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Nutrients May 2024An imbalance of energy intake and expenditure is commonly considered as the fundamental cause of obesity. However, individual variations in susceptibility to obesity do...
An imbalance of energy intake and expenditure is commonly considered as the fundamental cause of obesity. However, individual variations in susceptibility to obesity do indeed exist in both humans and animals, even among those with the same living environments and dietary intakes. To further explore the potential influencing factors of these individual variations, male C57BL/6J mice were used for the development of obesity-prone and obesity-resistant mice models and were fed high-fat diets for 16 weeks. Compared to the obesity-prone mice, the obesity-resistant group showed a lower body weight, liver weight, adipose accumulation and pro-inflammatory cytokine levels. 16S rRNA sequencing, which was conducted for fecal microbiota analysis, found that the fecal microbiome's structural composition and biodiversity had changed in the two groups. The genera , , and increased in the obesity-prone mice, and the genera , and were enriched in the obesity-resistant mice. Using widely targeted metabolomics analysis, 166 differential metabolites were found, especially those products involved in arachidonic acid (AA) metabolism, which were significantly reduced in the obesity-resistant mice. Moreover, KEGG pathway analysis exhibited that AA metabolism was the most enriched pathway. Significantly altered bacteria and obesity-related parameters, as well as AA metabolites, exhibited strong correlations. Overall, the phenotypes of the obesity-prone and obesity-resistant mice were linked to gut microbiota and AA metabolism, providing new insight for developing an in-depth understanding of the driving force of obesity resistance and a scientific reference for the targeted prevention and treatment of obesity.
Topics: Animals; Gastrointestinal Microbiome; Diet, High-Fat; Obesity; Male; Mice, Inbred C57BL; Arachidonic Acid; Mice; Feces; RNA, Ribosomal, 16S; Disease Models, Animal; Bacteria; Body Weight
PubMed: 38892512
DOI: 10.3390/nu16111579 -
PLoS Computational Biology Jun 2024Microbial communities play fundamental roles in every complex ecosystem, such as soil, sea and the human body. The stability and diversity of the microbial community...
Microbial communities play fundamental roles in every complex ecosystem, such as soil, sea and the human body. The stability and diversity of the microbial community depend precisely on the composition of the microbiota. Any change in the composition of these communities affects microbial functions. An important goal of studying the interactions between species is to understand the behavior of microbes and their responses to perturbations. These interactions among species are mediated by the exchange of metabolites within microbial communities. We developed a computational model for the microbial community that has a separate compartment for exchanging metabolites. This model can predict possible metabolites that cause competition, commensalism, and mutual interactions between species within a microbial community. Our constraint-based community metabolic modeling approach provides insights to elucidate the pattern of metabolic interactions for each common metabolite between two microbes. To validate our approach, we used a toy model and a syntrophic co-culture of Desulfovibrio vulgaris and Methanococcus maripaludis, as well as another in co-culture between Geobacter sulfurreducens and Rhodoferax ferrireducens. For a more general evaluation, we applied our algorithm to the honeybee gut microbiome, composed of seven species, and the epiphyte strain Pantoea eucalypti 299R. The epiphyte strain Pe299R has been previously studied and cultured with six different phyllosphere bacteria. Our algorithm successfully predicts metabolites, which imply mutualistic, competitive, or commensal interactions. In contrast to OptCom, MRO, and MICOM algorithms, our COMMA algorithm shows that the potential for competitive interactions between an epiphytic species and Pe299R is not significant. These results are consistent with the experimental measurements of population density and reproductive success of the Pe299R strain.
PubMed: 38900842
DOI: 10.1371/journal.pcbi.1012233 -
Journal of Microbiology and... Dec 2023This study aimed to evaluate the effects of and isolated from human feces coordinating with inulin on the composition of gut microbiota and metabolic profiles in db/db...
