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IScience Oct 2023Alcohol-related liver disease (ALD) is one of the leading causes of liver-related death worldwide. However, roles of oral microbiota in regulating the progression of ALD...
Alcohol-related liver disease (ALD) is one of the leading causes of liver-related death worldwide. However, roles of oral microbiota in regulating the progression of ALD remain unknown. Here, we fed mice with control or ethanol diet to establish chronic-plus-binge ALD model. 16S ribosomal DNA sequencing was performed on oral and cecum samples. We demonstrated that alcohol drinking influenced bacterial richness, microbial structure, and composition in oral samples of ethanol-fed mice compared with control mice. Alcohol consumption also remodeled relationships among oral microbes and altered functions of oral microbiota. Furthermore, oral microbiota, such as , , , and were closely associated with ALD parameters. Finally, we observed , , and possibly translocated along with oral-gut axis and positively correlated with the severity of ALD. Altogether, alcohol consumption reprogramed composition and functions of oral microbiota to promote ALD progression, suggesting that oral microbes might become a new target for ALD therapy.
PubMed: 37810215
DOI: 10.1016/j.isci.2023.107977 -
Nature Feb 2024To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage. In...
To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage. In bacteria, two families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats and environmental stressors have confounded their discovery. Here, by combining cryogenic electron microscopy, genetics and biochemistry, we identify Balon, a new hibernation factor in the cold-adapted bacterium Psychrobacter urativorans. We show that Balon is a distant homologue of the archaeo-eukaryotic translation factor aeRF1 and is found in 20% of representative bacteria. During cold shock or stationary phase, Balon occupies the ribosomal A site in both vacant and actively translating ribosomes in complex with EF-Tu, highlighting an unexpected role for EF-Tu in the cellular stress response. Unlike typical A-site substrates, Balon binds to ribosomes in an mRNA-independent manner, initiating a new mode of ribosome hibernation that can commence while ribosomes are still engaged in protein synthesis. Our work suggests that Balon-EF-Tu-regulated ribosome hibernation is a ubiquitous bacterial stress-response mechanism, and we demonstrate that putative Balon homologues in Mycobacteria bind to ribosomes in a similar fashion. This finding calls for a revision of the current model of ribosome hibernation inferred from common model organisms and holds numerous implications for how we understand and study ribosome hibernation.
Topics: Bacterial Proteins; Peptide Elongation Factor Tu; Protein Biosynthesis; Ribosomal Proteins; Ribosomes; Psychrobacter; Cryoelectron Microscopy; Cold-Shock Response; Peptide Termination Factors
PubMed: 38355796
DOI: 10.1038/s41586-024-07041-8 -
Food Research International (Ottawa,... Oct 2023Fermented fish and fermented fish-based products are part of the diet of many countries all over the world. Their popularity is not only due to the unique flavor, the... (Review)
Review
Fermented fish and fermented fish-based products are part of the diet of many countries all over the world. Their popularity is not only due to the unique flavor, the distinct texture, and the good nutritional quality, but also to the easiness of the production process, that is commonly based on empirical traditional methods. Fish fermentation techniques ususally rely on the combination of some key steps, including salting, addition of spices or additives, and maintenance of anaerobic conditions, thus selecting for the multiplication of some pro-technological microorganisms. The objective of the present review was to provide an overview of the current knowledge of the microbial communities occurring in fermented fish and fish-based products. Specific information was collected from scientific publications published from 2000 to 2022 with the aim of generating a comprehensive database. The production of fermented fish and fish-based foods was mostly localized in West African countries, Northern European countries, and Southeast Asian countries. Based on the available literature, the microbial composition of fermented fish and fish-based products was delineated by using viable counting combined with identification of isolates, and culture-independent techniques. The data obtained from viable counting highlighted the occurrence of microbial groups usually associated with food fermentation, namely lactic acid bacteria, staphylococci, Bacillus spp., and yeasts. The identification of isolates combined with culture-independent methods showed that the fermentative process of fish-based products was generally guided by lactobacilli (Lactiplantibacillus plantarum, Latilactobacillus sakei, and Latilactobacillus curvatus) or Tetragenococcus spp. depending on the salt concentration. Among lactic acid bacteria populations, Lactococcus spp., Pediococcus spp., Leuconostoc spp., Weissella spp., Enterococcus spp., Streptococcus spp., and Vagococcus spp. were frequently identified. Staphylococcus spp. and Bacillus spp. confirmed a great adaptation to fermented fish-based products. Other noteworthy bacterial taxa included Micrococcus spp., Pseudomonas spp., Psychrobacter spp., Halanaerobium spp., and Halomonas spp. Among human pathogenic bacteria, the occurrence of Clostridium spp. and Vibrio spp. was documented. As for yeast populations, the predominance of Candida spp., Debaryomyces spp., and Saccharomyces spp. was evidenced. The present literature review could serve as comprehensive database for the scientific community, and as a reference for the food industry in order to formulate tailored starter or adjunctive cultures for product improvement.
