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1.
BMC Microbiol ; 24(1): 245, 2024 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-38970021

RESUMO

BACKGROUND: The phylum Bacteroidota represents a significant proportion of heterotrophic bacteria found in marine ecosystems. Members of the phylum Bacteroidota are actively involved in the degradation of biopolymers such as polysaccharides and proteins. Bacteroidota genomes exhibit a significant enrichment of various enzymes, including carbohydrate-active enzymes (CAZymes), carboxypeptidases, esterases, isomerases, peptidases, phosphatases, and sulfatases. The genus Marivirga, a member of the family Marivirgaceae within the phylum Bacteroidota, comprises six documented species. During a microbial diversity study, three novel Marivirga strains (BKB1-2 T, ABR2-2, and BDSF4-3 T) were isolated from the West Sea, Republic of Korea. RESULTS: To explore the taxonomic status and genomic characteristics of the novel isolates, we employed a polyphasic taxonomic approach, which included phylogenetic, chemotaxonomic and comprehensive genome analysis. The three isolates were Gram-stain-negative, aerobic, rod-shaped, moderately halophilic, and had a gliding motility. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among the two isolates, BKB1-2 T and BDSF4-3 T, and the six reference strains were 70.5-76.5% for ANI and 18.1-25.7% for dDDH. Interestingly, the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the strains harbor genes for a comprehensive pathway for dissimilatory nitrate reduction to ammonium (DNRA), as well as other nitrogen pathways for the reduction of nitrite, nitric oxide, and nitrous oxide. Additionally, the antiSMASH analysis indicated that the strains contained three to eight biosynthetic gene clusters (BGCs) associated with the synthesis of secondary metabolites. Furthermore, the strains carried a high number of CAZyme ranging from 53 to 152, which was also demonstrated by an in vitro analysis of degradation of the polysaccharide cellulose, chitin, laminarin, starch, and xylan. Additionally, all the strains carried genes for the metabolism of heavy metals, and exhibited tolerance to heavy metals, with minimum inhibitory concentrations (MICs) in millimoles (mM) in ranges of Co2+ (3-6), Cu2+ (0.2-0.4), Ni2+ (3-5), Zn2+ (2-4), Mn2+ (20-50), and Hg2+ (0.3). CONCLUSIONS: Based on polyphasic taxonomic approach, the three isolated strains represent two novel species names Marivirga arenosa sp. nov. (BKB1-2 T = KCTC 82989 T = InaCC B1618T), and Marivirga salinae sp. nov. (BDSF4-3 T = KCTC 82973 T = InaCC B1619T).


Assuntos
DNA Bacteriano , Genoma Bacteriano , Filogenia , RNA Ribossômico 16S , República da Coreia , DNA Bacteriano/genética , RNA Ribossômico 16S/genética , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Bacteroidetes/classificação , Análise de Sequência de DNA , Hibridização de Ácido Nucleico
2.
BMC Microbiol ; 24(1): 237, 2024 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-38961326

RESUMO

OBJECTIVE: Bladder cancer(BCa) was a disease that seriously affects patients' quality of life and prognosis. To address this issue, many researches suggested that the gut microbiota modulated tumor response to treatment; however, this had not been well-characterized in bladder cancer. In this study, our objective was to determine whether the diversity and composition of the gut microbiota or the density of specific bacterial genera influence the prognosis of patients with bladder cancer. METHODS: We collected fecal samples from a total of 50 bladder cancer patients and 22 matched non-cancer individuals for 16S rDNA sequencing to investigate the distribution of Parabacteroides in these two groups. Further we conducted follow-up with cancer patients to access the impact of different genera of microorganisms on patients survival. We conducted a Fecal Microbiota Transplantation (FMT) and mono-colonization experiment with Parabacteroides distasonis to explore its potential enhancement of the efficacy of anti-PD-1 immunotherapy in MB49 tumor-bearing mice. Immunohistochemistry, transcriptomics and molecular experiment analyses were employed to uncover the underlying mechanisms. RESULTS: The 16S rDNA showed that abundance of the genus Parabacteroides was elevated in the non-cancer control group compared to bladder cancer group. The results of tumor growth curves showed that a combination therapy of P. distasonis and ICIs treatment significantly delayed tumor growth and increased the intratumoral densities of both CD4+T and CD8+T cells. The results of transcriptome analysis demonstrated that the pathways associated with antitumoral immune response were remarkably upregulated in the P. distasonis gavage group. CONCLUSION: P. distasonis delivery combined with α-PD-1 mAb could be a new strategy to enhance the effect of anti-PD-1 immunotherapy. This effect might be achieved by activating immune and antitumor related pathways.