This study aimed to evaluate the effects of and isolated from human feces coordinating with inulin on the composition of gut microbiota and metabolic profiles in db/db mice. These supplements were administered to db/db mice for 12 weeks. The results showed that the coordinating with inulin group (LI) exhibited lower fasting blood glucose levels than the model control group (MC). Additionally, LI was found to enhance colon tissue and increase the levels of short-chain fatty acids. 16S rRNA sequencing revealed that the abundance of and , which were significantly increased in the MC group compared with NC group, were significantly decreased by the treatment of LI that also restored the key genera of the _NK4A136_group, , , , and . Untargeted metabolomics analysis showed that lotaustralin, 5-hydroxyindoleacetic acid, and 13(S)-HpODE were increased while L-phenylalanine and L-tryptophan were decreased in the MC group compared with the NC group. However, the intervention of LI reversed the levels of these metabolites in the intestine. Correlation analysis revealed that and _group were negatively correlated with 5-hydroxyindoleacetic acid and 13(S)-HpODE, but positively correlated with L-tryptophan. 13(S)-HpODE was involved in the "linoleic acid metabolism". L-tryptophan and 5-hydroxyindoleacetic acid were involved in "tryptophan metabolism" and "serotonergic synapse". These findings suggest that LI may alleviate type 2 diabetes symptoms by modulating the abundance of and to regulate the pathways of "linoleic acid metabolism", "serotonergic synapse", and" tryptophan metabolism". Our results provide new insights into prevention and treatment of type 2 diabetes.
Topics: Humans; Animals; Mice; Lactobacillaceae; Gastrointestinal Microbiome; Inulin; Tryptophan; Diabetes Mellitus, Type 2; Hydroxyindoleacetic Acid; RNA, Ribosomal, 16S; Metabolome; Linoleic Acids
PubMed: 37734909
DOI: 10.4014/jmb.2304.04039 -
Gut Microbes 2024Diarrhea-predominant irritable bowel syndrome (IBS-D), associated with increased intestinal permeability, inflammation, and small intestinal bacterial overgrowth, can be...
Diarrhea-predominant irritable bowel syndrome (IBS-D), associated with increased intestinal permeability, inflammation, and small intestinal bacterial overgrowth, can be triggered by acute gastroenteritis. Cytolethal distending toxin B (CdtB) is produced by gastroenteritis-causing pathogens and may underlie IBS-D development, through molecular mimicry with vinculin. Here, we examine the effects of exposure to CdtB alone on gut microbiome composition, host intestinal gene expression, and IBS-D-like phenotypes in a rat model. CdtB-inoculated rats exhibited increased anti-CdtB levels, which correlated with increased stool wet weights, pro-inflammatory cytokines (TNFα, IL2) and predicted microbial metabolic pathways including inflammatory responses, TNF responses, and diarrhea. Three distinct ileal microbiome profiles (microtypes) were identified in CdtB-inoculated rats. The first microtype (most like controls) had altered relative abundance (RA) of genera and . The second had lower microbial diversity, higher RA, higher absolute abundance, and altered host ileal tissue expression of immune-response and TNF-response genes compared to controls. The third microtype had higher microbial diversity, higher RA of hydrogen sulfide (HS)-producer , and increased expression of HS-associated pain/serotonin response genes. All CdtB-inoculated rats exhibited decreased ileal expression of cell junction component mRNAs, including vinculin-associated proteins. Significantly, cluster-specific microRNA-mRNA interactions controlling intestinal permeability, visceral hypersensitivity/pain, and gastrointestinal motility genes, including several previously associated with IBS were seen. These findings demonstrate that exposure to CdtB toxin alone results in IBS-like phenotypes including inflammation and diarrhea-like stool, decreased expression of intestinal barrier components, and altered ileal microtypes that influenced changes in microRNA-modulated gene expression and predicted metabolic pathways consistent with specific IBS-D symptoms.
Topics: Rats; Animals; Irritable Bowel Syndrome; Rodentia; Vinculin; Escherichia coli; Gastrointestinal Microbiome; Diarrhea; Inflammation; Gastroenteritis; Gene Expression; Pain
PubMed: 38108386
DOI: 10.1080/19490976.2023.2293170 -
Revista Brasileira de Parasitologia... 2023In vitro excystation of cysts of microscopically identified Chilomastix mesnili and Retortamonas sp. isolated from Japanese macaques and Retortamonas sp. isolated from...