Topics: Animals; Humans; Acclimatization; Africa, Western; Bacillus; Candida; Databases, Factual; Enterococcaceae; Fishes
PubMed: 37689879
DOI: 10.1016/j.foodres.2023.113112 -
Neurobiology of Disease Feb 2024Studies from rodents to primates and humans indicate that individuals vary in how resilient they are to stress, and understanding the basis of these variations may help...
Studies from rodents to primates and humans indicate that individuals vary in how resilient they are to stress, and understanding the basis of these variations may help improve treatments for depression. Here we explored the potential contribution of the gut microbiome to such variation. Mice were exposed to chronic unpredictable mild stress (CUMS) for 4 weeks then allowed to recover for 3 weeks, after which they were subjected to behavioral tests and categorized as showing low or high stress resilience. The two types of mouse were compared in terms of hippocampal gene expression using RNA sequencing, fecal microbiomes using 16S RNA sequencing, and extent of neurogenesis in the hippocampus using immunostaining of brain sections. Fecal microbiota were transplanted from either type of mouse into previously stress-exposed and stress-naïve animals, and the effects of the transplantation on stress-induced behaviors and neurogenesis in the hippocampus were examined. Finally, we blocked neurogenesis using temozolomide to explore the role of neurogenesis promoted by fecal microbiota transplantation in enhancing resilience to stress. Results showed that highly stress-resilient mice, but not those with low resilience, improved significantly on measures of anhedonia, behavioral despair, and anxiety after 3-week recovery from CUMS. Their feces showed greater abundance of Lactobacillus, Bifidobacterium and Romboutsia than feces from mice with low stress resilience, as well as lower abundance of Staphylococcus, Psychrobacter and Corynebacterium. Similarly, highly stress-resilient mice showed greater neurogenesis in hippocampus than animals with low stress resilience. Transplanting fecal microbiota from mice with high stress resilience into previously CUMS-exposed recipients rescued neurogenesis in hippocampus, facilitating recovery from stress-induced depression and cognitive decline. Blockade of neurogenesis with temozolomide abolished recovery of recipients from CUMS-induced depression and cognitive decline in mice transplanted with fecal microbiota from mice with high stress resilience. In conclusion, our results suggested that remodeling of the gut microbiome after stress may reverse stress-induced impairment of hippocampal neurogenesis and thereby promote recovery from stress-induced depression.
Topics: Humans; Mice; Animals; Depression; Gastrointestinal Microbiome; Temozolomide; Hippocampus; Neurogenesis; Stress, Psychological
PubMed: 38176570
DOI: 10.1016/j.nbd.2023.106396 -
Microbiology Spectrum Aug 2023is an important bacterial genus that is widespread in Antarctic and marine environments. However, to date, only two complete phage sequences have been deposited in the...