Assuntos
Bacteroidetes , Transplante de Microbiota Fecal , Microbioma Gastrointestinal , Imunoterapia , Neoplasias da Bexiga Urinária , Neoplasias da Bexiga Urinária/terapia , Neoplasias da Bexiga Urinária/imunologia , Neoplasias da Bexiga Urinária/microbiologia , Animais , Humanos , Camundongos , Imunoterapia/métodos , Bacteroidetes/genética , Bacteroidetes/imunologia , Feminino , Masculino , RNA Ribossômico 16S/genética , Fezes/microbiologia , Pessoa de Meia-Idade , Idoso , Camundongos Endogâmicos C57BL
3.
Artigo em Inglês | MEDLINE | ID: mdl-38963413

RESUMO

A Gram-stain-negative, yellow-pigmented, and facultatively aerobic bacterium, designated strain GPA1T, was isolated from plastic waste landfill soil in the Republic of Korea. The cells were non-motile short rods exhibiting oxidase-negative and catalase-positive activities. Growth was observed at 15-40 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 0-2.5 % (w/v) NaCl (optimum, 0 %). Menaquinone-7 was the sole respiratory quinone, and iso-C15 : 0, C16 : 1 ω5c, and iso-C17 : 0 3-OH were the major cellular fatty acids (>10 % of the total fatty acids). Phosphatidylethanolamine was identified as a major polar lipid. Phylogenetic analyses based on 16S rRNA gene sequences and 120 concatenated marker protein sequences revealed that strain GPA1T formed a distinct lineage within the genus Chitinophaga. The genome of strain GPA1T was 6078 kb in size with 53.8 mol% G+C content. Strain GPA1T exhibited the highest similarity to Chitinophaga rhizosphaerae T16R-86T, with a 98.6 % 16S rRNA gene sequence similarity, but their average nucleotide identity and digital DNA-DNA hybridization values were 82.5 and 25.9 %, respectively. Based on its phenotypic, chemotaxonomic, and phylogenetic characteristics, strain GPA1T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga pollutisoli sp. nov. is proposed. The type strain is GPA1T (=KACC 23415T=JCM 36644T).


Assuntos
Técnicas de Tipagem Bacteriana , Bacteroidetes , Composição de Bases , DNA Bacteriano , Ácidos Graxos , Sedimentos Geológicos , Fosfatidiletanolaminas , Filogenia , RNA Ribossômico 16S , Análise de Sequência de DNA , Microbiologia do Solo , Vitamina K 2 , RNA Ribossômico 16S/genética , República da Coreia , Ácidos Graxos/química , Vitamina K 2/análogos & derivados , Vitamina K 2/química , Vitamina K 2/análise , DNA Bacteriano/genética , Sedimentos Geológicos/microbiologia , Bacteroidetes/isolamento & purificação , Bacteroidetes/classificação , Bacteroidetes/genética , Hibridização de Ácido Nucleico , Instalações de Eliminação de Resíduos , Genoma Bacteriano
4.
Sci Rep ; 14(1): 13819, 2024 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-38879636

RESUMO

Culture-dependent and metagenomic binning techniques were employed to gain an insight into the diversification of gut bacteria in Rhinopithecius bieti, a highly endangered primate endemic to China. Our analyses revealed that Bacillota_A and Bacteroidota were the dominant phyla. These two phyla species are rich in carbohydrate active enzymes, which could provide nutrients and energy for their own or hosts' survival under different circumstances. Among the culturable bacteria, one novel bacterium, designated as WQ 2009T, formed a distinct branch that had a low similarity to the known species in the family Sphingobacteriaceae, based on the phylogenetic analysis of its 16S rRNA gene sequence or phylogenomic analysis. The ANI, dDDH and AAI values between WQ 2009T and its most closely related strains S. kitahiroshimense 10CT, S. pakistanense NCCP-246T and S. faecium DSM 11690T were significantly lower than the accepted cut-off values for microbial species delineation. All results demonstrated that WQ 2009T represent a novel genus, for which names Rhinopithecimicrobium gen. nov. and Rhinopithecimicrobium faecis sp. nov. (Type strain WQ 2009T = CCTCC AA 2021153T = KCTC 82941T) are proposed.


Assuntos
Microbioma Gastrointestinal , Metagenômica , Filogenia , RNA Ribossômico 16S , Animais , Microbioma Gastrointestinal/genética , Metagenômica/métodos , RNA Ribossômico 16S/genética , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Bacteroidetes/classificação
5.
Gut Microbes ; 16(1): 2350150, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38841888

RESUMO

Comensal Bacteroidota (Bacteroidota) and Enterobacteriacea are often linked to gut inflammation. However, the causes for variability of pro-inflammatory surface antigens that affect gut commensal/opportunistic dualism in Bacteroidota remain unclear. By using the classical lipopolysaccharide/O-antigen 'rfb operon' in Enterobacteriaceae as a surface antigen model (5-rfb-gene-cluster rfbABCDX), and a recent rfbA-typing strategy for strain classification, we characterized the integrity and conservancy of the entire rfb operon in Bacteroidota. Through exploratory analysis of complete genomes and metagenomes, we discovered that most Bacteroidota have the rfb operon fragmented into nonrandom patterns of gene-singlets and doublets/triplets, termed 'rfb-gene-clusters', or rfb-'minioperons' if predicted as transcriptional. To reflect global operon integrity, contiguity, duplication, and fragmentation principles, we propose a six-category (infra/supra-numerary) cataloging system and a Global Operon Profiling System for bacteria. Mechanistically, genomic sequence analyses revealed that operon fragmentation is driven by intra-operon insertions of predominantly Bacteroides-DNA (thetaiotaomicron/fragilis) and likely natural selection in gut-wall specific micro-niches or micropathologies. Bacteroides-insertions, also detected in other antigenic operons (fimbriae), but not in operons deemed essential (ribosomal), could explain why Bacteroidota have fewer KEGG-pathways despite large genomes. DNA insertions, overrepresenting DNA-exchange-avid (Bacteroides) species, impact our interpretation of functional metagenomics data by inflating by inflating gene-based pathway inference and by overestimating 'extra-species' abundance. Of disease relevance, Bacteroidota species isolated from cavitating/cavernous fistulous tract (CavFT) microlesions in Crohn's Disease have supra-numerary fragmented operons, stimulate TNF-alpha from macrophages with low potency, and do not induce hyperacute peritonitis in mice compared to CavFT Enterobacteriaceae. The impact of 'foreign-DNA' insertions on pro-inflammatory operons, metagenomics, and commensalism/opportunism requires further studies to elucidate their potential for novel diagnostics and therapeutics, and to elucidate the role of co-existing pathobionts in Crohn's disease microlesions.