In vitro excystation of cysts of microscopically identified Chilomastix mesnili and Retortamonas sp. isolated from Japanese macaques and Retortamonas sp. isolated from small Indian mongooses could be induced using an established protocol for Giardia intestinalis and subsequently by culturing with H2S-rich Robinson's medium supplemented with Desulfovibrio desulfuricans. Excystation usually began 2 h after incubation in Robinson's medium. DNA was isolated from excysted flagellates after 4 h of incubation or from cultured excysted flagellates. Phylogenetic analysis based on their 18S rRNA genes revealed that two isolates of C. mesnili from Japanese macaques belonged to the same cluster as a C. mesnili isolate from humans, whereas a mammalian Retortamonas sp. isolate from a small Indian mongoose belonged to the same cluster as that of an amphibian Retortamonas spp. isolate from a 'poison arrow frog' [sequence identity to AF439347 (94.9%)]. These results suggest that the sequence homology of the 18S rRNA gene of the two C. mesnili isolates from Japanese macaques was similar to that of humans, in addition to the morphological similarity, and Retortamonas sp. infection of the amphibian type in the small Indian mongoose highlighted the possibility of the effect of host feeding habitats.
Topics: Humans; Animals; Phylogeny; Retortamonadidae; Herpestidae; Macaca fuscata; Parasites; RNA, Ribosomal, 18S
PubMed: 38055438
DOI: 10.1590/S1984-29612023070 -
Ecotoxicology and Environmental Safety Aug 2023Di-n-butyl phthalate (DBP) is a ubiquitous environmental contaminant linked with various adverse health effects, including immune system dysfunction. Gut microbial...
Di-n-butyl phthalate (DBP) is a ubiquitous environmental contaminant linked with various adverse health effects, including immune system dysfunction. Gut microbial dysbiosis can contribute to a wide range of pathogenesis, particularly immune disease. Here, we investigated the impact of DBP on the gut microbiome and examined correlations with immune system changes after five weeks oral exposure (10 or 100 mg/kg/day) in adult male mice. The fecal microbiome composition was characterized using 16S rRNA sequencing. DBP-treated mice displayed a significantly distinct microbial community composition, indicated by Bray-Curtis distance. Numerous amplicon sequence variants (ASVs) at the genus level were altered. Compared to the vehicle control group, the 10 mg/kg/day DBP group had 63 more abundant and 65 less abundant ASVs, while 60 ASVs were increased and 76 ASVs were decreased in the 100 mg/kg/day DBP group. Both DBP treatment groups showed higher abundances of ASVs assigned to Desulfovibrio (Proteobacteria phylum) and Enterorhabdus genera, while ASVs belonging to Parabacteroides, Lachnospiraceae UCG-006 and Lachnoclostridium were less common compared to the control group. Interestingly, an ASV belonging to Rumniniclostridium 6, which was less abundant in DBP-treated mice, demonstrated a negative correlation with the increased number of non-classical monocytes observed in the blood of DBP-treated animals. In addition, an ASV from Lachnospiraceae UCG-001, which was more abundant in the DBP-treated animals, showed a positive correlation with the non-classical monocyte increase. This study shows that DBP exposure greatly modifies the gut bacterial microbiome and indicates a potential contribution of microbial dysbiosis to DBP-induced immune system impairment, illustrating the importance of investigating how interactions between exposome components can affect health.
PubMed: 37549549
DOI: 10.1016/j.ecoenv.2023.115321 -
Environmental Research Oct 2023Our current understanding of the susceptibility of hazardous polycyclic aromatic hydrocarbons (PAHs) to anaerobic microbial degradation is very limited. In the present...