is an important bacterial genus that is widespread in Antarctic and marine environments. However, to date, only two complete phage sequences have been deposited in the NCBI database. Here, the novel phage vB_PmaS_Y8A, infecting HM08A, was isolated from sewage in the Qingdao area, China. The morphology of vB_PmaS_Y8A was characterized by transmission electron microscopy, revealing an icosahedral head and long tail. The genomic sequence of vB_PmaS_Y8A is linear, double-stranded DNA with a length of 40,226 bp and 44.1% G+C content, and encodes 69 putative open reading frames. Two auxiliary metabolic genes (AMGs) were identified, encoding phosphoadenosine phosphosulfate reductase and MarR protein. The first AMG uses thioredoxin as an electron donor for the reduction of phosphoadenosine phosphosulfate to phosphoadenosine phosphate. MarR regulates multiple antibiotic resistance mechanisms in Escherichia coli and is rarely found in viruses. No tRNA genes were identified and no lysogeny-related feature genes were detected. However, many similar open reading frames (ORFs) were found in the host genome, which may indicate that Y8A also has a lysogenic stage. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analysis indicate that vB_PmaS_Y8A contains a novel genomic architecture similar only to that of phage pOW20-A, although at a low similarity. vB_PmaS_Y8A represents a new family-level virus cluster with 22 metagenomic assembled viral genomes, here named . Although is a well-known and important bacterial genus that is widespread in Antarctic and marine environments, genetic characterization of its phages is still rare. This study describes a novel phage containing an uncharacterized antibiotic resistance gene and representing a new virus family, . The characterization provided here will bolster current understanding of genomes, diversity, evolution, and phage-host interactions in populations.
Topics: Bacteriophages; Psychrobacter; Phylogeny; Phosphoadenosine Phosphosulfate; DNA, Viral; Genome, Viral; Escherichia coli; Open Reading Frames
PubMed: 37272818
DOI: 10.1128/spectrum.05335-22 -
Frontiers in Microbiology 2023In Goa, salt production from the local salt pans is an age-old practice. These salt pans harbor a rich diversity of halophilic microbes with immense biotechnological...
In Goa, salt production from the local salt pans is an age-old practice. These salt pans harbor a rich diversity of halophilic microbes with immense biotechnological applications, as they tolerate extremely harsh conditions. Detecting the existence of these microbes by a metabarcoding approach could be a primary step to harness their potential. Three salt pans Agarwado, Curca, and Nerul adjoining prominent estuaries of Goa were selected based on their unique geographical locations. The sediments of these salt pans were examined for their bacterial community and function by 16S rRNA amplicon-sequencing. These salt pans were hypersaline (400-450 PSU) and alkaline (pH 7.6-8.25), with 0.036-0.081 mg/L nitrite, 0.0031-0.016 mg/L nitrate, 6.66-15.81 mg/L sulfate, and 20.8-25.6 mg/L sulfide. The relative abundance revealed that the was dominant in salt pans of Nerul (13.9%), Curca (19.6%), and Agarwado (32.4%). The predominant genera in Nerul, Curca, and Agarwado salt pan sediments were (1.12%), (1.28%), and (25.5%) respectively. The highest alpha diversity (Shannon-diversity Index) was observed in the Nerul salt pan (4.8) followed by Curca (4.3) and Agarwado (2.03). Beta diversity indicated the highest dissimilarity between Agarwado and the other two salt pans (0.73) Nerul and Curca and the lowest dissimilarity was observed between Nerul and Curca salt pans (0.48). Additionally, in the Agarwado salt pan, 125 unique genera were detected, while in Nerul 119, and in Curca 28 distinct genera were noted. The presence of these exclusive microorganisms in a specific salt pan and its absence in the others indicate that the adjacent estuaries play a critical role in determining salt pan bacterial diversity. Further, the functional prediction of bacterial communities indicated the predominance of stress adaptation genes involved in osmotic balance, membrane modification, and DNA repair mechanisms. This is the first study to report the bacterial community structure and its functional genes in these three salt pans using Next-Generation Sequencing. The data generated could be used as a reference by other researchers across the world for bioprospecting these organisms for novel compounds having biotechnological and biomedical potential.
PubMed: 38111647
DOI: 10.3389/fmicb.2023.1230929 -
Eco-Environment & Health Dec 2023Indoor microorganisms impact asthma and allergic rhinitis (AR), but the associated microbial taxa often vary extensively due to climate and geographical variations. To...