Assuntos
Doença de Crohn , Microbioma Gastrointestinal , Metagenômica , Óperon , Camundongos , Animais , Humanos , Doença de Crohn/microbiologia , Doença de Crohn/genética , Bacteroidetes/genética , Bacteroidetes/classificação , Antígenos de Bactérias/genética , Genoma Bacteriano , Enterobacteriaceae/genética , Enterobacteriaceae/classificação
6.
PeerJ ; 12: e17450, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38860210

RESUMO

Background: Spodoptera frugiperda, the fall armyworm is a destructive invasive pest, and S. litura the tobacco cutworm, is a native species closely related to S. frugiperda. The gut microbiota plays a vital role in insect growth, development, metabolism and immune system. Research on the competition between invasive species and closely related native species has focused on differences in the adaptability of insects to the environment. Little is known about gut symbiotic microbe composition and its role in influencing competitive differences between these two insects. Methods: We used a culture-independent approach targeting the 16S rRNA gene of gut bacteria of 5th instar larvae of S. frugiperda and S. litura. Larvae were reared continuously on maize leaves for five generations. We analyzed the composition, abundance, diversity, and metabolic function of gut microbiomes of S. frugiperda and S. litura larvae. Results: Firmicutes, Proteobacteria, and Bacteroidetes were the dominant bacterial phyla in both species. Enterococcus, ZOR0006, Escherichia, Bacteroides, and Lactobacillus were the genera with the highest abundance in S. frugiperda. Enterococcus, Erysipelatoclostridium, ZOR0006, Enterobacter, and Bacteroides had the highest abundance in S. litura. According to α-diversity analysis, the gut bacterial diversity of S. frugiperda was significantly higher than that of S. litura. KEGG analysis showed 15 significant differences in metabolic pathways between S. frugiperda and S. litura gut bacteria, including transcription, cell growth and death, excretory system and circulatory system pathways. Conclusion: In the same habitat, the larvae of S. frugiperda and S. litura showed significant differences in gut bacterial diversity and community composition. Regarding the composition and function of gut bacteria, the invasive species S. frugiperda may have a competitive advantage over S. litura. This study provides a foundation for developing control strategies for S. frugiperda and S. litura.


Assuntos
Microbioma Gastrointestinal , Larva , RNA Ribossômico 16S , Spodoptera , Animais , Microbioma Gastrointestinal/genética , Spodoptera/microbiologia , Spodoptera/genética , Larva/microbiologia , RNA Ribossômico 16S/genética , Proteobactérias/genética , Proteobactérias/isolamento & purificação , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Firmicutes/genética , Firmicutes/isolamento & purificação , Bactérias/genética , Bactérias/classificação , Lactobacillus/genética , Lactobacillus/isolamento & purificação , Enterococcus/genética , Bacteroides/genética , Simbiose
7.
Sci Rep ; 14(1): 12827, 2024 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-38834834

RESUMO

Gut microbiota plays a crucial role in gastrointestinal tumors. Additionally, gut microbes influence the progression of esophageal cancer. However, the major bacterial genera that affect the invasion and metastasis of esophageal cancer remain unknown, and the underlying mechanisms remain unclear. Here, we investigated the gut flora and metabolites of patients with esophageal squamous cell carcinoma and found abundant Bacteroides and increased secretion and entry of the surface antigen lipopolysaccharide (LPS) into the blood, causing inflammatory changes in the body. We confirmed these results in a mouse model of 4NQO-induced esophageal carcinoma in situ and further identified epithelial-mesenchymal transition (EMT) occurrence and TLR4/Myd88/NF-κB pathway activation in mouse esophageal tumors. Additionally, in vitro experiments revealed that LPS from Bacteroides fragile promoted esophageal cancer cell proliferation, migration, and invasion, and induced EMT by activating the TLR4/Myd88/NF-κB pathway. These results reveal that Bacteroides are closely associated with esophageal cancer progression through a higher inflammatory response level and signaling pathway activation that are both common to inflammation and tumors induced by LPS, providing a new biological target for esophageal cancer prevention or treatment.