Our current understanding of the susceptibility of hazardous polycyclic aromatic hydrocarbons (PAHs) to anaerobic microbial degradation is very limited. In the present study, we obtained phenanthrene- and pyrene-degrading strictly anaerobic sulfate-reducing enrichments using contaminated freshwater lake sediments as the source material. The highly enriched phenanthrene-degrading culture, MMKS23, was dominated (98%) by a sulfate-reducing bacterium belonging to the genus Desulfovibrio. While Desulfovibrio sp. was also predominant (79%) in the pyrene-degrading enrichment culture, MMKS44, an anoxygenic purple non-sulfur bacterium, Rhodopseudomonas sp., constituted a significant fraction (18%) of the total microbial community. Phenanthrene or pyrene biodegradation by the enrichment cultures was coupled with sulfate reduction, as evident from near stoichiometric consumption of sulfate and accumulation of sulfide. Also, there was almost complete inhibition of substrate degradation in the presence of an inhibitor of sulfate reduction, i.e., 20 mM MoO, in the culture medium. After 180 days of incubation, about 79.40 μM phenanthrene was degraded in the MMKS23 culture, resulting in the consumption of 806.80 μM sulfate and accumulation of 625.80 μM sulfide. Anaerobic pyrene biodegradation by the MMKS44 culture was relatively slow. About 22.30 μM of the substrate was degraded after 180 days resulting in the depletion of 239 μM sulfate and accumulation of 196.90 μM sulfide. Biodegradation of phenanthrene by the enrichment yielded a metabolite, phenanthrene-2-carboxylic acid, suggesting that carboxylation could be a widespread initial step of phenanthrene activation under sulfate-reducing conditions. Overall, this novel study demonstrates the ability of sulfate-reducing bacteria (SRB), dwelling in contaminated freshwater sediments to anaerobically biodegrade three-ringed phenanthrene and highly recalcitrant four-ringed pyrene. Our findings suggest that SRB could play a crucial role in the natural attenuation of PAHs in anoxic freshwater sediments.
Topics: Anaerobiosis; Lakes; Sulfates; Phenanthrenes; Polycyclic Aromatic Hydrocarbons; Pyrenes; Bacteria; Biodegradation, Environmental; Geologic Sediments
PubMed: 37437866
DOI: 10.1016/j.envres.2023.116616 -
Frontiers in Cellular and Infection... 2023As a potential antibiotic alternative, macleaya cordata extract (MCE) has anti-inflammatory, antioxidant, and antimicrobial properties. This study was conducted to...
Microbiome-transcriptome analysis reveals that dietary supplementation with macleaya cordata extract alters multiple immune pathways with minimal impact on microbial structure.
BACKGROUND
As a potential antibiotic alternative, macleaya cordata extract (MCE) has anti-inflammatory, antioxidant, and antimicrobial properties. This study was conducted to assess the impact of MCE supplementation on the gut microbiota and its interplay with the host in young goats. Thirty female black goats with similar body weight (5.63 ± 0.30 kg) were selected and randomly allotted into one of three diets: a control diet (Control), a control diet with antibiotics (Antibiotics, 21 mg/kg/day vancomycin and 42 mg/kg/day neomycin), and a control diet with MCE (MCE, 3.75% w/w premix).
RESULTS
Principal coordinate analysis of the microbial community showed that samples of Antibiotic clustered separately from both Control and MCE ( < 0.001). The random forest analysis revealed that, in comparison to the Control group, the impact of Antibiotics on the microbiota structure was more pronounced than that of MCE (number of featured microbiota, 13 in Antibiotics and >6 in MCE). In addition, the pathways of significant enrichment either from DEGs between Antibiotics and Control or from DEGs between MCE and Control were almost identical, including Th17 cell differentiation, butanoate metabolism, T-cell receptor signaling pathway, intestinal immune network for IgA production, antigen processing and presentation, and ABC transporters. Furthermore, an integrative analysis indicated that significant positive correlations ( < 0.05) were observed between and the featured biomarkers , , , and in the MCE group. Conversely, several significant negative correlations ( < 0.05) were identified between and the featured biomarkers , , , , , , , , , and in the Antibiotics group.
CONCLUSION
Collectively, the analysis of microbiome-transcriptome data revealed that dietary supplementation with MCE produced significant alterations in multiple immune pathways, while having minimal impact on the microbial structure.