Indoor microorganisms impact asthma and allergic rhinitis (AR), but the associated microbial taxa often vary extensively due to climate and geographical variations. To provide more consistent environmental assessments, new perspectives on microbial exposure for asthma and AR are needed. Home dust from 97 cases (32 asthma alone, 37 AR alone, 28 comorbidity) and 52 age- and gender-matched controls in Shanghai, China, were analyzed using high-throughput shotgun metagenomic sequencing and liquid chromatography-mass spectrometry. Homes of healthy children were enriched with environmental microbes, including , , and , and metabolites like keto acids, indoles, pyridines, and flavonoids (astragalin, hesperidin) (False Discovery Rate < 0.05). A neural network co-occurrence probability analysis revealed that environmental microorganisms were involved in producing these keto acids, indoles, and pyridines. Conversely, homes of diseased children were enriched with mycotoxins and synthetic chemicals, including herbicides, insecticides, and food/cosmetic additives. Using a random forest model, characteristic metabolites and microorganisms in Shanghai homes were used to classify high and low prevalence of asthma/AR in an independent dataset in Malaysian schools (N = 1290). Indoor metabolites achieved an average accuracy of 74.9% and 77.1% in differentiating schools with high and low prevalence of asthma and AR, respectively, whereas indoor microorganisms only achieved 51.0% and 59.5%, respectively. These results suggest that indoor metabolites and chemicals rather than indoor microbiome are potentially superior environmental indicators for childhood asthma and AR. This study extends the traditional risk assessment focusing on allergens or air pollutants in childhood asthma and AR, thereby revealing potential novel intervention strategies for these diseases.
PubMed: 38435359
DOI: 10.1016/j.eehl.2023.08.001 -
Antibiotics (Basel, Switzerland) Aug 2023This study investigated the longitudinal impact of methods for the drying off of cows with and without dry cow therapy (DCT) on the microbiota and resistome profile in...
This study investigated the longitudinal impact of methods for the drying off of cows with and without dry cow therapy (DCT) on the microbiota and resistome profile in colostrum and milk samples from cows. Three groups of healthy dairy cows ( = 24) with different antibiotic treatments during DCT were studied. Colostrum and milk samples from Month 0 (M0), 2 (M2), 4 (M4) and 6 (M6) were analysed using whole-genome shotgun-sequencing. The microbial diversity from antibiotic-treated groups was different and higher than that of the non-antibiotic group. This difference was more evident in milk compared to colostrum, with increasing diversity seen only in antibiotic-treated groups. The microbiome of antibiotic-treated groups clustered separately from the non-antibiotic group at M2-, M4- and M6 milk samples, showing the effect of antibiotic treatment on between-group (beta) diversity. The non-antibiotic group did not show a high relative abundance of mastitis-causing pathogens during early lactation and was more associated with genera such as , , and . A high relative abundance of antibiotic resistance genes (ARGs) was observed in the milk of antibiotic-treated groups with the Cephaguard group showing a significantly high abundance of genes conferring resistance to cephalosporin, aminoglycoside and penam classes. The data support the use of non-antibiotic alternatives for drying off in cows.
PubMed: 37627735
DOI: 10.3390/antibiotics12081315 -
Frontiers in Endocrinology 2023Non-alcoholic fatty liver disease (NAFLD) is a multifactorial disease. As a clinical empirical prescription of traditional Chinese medicine, Qushi Huayu decoction (QHD)...
INTRODUCTION
Non-alcoholic fatty liver disease (NAFLD) is a multifactorial disease. As a clinical empirical prescription of traditional Chinese medicine, Qushi Huayu decoction (QHD) has attracted considerable attention for its advantages in multi-target treatment of NAFLD. However, the intervention mechanism of QHD on abnormal lipid levels and gut microbiota in NAFLD has not been reported.