Assuntos
Transição Epitelial-Mesenquimal , Neoplasias Esofágicas , Carcinoma de Células Escamosas do Esôfago , Lipopolissacarídeos , Fator 88 de Diferenciação Mieloide , NF-kappa B , Transdução de Sinais , Receptor 4 Toll-Like , Receptor 4 Toll-Like/metabolismo , Fator 88 de Diferenciação Mieloide/metabolismo , Animais , NF-kappa B/metabolismo , Humanos , Neoplasias Esofágicas/patologia , Neoplasias Esofágicas/metabolismo , Neoplasias Esofágicas/microbiologia , Camundongos , Carcinoma de Células Escamosas do Esôfago/metabolismo , Carcinoma de Células Escamosas do Esôfago/patologia , Carcinoma de Células Escamosas do Esôfago/microbiologia , Transição Epitelial-Mesenquimal/efeitos dos fármacos , Linhagem Celular Tumoral , Invasividade Neoplásica , Inflamação/metabolismo , Inflamação/patologia , Bacteroidetes , Microbioma Gastrointestinal , Movimento Celular/efeitos dos fármacos , Masculino , Metástase Neoplásica , Proliferação de Células , Feminino
8.
Benef Microbes ; 15(4): 343-355, 2024 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-38879179

RESUMO

Chronic intestinal inflammation is associated with strong alterations of the microbial composition of the gut. Probiotic treatments and microbiota-targeting approaches have been considered to reduce the inflammation, improve both gut barrier function as well as overall gastrointestinal health. Here, a murine model of experimental colitis was used to assess the beneficial health effects of Bacillus subtilis SF106 and Bacillus clausii (recently renamed Shouchella clausii) SF174, two spore-forming strains previously characterised in vitro as potential probiotics. Experimental colitis was induced in BALB/c mice by the oral administration of dextran sodium sulphate (DSS) and groups of animals treated with spores of either strain. Spores of both strains reduced the DSS-induced inflammation with spores of B. clausii SF174 more effective than B. subtilis SF106. Spores of both strains remodelled the mouse gut microbiota favouring the presence of beneficial microbes such as members of the Bacteroidetes and Akkermansia genera.


Assuntos
Bacillus clausii , Bacillus subtilis , Colite , Sulfato de Dextrana , Modelos Animais de Doenças , Microbioma Gastrointestinal , Camundongos Endogâmicos BALB C , Probióticos , Esporos Bacterianos , Animais , Probióticos/administração & dosagem , Colite/microbiologia , Colite/induzido quimicamente , Colite/terapia , Camundongos , Sulfato de Dextrana/toxicidade , Inflamação/microbiologia , Bacteroidetes , Akkermansia , Feminino
9.
Skin Res Technol ; 30(7): e13792, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38940462

RESUMO

BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin disease that affects 15%-30% of children and 10% of adults globally, with its incidence being influenced by genetic, environmental, and various other factors. While the immune plays a crucial role in the development, the composition of gut microbiota and serum metabolites also contribute to its pathogenesis. SUBJECT: Study the characteristics of gut microbiota and serum metabolites in patients with atopic dermatitis METHOD: In this study, we collected stool and serum samples from 28 AD patients and 23 healthy individuals (NC) for metagenomic sequencing of gut microbiota and non-targeted metabolomic sequencing of serum. RESULT: Our results revealed a lower diversity of gut microbiota in the AD group compared to the NC group. The predominant Phylum in AD patients were Bacteroidetes, Pseudomonas, and Verrucomicrobia, with the most dominant bacterial genus being Faecalibacterium. At the species level, Prevotella copri and Faecalibacterium prausnitzii were found to be the most abundant bacteria. Significant differences in serum metabolite profiles were observed between NC and AD patients, with noticeable variations in metabolite expression levels. The majority of metabolites in the serum of AD patients exhibited low expression, while a few showed high expression levels. Notably, metabolites such as Cholesterol glucuronide, Styrene, Lutein, Betaine, Phosphorylcholine, Taurine, and Creatinine displayed the most pronounced alterations. CONCLUSION: These findings contribute to a further understanding of the complexities underlying this disease.


Assuntos
Dermatite Atópica , Fezes , Microbioma Gastrointestinal , Humanos , Dermatite Atópica/microbiologia , Dermatite Atópica/sangue , Microbioma Gastrointestinal/fisiologia , Masculino , Feminino , Adulto , Fezes/microbiologia , Criança , Adulto Jovem , Pessoa de Meia-Idade , Adolescente , Metaboloma/fisiologia , Bacteroidetes
10.
Open Biol ; 14(6): 230448, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38862016

