohydrate-active enzymes were observed to be Prolixibacteracea, Flavobacteriaceae, Cellvibrionaceae, Saccharospirillaceae, Alteromonadaceae, Vibrionaceae and Cytophagaceae. These families secreted lignocellulose-active glycoside hydrolase (GH) family enzymes GH3, GH5, GH6, GH9, GH10, GH11, GH13 and GH43 that were associated with degrading Spartina biomass. While fungi were present, we did not detect a lignocellulolytic contribution from fungi which are major contributors to terrestrial lignocellulose deconstruction. Oxidative enzymes such as laccases, peroxidases and lytic polysaccharide monooxygenases that are important for lignocellulose degradation in the terrestrial environment were present but not abundant, while a notable abundance of putative esterases (such as carbohydrate esterase family 1) associated with decoupling lignin from polysaccharides in lignocellulose was observed. Conclusions Here, we identify a diverse cohort of previously undefined bacteria that drive lignocellulose degradation in the surface sediments of the salt marsh environment and describe the enzymatic mechanisms they employ to facilitate this process. Our results increase the understanding of the microbial and molecular mechanisms that underpin carbon sequestration from lignocellulose within salt marsh surface sediments in situ and provide insights into the potential enzymatic mechanisms regulating the enrichment of polyphenolics in salt marsh sediments.

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Section: Discussionmentioning

confidence: 99%

Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh

et al. 2021

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“…The Butyrivibrio spp. from Lachnospriaceae detected only in SIBO patients could encode a more impressive repertoire of carbohydrate-active enzymes than most Firmicutes [ 40 ], capable of growing on a range of carbohydrates, from mono-or oligosaccharides to complex plant polysaccharides, such as pectins, mannans, starch, and hemicelluloses [ 51 , 52 ]. The end products were butyrate and many kinds of gas including hydrogen (H 2 ), carbon dioxide (CO 2 ), and hydrogen sulfide (H 2 S).…”

Section: Discussionmentioning

confidence: 99%

Fecal Coprococcus, hidden behind abdominal symptoms in patients with small intestinal bacterial overgrowth

Guo,

Chen,

Dong

et al. 2024

J Transl Med

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Background Small intestinal bacterial overgrowth (SIBO) is the presence of an abnormally excessive amount of bacterial colonization in the small bowel. Hydrogen and methane breath test has been widely applied as a non-invasive method for SIBO. However, the positive breath test representative of bacterial overgrowth could also be detected in asymptomatic individuals. Methods To explore the relationship between clinical symptoms and gut dysbiosis, and find potential fecal biomarkers for SIBO, we compared the microbial profiles between SIBO subjects with positive breath test but without abdominal symptoms (PBT) and healthy controls (HC) using 16S rRNA amplicon sequencing. Results Fecal samples were collected from 63 SIBO who complained of diarrhea, distension, constipation, or abdominal pain, 36 PBT, and 55 HC. For alpha diversity, the Shannon index of community diversity on the genus level showed a tendency for a slight increase in SIBO, while the Shannon index on the predicted function was significantly decreased in SIBO. On the genus level, significantly decreased Bacteroides, increased Coprococcus_2, and unique Butyrivibrio were observed in SIBO. There was a significant positive correlation between saccharolytic Coprococcus_2 and the severity of abdominal symptoms. Differently, the unique Veillonella in the PBT group was related to amino acid fermentation. Interestingly, the co-occurrence network density of PBT was larger than SIBO, which indicates a complicated interaction of genera. Coprococcus_2 showed one of the largest betweenness centrality in both SIBO and PBT microbiota networks. Pathway analysis based on the Kyoto Encyclopedia of Genes and Genome (KEGG) database reflected that one carbon pool by folate and multiple amino acid metabolism were significantly down in SIBO. Conclusions This study provides valuable insights into the fecal microbiota composition and predicted metabolic functional changes in patients with SIBO. Butyrivibrio and Coprococcus_2, both renowned for their role in carbohydrate fermenters and gas production, contributed significantly to the symptoms of the patients. Coprococcus’s abundance hints at its use as a SIBO marker. Asymptomatic PBT individuals show a different microbiome, rich in Veillonella. PBT’s complex microbial interactions might stabilize the intestinal ecosystem, but further study is needed due to the core microbiota similarities with SIBO. Predicted folate and amino acid metabolism reductions in SIBO merit additional validation.

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“…However, randomized controlled trials are required to establish the beneficial effects of probiotics against hypothyroidism and their specific protective mechanisms. Butyrivibrio bacteria are predominantly located in the rumen of ruminant animals, where they have a crucial function in breaking down plant fibers and producing butyric acid (51). The connection between Butyrivibrio and disease was established by observing a decrease in the proportion of Butyrivibrio species in the intestinal tracts of patients with Behcet's disease.…”

Section: Discussionmentioning

confidence: 99%

Cross-talk between the gut microbiota and hypothyroidism: a bidirectional two-sample Mendelian randomization study

Shi,

Chen,

et al. 2024

Front. Nutr.

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BackgroundMultiple observational studies suggest a connection between the composition of the gut microbiota and hypothyroidism. However, it has yet to be determined whether the gut microbiota has a causal effect on hypothyroidism.MethodsTo investigate the connection between the gut microbiota and hypothyroidism, two-sample Mendelian randomization was performed using data from a genome-wide association study meta-analysis (n = 18,430) conducted by the MiBioGen consortium. Summary statistics for hypothyroidism (26,342 cases and 59,827 controls) were obtained using the data from the FinnGen consortium R8 release data. To investigate the causal link between the gut microbiota and hypothyroidism, various methods, including MR-Egger, weighted median, weighted model, simple model, MR-PRESSO, and inverse variance weighted (IVW), were employed. The bacteria that were causally linked to hypothyroidism in forward Mendelian randomization analysis were subjected to reverse Mendelian randomization analysis. Cochran’s Q statistics were utilized to gauge the heterogeneity of the instrumental variables.ResultsThe results indicated that Akkermansia had a positive impact on hypothyroidism, with an odds ratio of 0.84 (95% CI 0.74–0.95, p = 0.01) based on the inverse variance-weighted estimates. Additionally, Anaerostipes (OR = 1.17, 95% CI 1.01–1.36, p = 0.04), Butyrivibrio (OR = 0.93, 95% CI 0.88–0.99, p = 0.02), Holdemania (OR = 0.89, 95% CI 0.81–0.99, p = 0.03), Intestinimonas (OR = 1.13, 95% CI 1.02–1.26, p = 0.03), Ruminiclostridium5 (OR = 1.19, 95% CI 1.01–1.41, p = 0.04), and Ruminococcaceae UCG-011 (OR = 0.91, 95% CI 0.84–0.99, p = 0.03) were identified. The gut microbiota was not significantly affected by hypothyroidism, as indicated by the results of the reverse MR analysis. There was no significant variation in the instrumental variables or horizontal pleiotropy.ConclusionThe findings of this study using two-sample Mendelian randomization indicate a causal relationship between Akkermansia and hypothyroidism. Increased Akkermansia inhibits the onset and progression of hypothyroidism. Additional randomized controlled experiments are necessary to elucidate the beneficial impact of probiotics on hypothyroidism and their distinct protective mechanisms.

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Comparison of enzymatic activities and proteomic profiles of Butyrivibrio fibrisolvens grown on different carbon sources

Cited by 10 publications

References 62 publications

Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh

Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh

Fecal Coprococcus, hidden behind abdominal symptoms in patients with small intestinal bacterial overgrowth

Cross-talk between the gut microbiota and hypothyroidism: a bidirectional two-sample Mendelian randomization study

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