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1.
J Agric Food Chem ; 67(30): 8303-8311, 2019 Jul 31.
Artigo em Inglês | MEDLINE | ID: mdl-31298535

RESUMO

Exposure to chiral pesticides poses many potential health risks. In this study, we examined the impacts of exposure to penconazole and its enantiomers on gut microbiota and metabolic profiles in mice. The relative abundance of microbiota in cecal content significantly changed following exposure to penconazole and its enantiomers. At the genus level, the relative abundances of seven gut microflora were altered following exposure to (-)-penconazole. Both (±)-penconazole and (+)-penconazole caused significant changes in the relative abundances of five gut microflora. In addition, targeted serum metabolomics analysis showed disturbed metabolic profiles following exposure. Respectively, (±)-penconazole, (+)-penconazole, and (-)-penconazole exposure significantly altered the relative levels of 29, 23, and 36 metabolites. In general, exposure to penconazole and its enantiomers caused disorders in gut microbiota and metabolic profiles of mice. The potential health risks of penconazole and its enantiomers now require further evaluation.


Assuntos
Microbioma Gastrointestinal/efeitos dos fármacos , Camundongos/metabolismo , Praguicidas/química , Praguicidas/farmacologia , Triazóis/química , Triazóis/farmacologia , Animais , Bactérias/efeitos dos fármacos , Bactérias/genética , Bactérias/isolamento & purificação , Trato Gastrointestinal/microbiologia , Masculino , Camundongos Endogâmicos ICR , Filogenia , Estereoisomerismo
2.
J Agric Food Chem ; 67(28): 7869-7879, 2019 Jul 17.
Artigo em Inglês | MEDLINE | ID: mdl-31287296

RESUMO

Carnitine, a dietary quaternary amine mainly from red meat, is metabolized to trimethylamine (TMA) by gut microbiota and subsequently oxidized to trimethylamine-N-oxide (TMAO) by host hepatic enzymes, flavin monooxygenases (FMOs). The objective of this study aims to investigate the effects of flavonoids from oolong tea and citrus peels on reducing TMAO formation and protecting vascular inflammation in carnitine-feeding mice. The results showed that mice treated with 1.3% carnitine in drinking water significantly (p < 0.05) increased the plasma levels of TMAO compared to control group, whereas the plasma TMAO was remarkedly reduced by flavonoids used. Meanwhile, these dietary phenolic compounds significantly (p < 0.05) decreased hepatic FMO3 mRNA levels compared to carnitine only group. Additionally, oolong tea extract decreased mRNA levels of vascular inflammatory markers such as tissue necrosis factor-alpha (TNF-α), vascular cell adhesion molecule-1 (VCAM-1) and E-selectin. Polymethoxyflavones significantly lowered the expression of VCAM-1 and showed a decreasing trend in TNF-α and E-selectin mRNA expression compared to the carnitine group. Genus-level analysis of the gut microbiota in the cecum showed that these dietary phenolic compounds induced an increase in the relative abundances of Bacteroides. Oolong tea extract-treated group up-regulated Lactobacillus genus, compared to the carnitine only group. Administration of polymethoxyflavones increased Akkermansia in mice.


Assuntos
Aterosclerose/tratamento farmacológico , Aterosclerose/metabolismo , Camellia sinensis/química , Carnitina/metabolismo , Citrus/química , Flavonas/administração & dosagem , Extratos Vegetais/administração & dosagem , Animais , Aterosclerose/genética , Aterosclerose/microbiologia , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo , Biotransformação/efeitos dos fármacos , Feminino , Flavonas/análise , Microbioma Gastrointestinal/efeitos dos fármacos , Trato Gastrointestinal/metabolismo , Trato Gastrointestinal/microbiologia , Humanos , Metilaminas/metabolismo , Camundongos , Camundongos Endogâmicos C57BL , Extratos Vegetais/análise , Fator de Necrose Tumoral alfa/genética , Fator de Necrose Tumoral alfa/metabolismo , Molécula 1 de Adesão de Célula Vascular/genética , Molécula 1 de Adesão de Célula Vascular/metabolismo
3.
Z Gastroenterol ; 57(7): 871-882, 2019 Jul.
Artigo em Alemão | MEDLINE | ID: mdl-31288283