RESUMO

Gram-negative bacteria from the Bacteroidota phylum possess a type-IX secretion system (T9SS) for protein secretion, which requires cargoes to have a C-terminal domain (CTD). Structurally analysed CTDs are from Porphyromonas gingivalis proteins RgpB, HBP35, PorU and PorZ, which share a compact immunoglobulin-like antiparallel 3+4 ß-sandwich (ß1-ß7). This architecture is essential as a P. gingivalis strain with a single-point mutant of RgpB disrupting the interaction of the CTD with its preceding domain prevented secretion of the protein. Next, we identified the C-terminus ('motif C-t.') and the loop connecting strands ß3 and ß4 ('motif Lß3ß4') as conserved. We generated two strains with insertion and replacement mutants of PorU, as well as three strains with ablation and point mutants of RgpB, which revealed both motifs to be relevant for T9SS function. Furthermore, we determined the crystal structure of the CTD of mirolase, a cargo of the Tannerella forsythia T9SS, which shares the same general topology as in Porphyromonas CTDs. However, motif Lß3ß4 was not conserved. Consistently, P. gingivalis could not properly secrete a chimaeric protein with the CTD of peptidylarginine deiminase replaced with this foreign CTD. Thus, the incompatibility of the CTDs between these species prevents potential interference between their T9SSs.


Assuntos
Proteínas de Bactérias , Sistemas de Secreção Bacterianos , Porphyromonas gingivalis , Porphyromonas gingivalis/metabolismo , Porphyromonas gingivalis/genética , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Sistemas de Secreção Bacterianos/metabolismo , Sistemas de Secreção Bacterianos/genética , Sistemas de Secreção Bacterianos/química , Modelos Moleculares , Cristalografia por Raios X , Sequência de Aminoácidos , Sinais Direcionadores de Proteínas , Domínios Proteicos , Bacteroidetes/metabolismo , Bacteroidetes/genética , Tannerella forsythia/metabolismo , Tannerella forsythia/genética , Tannerella forsythia/química , Relação Estrutura-Atividade , Conformação Proteica
11.
FEBS Open Bio ; 14(7): 1133-1146, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38735878

RESUMO

Proteins featuring the Domain of Unknown Function 1735 are frequently found in Polysaccharide Utilization Loci, yet their role remains unknown. The domain and vicinity analyzer programs we developed mine the Kyoto Encyclopedia of Genes and Genomes and UniProt to enhance the functional prediction of DUF1735. Our datasets confirmed the exclusive presence of DUF1735 in Bacteroidota genomes, with Bacteroidetes thetaiotaomicron harboring 46 copies. Notably, 97.8% of DUF1735 are encoded in PULs, and 89% are N-termini of multimodular proteins featuring C-termini like Laminin_G_3, F5/8-typeC, and GH18 domains. Predominantly possessing a predicted lipoprotein signal peptide and sharing an immunoglobulin-like ß-sandwich fold with the BACON domain and the N-termini of SusE/F, DUF1735 likely functions as N-terminal, membrane-bound spacer for diverse C-termini involved in PUL-mediated carbohydrate utilization.


Assuntos
Polissacarídeos , Polissacarídeos/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Metabolismo dos Carboidratos/genética , Bacteroidetes/genética
12.
J Microbiol Biotechnol ; 34(6): 1214-1221, 2024 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-38783719

RESUMO

The accumulating evidence substantiates the indispensable role of gut microbiota in modulating the pathogenesis of type 2 diabetes. Uncovering the intricacies of the mechanism is imperative in aiding disease control efforts. Revealing key bacterial species, their metabolites and/or metabolic pathways from the vast array of gut microorganisms can significantly contribute to precise treatment of the disease. With a high prevalence of type 2 diabetes in Inner Mongolia, China, we recruited volunteers from among the Mongolian population to investigate the relationship between gut microbiota and the disease. Fecal samples were collected from the Volunteers of Mongolia with Type 2 Diabetes group and a Control group, and detected by metagenomic analysis and untargeted metabolomics analysis. The findings suggest that Firmicutes and Bacteroidetes phyla are the predominant gut microorganisms that exert significant influence on the pathogenesis of type 2 diabetes in the Mongolian population. In the disease group, despite an increase in the quantity of most gut microbial metabolic enzymes, there was a concomitant weakening of gut metabolic function, suggesting that the gut microbiota may be in a compensatory state during the disease stage. ß-Tocotrienol may serve as a pivotal gut metabolite produced by gut microorganisms and a potential biomarker for type 2 diabetes. The metabolic biosynthesis pathways of ubiquinone and other terpenoid quinones could be the crucial mechanism through which the gut microbiota regulates type 2 diabetes. Additionally, certain Clostridium gut species may play a pivotal role in the progression of the disease.


Assuntos
Bactérias , Diabetes Mellitus Tipo 2 , Fezes , Microbioma Gastrointestinal , Humanos , Diabetes Mellitus Tipo 2/microbiologia , Fezes/microbiologia , Pessoa de Meia-Idade , Masculino , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo , Mongólia , Feminino , China , Adulto , Metabolômica , Firmicutes/isolamento & purificação , Metagenômica , Bacteroidetes/isolamento & purificação , Bacteroidetes/metabolismo , Bacteroidetes/genética , Redes e Vias Metabólicas , Idoso
13.
Microb Pathog ; 192: 106647, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38788811