Topics: Female; Animals; Plant Extracts; Microbiota; Papaveraceae; Gene Expression Profiling; Anti-Bacterial Agents; Dietary Supplements; Biomarkers; Goats
PubMed: 37842002
DOI: 10.3389/fcimb.2023.1264550 -
BioRxiv : the Preprint Server For... Nov 2023Biofilms of the sulfate reducing bacterium (SRB) Hildenborough (DvH) can facilitate metal corrosion in various industrial and environmental settings leading to...
Biofilms of the sulfate reducing bacterium (SRB) Hildenborough (DvH) can facilitate metal corrosion in various industrial and environmental settings leading to substantial economic losses; however, the mechanisms of biofilm formation by DvH are not yet well-understood. Evidence suggests that a large adhesin, DvhA, may be contributing to biofilm formation in DvH. The gene and its neighbors encode proteins that resemble the Lap system, which regulates biofilm formation by , including a LapG-like protease DvhG and effector protein DvhD, which has key differences from the previously described LapD. By expressing the Lap-like adhesion components of DvH in , our data support the model that the N-terminal fragment of the large adhesin DvhA serves as an adhesin "retention module" and is the target of the DvhG/DvhD regulatory module, thereby controlling cell-surface location of the adhesin. By heterologously expressing the DvhG/DvhD-like proteins in a background lacking native regulation (ΔΔ) we also show that cell surface regulation of the adhesin is dependent upon the intracellular levels of c-di-GMP. This study provides insight into the key players responsible for biofilm formation by DvH, thereby expanding our understanding of Lap-like systems.
PubMed: 38045380
DOI: 10.1101/2023.11.22.568322 -
Frontiers in Microbiology 2024Previous studies have indicated that diarrhea with kidney-yang deficiency syndrome leads to a disorder of small intestine contents and mucosal microbiota. However, the...
OBJECTIVE
Previous studies have indicated that diarrhea with kidney-yang deficiency syndrome leads to a disorder of small intestine contents and mucosal microbiota. However, the relationship of TMA-lyase (CutC) activity and TMAO with diarrhea with kidney-yang deficiency syndrome remains unexplored. Therefore, this study explores the relationship between cecal microbiota and choline TMA-lyase (CutC) activity, as well as the correlation between trimethylamine oxide (TMAO), inflammatory index, and CutC activity.
METHOD
Twenty SPF-grade male KM mice were randomly divided into the normal group (CN) and the diarrhea model group (CD). Diarrhea mouse models were established by adenine combined with administration. CutC activity, TMAO, interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) levels were detected, and the cecal content microbiota was sequenced.
RESULT
After 14 days, diarrhea occurred in the CD group. Compared with the CN group, there was no significant change in the activity of CutC in the small intestine of the CD group, while the activity of CutC in the cecum was significantly increased, and the levels of TMAO, IL-6, and TNF-α showed a significant increase. The Chao1 index, Observed_species index, Shannon index, and Simpson index all exhibited a decreasing trend. The main changes at the bacterial genus level were , , , , , and . The results of LEfSe analysis, random forest analysis and ROC curve analysis revealed , , , , , , , , , , and as characteristic bacteria in the CD group. Correlation analysis showed a significant negative correlation between cecal CutC activity and , and a significant positive correlation with and . The level of TMAO was significantly positively correlated with CutC activity and IL-6.
CONCLUSION
Diarrhea with kidney-yang deficiency syndrome significantly affects the physiological status, digestive enzyme activity, CutC activity, TMAO levels, and inflammatory response in mice. Additionally, there are changes in the composition and function of cecal microbiota, indicating an important impact of diarrhea with kidney-yang deficiency syndrome on the host intestinal microbiota balance. The occurrence of diarrhea with kidney-yang deficiency syndrome may be associated with dysbiosis of intestinal microbiota, increased CutC activity, elevated TMAO levels, and heightened inflammatory factor levels.
PubMed: 38500584
DOI: 10.3389/fmicb.2024.1354823