METHODS
Therefore, we verified the therapeutic effect of QHD on high-fat diet (HFD)-induced NAFLD in rats by physiological parameters and histopathological examination. In addition, studies on gut microbiota and serum lipidomics based on 16S rRNA sequencing and ultra-high performance liquid chromatography-mass spectrometry (UPLC-MS) were conducted to elucidate the therapeutic mechanism of NAFLD in QHD.
RESULTS
The changes in gut microbiota in NAFLD rats are mainly reflected in their diversity and composition, while QHD treated rats restored these changes. The genera and were predominant in the NAFLD group, whereas, , and were predominant in the NAFLD+QHD group. Lipid subclasses, including diacylglycerol (DG), triglycerides (TG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidic acid (PA), phosphatidylserine (PS), lysophosphatidylinositol (LPI), and phosphatidylglycerol (PG), were significantly different between the NAFLD and the control groups, while QHD treatment significantly altered the levels of DG, TG, PA, lysophosphatidylcholine (LPC), lysophosphatidylethanolamine (LPE), and platelet activating factor (PAF). Finally, Spearman's correlation analysis showed that NAFLD related differential lipid molecules were mainly associated with the genera of , and , which were also significantly correlated with the biological parameters of NAFLD.
DISCUSSION
Taken together, QHD may exert beneficial effects by regulating the gut microbiota and thus intervening in serum lipids.
Topics: Rats; Animals; Non-alcoholic Fatty Liver Disease; Gastrointestinal Microbiome; RNA, Ribosomal, 16S; Chromatography, Liquid; Rats, Sprague-Dawley; Tandem Mass Spectrometry; Triglycerides
PubMed: 37900123
DOI: 10.3389/fendo.2023.1272214 -
Frontiers in Microbiology 2024With the development of healthcare services, drug efficacy, and safety have become the focus of drug use, and processing alters drug toxicity and efficacy, exploring the...
BACKGROUND
With the development of healthcare services, drug efficacy, and safety have become the focus of drug use, and processing alters drug toxicity and efficacy, exploring the effects of processing on Evodiae fructus (EF) can guide the clinical use of drugs.
METHODS
Fifty male Kunming mice were randomly divided into the control group (CCN), raw small-flowered EF group (CRSEF), raw medium-flowered EF group (CRMEF), processing small-flowered EF group (CPSEF), and processing medium-flowered EF group (CPMEF). The CRSEF, CRMEF, CPSEF, and CPMEF groups were gavaged with aqueous extracts of raw small-flowered EF dry paste (RSEF), medium-flowered EF dry paste (RMEF), processing small-flowered EF dry paste (PSEF) and processing medium-flowered EF dry paste (PMEF), respectively, for 21 days at 5 times the pharmacopeial dosage. Upon concluding the experiment, histopathological sections of liver and kidney tissues were examined. Additionally, levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT), serum creatinine (SCr), and blood urea nitrogen (BUN) were determined. DNA from the intestinal contents of the mice was extracted, and 16S rRNA full-length high-throughput sequencing was performed.
RESULTS
After fed EF 21 days, mice exhibited a decreasing trend in body weight. Comparative analysis with the CCN group revealed an upward trend in SCr, BUN, AST, and ALT levels in both CRSEF and CRMEF groups. The CRMEF group displayed notably elevated BUN and AST levels, with an observed increasing trend in Scr and ALT. Kidney sections unveiled cellular edema and considerable inflammatory cell infiltrates, whereas significant liver damage was not evident. Compared with CRSEF, Bun levels were significantly lower while AST levels were significantly higher in the CPMEF group. Additionally, the intestinal microbiota diversity and the relative abundance of decreased significantly, and the relative abundance of , , and increased significantly in the CPMEF group. AST, ALT, and SCr were positively correlated with , , and .
CONCLUSION
In conclusion, PMEF significantly increased harmful bacteria (, , and ) and decreased beneficial bacteria. SEF with 5 times the clinical dose showed nephrotoxicity and SEF nephrotoxicity decreased after processing, but EF hepatotoxicity was not significant, which may be due to insufficient dose concentration and time.
PubMed: 38435687
DOI: 10.3389/fmicb.2024.1336777