RESUMO

Recent research has revealed that alterations of the gut microbiome (GM) play a comprehensive role in the pathophysiology of HF. However, findings in this field remain controversial. In this study, we focus on differences in GM diversity and abundance between HF patients and non-HF people, based on previous 16 S ribosomal RNA (16rRNA) gene sequencing. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we conducted a comprehensive search of PubMed, Web of Science, Embase, Cochrane Library, and Ovid databases using the keyword "Heart failure" and "Gastrointestinal Microbiome". A significant decrease in alpha diversity was observed in the HF patients (Chao1, I2 = 87.5 %, p < 0.001; Shannon index, I2 = 62.8 %, p = 0.021). At the phylum level, the HF group exhibited higher abundances of Proteobacteria (I2 = 92.0 %, p = 0.004) and Actinobacteria (I2 = 82.5 %, p = 0.010), while Bacteroidetes (I2 = 45.1 %, p = 0.017) and F/B ratio (I2 = 0.0 %, p<0.001) were lower. The Firmicutes showed a decreasing trend but did not reach statistical significance (I2 = 82.3 %, p = 0.127). At the genus level, the relative abundances of Streptococcus, Bacteroides, Alistipes, Bifidobacterium, Escherichia-Shigella, Enterococcus and Klebsiella were increased in the HF group, whereas Ruminococcus, Faecalibacterium, Dorea and Megamona exhibited decreased relative abundances. Dialister, Blautia and Prevotella showed decreasing trends but without statistical significance. This observational meta-analysis suggests that GM changes are associated with HF, manifesting as alterations in GM abundance, disruptions in the production of short-chain fatty acids (SCFAs) bacteria, and an increase in trimethylamine N-oxide (TMAO) producing bacteria.


Assuntos
Bactérias , Microbioma Gastrointestinal , Insuficiência Cardíaca , Humanos , Insuficiência Cardíaca/microbiologia , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , RNA Ribossômico 16S/genética , Proteobactérias/genética , Proteobactérias/isolamento & purificação , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação
14.
PLoS One ; 19(5): e0302522, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38758940

RESUMO

Paddlefish has high economic and ecological value. In this study, microbial diversity and community structure in intestine, stomach, and mouth of paddlefish were detected using high-throughput sequencing. The results showed that the diversity and richness indices decreased along the digestive tract, and significantly lower proportion of those were observed in intestine. Firmicutes, Bacteroidetes and Proteobacteria were the dominant phyla. In top 10 phyla, there was no significant difference in mouth and stomach. But compared with intestine, there were significant differences in 8 of the 10 phyla, and Firmicutes and Bacteroidetes increased significantly, while Proteobacteria decreased significantly. There was no dominant genus in mouth and stomach, but Clostridium_sensu_stricto_1 and uncultured_bacterium_o_Bacteroidales was predominant in intestine. In conclusion, the species and abundance of microbiota in the mouth and stomach of paddlefish were mostly the same, but significantly different from those in intestine. Moreover, there was enrichment of the dominant bacteria in intestine.


Assuntos
Peixes , Microbioma Gastrointestinal , Animais , Peixes/microbiologia , Trato Gastrointestinal/microbiologia , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Boca/microbiologia , Estômago/microbiologia , Proteobactérias/isolamento & purificação , Proteobactérias/genética , Sequenciamento de Nucleotídeos em Larga Escala , Intestinos/microbiologia , Bacteroidetes/isolamento & purificação , Bacteroidetes/genética , Firmicutes/isolamento & purificação , Firmicutes/genética , Firmicutes/classificação , RNA Ribossômico 16S/genética , Biodiversidade
15.
Chemosphere ; 360: 142339, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38754488

RESUMO

The environmental burden due to industrial activities has been quite observable in the last few years, with heavy metals (HMs) like lead, cadmium, and arsenic inducing serious perturbations to the microbial ecosystem of groundwater. Studies carried out in North China, a region known for interconnection of industrial and groundwater systems, sought to explore the natural mechanisms of adaptation of microbes to groundwater contamination. The results showed that heavy metals permeate from surface increased the diversity and abundance of microbial communities in groundwater, producing an average decrease of 40.84% and 34.62% in the relative abundance of Bacteroidetes and Proteobacteria in groundwater, respectively. Meanwhile, the key environmental factors driving the evolution of microbial communities shift from groundwater nutrients to heavy metals, which explained 50.80% of the change in the microbial community composition. Microbial indicators are more sensitive to HMs pollution and could accurately identify industrial area where HMs permeation occurred and other extraneous pollutants. The phylum Bacteroidetes could act as appropriate indicators for the identification. Significant genera that were identified, being Mesorhizobium, Clostridium, Bacillus and Mucilaginibacter, were found to play important roles in the microbial network in terms of the potential to assist in groundwater clean-up. Notably, pollution from heavy metals has diminished the effectiveness and resilience of microbial communities in groundwater, thereby heightening the susceptibility of these normally stable microbial ecosystems. These findings offer new perspectives on how to monitor and detect groundwater pollution, and provide scientific guidance for developing suitable remediation methods for groundwater contaminated with heavy metals. Future research is essential explore the application of metal-tolerant or resistant bacteria in bioremediation strategies to rehabilitate groundwater systems contaminated by HMs.


Assuntos
Monitoramento Ambiental , Água Subterrânea , Metais Pesados , Poluentes Químicos da Água , Metais Pesados/análise , Poluentes Químicos da Água/análise , Poluentes Químicos da Água/metabolismo , Água Subterrânea/química , Água Subterrânea/microbiologia , China , Monitoramento Ambiental/métodos , Microbiota/efeitos dos fármacos , Bactérias/metabolismo , Bactérias/efeitos dos fármacos , Bacteroidetes , Indústrias , Ecossistema
16.
Artigo em Inglês | MEDLINE | ID: mdl-38739684

RESUMO

The Bacteroidota is one of the dominant bacterial phyla in corals. However, the exact taxa of those coral bacteria under the Bacteroidota are still unclear. Two aerobic, Gram-stain-negative, non-motile rods, designated strains BMA10T and BMA12T, were isolated from stony coral Porites lutea collected from Weizhou Island, PR China. Global alignment of 16S rRNA gene sequences indicated that both strains are closest to species of Fulvivirga with the highest identities being lower than 93 %, and the similarity value between these two strains was 92.3 %. Phylogenetic analysis based on 16S rRNA gene and genome sequences indicated that these two strains form an monophylogenetic lineage alongside the families Fulvivirgaceae, Reichenbachiellaceae, Roseivirgaceae, Marivirgaceae, Cyclobacteriaceae, and Cesiribacteraceae in the order Cytophagales, phylum Bacteroidota. The genomic DNA G+C contents of BMA10T and BMA12T were 38.4 and 41.9 mol%, respectively. The major polar lipids of BMA10T were phosphatidylethanolamine, unidentified aminophospholipid, four unidentified aminolipids, and five unidentified lipids. While those of BMA12T were phosphatidylethanolamine, two unidentified aminolipids, and five unidentified lipids. The major cellular fatty acids detected in both isolates were iso-C15 : 0 and C16 : 1 ω5c. Carbohydrate-active enzyme analysis indicated these two strains may utilize coral mucus or chitin. Based on above characteristics, these two strains are suggested to represent two new species in two new genera of a new family in the order Cytophagales, for which the name Splendidivirga corallicola gen. nov., sp. nov., Agaribacillus aureus gen. nov., sp. nov. and Splendidivirgaceae fam. nov. are proposed. The type strain of S. corallicola is BMA10T (=MCCC 1K08300T=KCTC 102045T), and that for A. aureus is BMA12T (=MCCC 1K08309T=KCTC 102046T).


Assuntos
Antozoários , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano , Ácidos Graxos , Filogenia , RNA Ribossômico 16S , Análise de Sequência de DNA , Antozoários/microbiologia , Animais , RNA Ribossômico 16S/genética , Ácidos Graxos/análise , DNA Bacteriano/genética , China , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Bacteroidetes/classificação , Fosfolipídeos/análise
17.
Sci Rep ; 14(1): 10137, 2024 05 02.
Artigo em Inglês | MEDLINE | ID: mdl-38698108

RESUMO

Gut microbiota impact host physiology, though simultaneous investigations in ectothermic vertebrates are rare. Particularly, amphibians may exhibit more complex interactions between host physiology and the effects of gut microbiota due to the combination of seasonal changes and complex life histories. In this study, we assessed the relationships among food resources, gut bacterial communities, and host physiology in frogs (Phelophylax nigromaculatus), taking into account seasonal and life history variations. We found that food sources were not correlated with physiological parameters but had some relationships with the gut bacterial community. Variations in gut bacterial community and host physiology were influenced by the combined effects of seasonal differences and life history, though mostly driven by seasonal differences. An increase in Firmicutes was associated with higher fat content, reflecting potential fat storage in frogs during the non-breeding season. The increase in Bacteroidetes resulted in lower fat content in adult frogs and decreased immunity in juvenile frogs during the breeding season, demonstrating a direct link. Our results suggest that the gut microbiome may act as a link between food conditions and physiological status, and that the combined effect of seasons and life history could reinforce the relationship between gut microbiota and physiological status in ectothermic animals. While food sources may influence the gut microbiota of ectotherms, we contend that temperature-correlated seasonal variation, which predominately influences most ectotherms, is a significant factor.


Assuntos
Anuros , Microbioma Gastrointestinal , Estações do Ano , Animais , Microbioma Gastrointestinal/fisiologia , Anuros/fisiologia , Anuros/microbiologia , Bactérias , Bacteroidetes
18.
Sci Rep ; 14(1): 10237, 2024 05 03.
Artigo em Inglês | MEDLINE | ID: mdl-38702505

RESUMO

Enzymatic degradation of algae cell wall carbohydrates by microorganisms is under increasing investigation as marine organic matter gains more value as a sustainable resource. The fate of carbon in the marine ecosystem is in part driven by these degradation processes. In this study, we observe the microbiome dynamics of the macroalga Fucus vesiculosus in 25-day-enrichment cultures resulting in partial degradation of the brown algae. Microbial community analyses revealed the phylum Pseudomonadota as the main bacterial fraction dominated by the genera Marinomonas and Vibrio. More importantly, a metagenome-based Hidden Markov model for specific glycosyl hydrolyses and sulphatases identified Bacteroidota as the phylum with the highest potential for cell wall degradation, contrary to their low abundance. For experimental verification, we cloned, expressed, and biochemically characterised two α-L-fucosidases, FUJM18 and FUJM20. While protein structure predictions suggest the highest similarity to a Bacillota origin, protein-protein blasts solely showed weak similarities to defined Bacteroidota proteins. Both enzymes were remarkably active at elevated temperatures and are the basis for a potential synthetic enzyme cocktail for large-scale algal destruction.


Assuntos
Parede Celular , Fucus , Metagenômica , Parede Celular/metabolismo , Fucus/metabolismo , Fucus/genética , Fucus/microbiologia , Metagenômica/métodos , Bacteroidetes/genética , Bacteroidetes/enzimologia , Metagenoma , Microbiota , Filogenia
19.
BMC Genomics ; 25(1): 495, 2024 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-38769483

RESUMO

Bacteria of the genera Xylanibacter and Segatella are among the most dominant groups in the rumen microbiota. They are characterized by the ability to utilize different hemicelluloses and pectin of plant cell-wall as well as plant energy storage polysaccharides. The degradation is possible with the use of cell envelope bound multiprotein apparatuses coded in polysaccharide utilization loci (PULs), which have been shown to be substrate specific. The knowledge of PUL presence in rumen Xylanibacter and Segatella based on bioinformatic analyses is already established and transcriptomic and genetic approaches confirmed predicted PULs for a limited number of substrates. In this study, we transcriptomically identified additional different PULs in Xylanibacter ruminicola KHP1 and Segatella bryantii TF1-3. We also identified substrate preferences and found that specific growth rate and extent of growth impacted the choice of substrates preferentially used for degradation. These preferred substrates were used by both strains simultaneously as judged by their PUL upregulation. Lastly, ß-glucan and xyloglucan were used by these strains in the absence of bioinformatically and transcriptomically identifiable PUL systems.


Assuntos
Perfilação da Expressão Gênica , Polissacarídeos , Rúmen , Xilanos , Animais , Xilanos/metabolismo , Polissacarídeos/metabolismo , Rúmen/microbiologia , Rúmen/metabolismo , Glucanos/metabolismo , beta-Glucanas/metabolismo , Especificidade por Substrato , Bacteroidetes/genética , Bacteroidetes/metabolismo , Transcriptoma
20.
Microbiol Spectr ; 12(6): e0401323, 2024 Jun 04.
Artigo em Inglês | MEDLINE | ID: mdl-38712938

RESUMO

Laccases (EC 1.10.3.2) are oxidoreductases that belong to the multicopper oxidase subfamily and are classified as yellow/white or blue according to their absorption spectrum. Yellow laccases are more useful for industrial processes since they oxidize nonphenolic compounds in the absence of a redox mediator and stand out for being more stable and functional under extreme conditions. This study aimed to characterize a new laccase that was predicted to be present in the genome of Chitinophaga sp. CB10 - Lac_CB10. Lac_CB10, with a molecular mass of 100.06 kDa, was purified and characterized via biochemical assays using guaiacol as a substrate. The enzyme demonstrated extremophilic characteristics, exhibiting relative activity under alkaline conditions (CAPS buffer pH 10.5) and thermophilic conditions (80-90°C), as well as maintaining its activity above 50% for 5 h at 80°C and 90°C. Furthermore, Lac_CB10 presented a spectral profile typical of yellow laccases, exhibiting only one absorbance peak at 300 nm (at the T2/T3 site) and no peak at 600 nm (at the T1 site). When lignin was degraded using copper as an inducer, 52.27% of the material was degraded within 32 h. These results highlight the potential of this enzyme, which is a novel yellow laccase with thermophilic and alkaline activity and the ability to act on lignin. This enzyme could be a valuable addition to the biorefinery process. In addition, this approach has high potential for industrial application and in the bioremediation of contaminated environments since these processes often occur at extreme temperatures and pH values. IMPORTANCE: The characterization of the novel yellow laccase, Lac_CB10, derived from Chitinophaga sp. CB10, represents a significant advancement with broad implications. This enzyme displays exceptional stability and functionality under extreme conditions, operating effectively under both alkaline (pH 10.5) and thermophilic (80-90°C) environments. Its capability to maintain considerable activity over extended periods, even at high temperatures, showcases its potential for various industrial applications. Moreover, its distinctive ability to efficiently degrade lignin-demonstrated by a significant 52.27% degradation within 32 h-signifies a promising avenue for biorefinery processes. This newfound laccase's characteristics position it as a crucial asset in the realm of bioremediation, particularly in scenarios involving contamination at extreme pH and temperature levels. The study's findings highlight the enzyme's capacity to address challenges in industrial processes and environmental cleanup, signifying its vital role in advancing biotechnological solutions.


Assuntos
Estabilidade Enzimática , Lacase , Lignina , Lacase/metabolismo , Lacase/genética , Lacase/isolamento & purificação , Lacase/química , Lignina/metabolismo , Concentração de Íons de Hidrogênio , Bacteroidetes/enzimologia , Bacteroidetes/genética , Especificidade por Substrato , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/química , Temperatura , Biodegradação Ambiental , Guaiacol/metabolismo , Cobre/metabolismo
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