RESUMO

Along with the increasing prevalence of obesity, metabolic syndrome and type 2 diabetes, non-alcoholic fatty liver disease (NAFLD) is rapidly increasing and poses a major challenge for gastroenterologists. Many studies have demonstrated that the microbiome is closely associated with the progression of nutrition-related diseases, especially of fatty liver disease. Changes in the quantity and quality of the intestinal flora, commonly referred to as dysbiosis, result in altered food metabolism, increased permeability of the intestinal barrier ("leaky gut") and consecutive inflammatory processes in the liver. This favors both the progression of obesity and metabolic disorders as well as NAFLD towards non-alcoholic steatohepatitis (NASH), hepatic fibrosis, cirrhosis and hepatocellular carcinoma (HCC). Important molecular mechanisms include microbial metabolites, microbial and endogenous signaling substances (so-called PAMPs/DAMPs) as well as bile acids. Essential cellular mechanisms include immune cells in the gut and liver, especially macrophages and Kupffer cells, as well as intestinal epithelial cells and hepatocytes as central regulators of metabolism. In this review article, we briefly summarize the relevant species of the human microbiome, describe the microbial analytics, explain the most important molecular relationships between microbiome and NAFLD/NASH, and finally the opportunities and challenges of microbiome-modulating therapy for the treatment of fatty liver disease.


Assuntos
Microbioma Gastrointestinal , Trato Gastrointestinal/microbiologia , Microbiota , Hepatopatia Gordurosa não Alcoólica/microbiologia , Progressão da Doença , Humanos , Cirrose Hepática , Hepatopatia Gordurosa não Alcoólica/patologia
4.
J Sci Food Agric ; 99(13): 6076-6083, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31233219

RESUMO

BACKGROUND: This study was conducted to evaluate the health benefits to weaning pigs, raised under low sanitary conditions, of dietary supplementation with a multi-strain yeast fraction product (Cyberlindnera jadinii and Saccharomyces cerevisiae). In total, 160 weaning pigs (7.21 ± 1.05 kg) were randomly allotted to two dietary treatments in a 6-week feeding trial. The dietary treatments included a corn-soybean meal-based basal diet (CON) and CON + 2 g kg-1 multi-strain yeast fraction product (MsYF) during weeks 1-2 and 0.4 g kg-1 MsYF during weeks 3-6. RESULTS: The MsYF supplementation increased (P < 0.05) body weight (BW) at day 42 and average daily gain (ADG) during days 1-14 and days 1-42 (P < 0.05) compared to CON. The total tract digestibility of dry matter (DM), fecal Lactobacillus counts, and serum immunoglobulin G (IgG) concentration at day 42 were higher (P < 0.05) in pigs fed a MsYF supplemented diet. The concentration of serum haptoglobin in pigs receiving a MsYF-supplemented diet was higher (P < 0.05) at days 7, 14, and 42 than those receiving CON. The mRNA expression for INF-γ and TNF-α genes were lower (P < 0.05) at days 14 and 7 respectively and the expression of IL-6 and TLR-2 genes was lower (P < 0.01) at days 7 and 14 in pigs fed an MsFY supplemented diet than those fed CON. CONCLUSION: Supplementation with a multi-strain yeast fraction product had a positive effect on ADG during the early post-weaning period and led to better health in weaning pigs. © 2019 Society of Chemical Industry.


Assuntos
Saccharomyces cerevisiae/química , Suínos/crescimento & desenvolvimento , Leveduras/química , Ração Animal/análise , Fenômenos Fisiológicos da Nutrição Animal , Animais , Suplementos Nutricionais/análise , Fezes/microbiologia , Microbioma Gastrointestinal , Trato Gastrointestinal/metabolismo , Trato Gastrointestinal/microbiologia , Higiene , Interferon-alfa/genética , Interferon-alfa/imunologia , Interleucina-6/genética , Interleucina-6/imunologia , Suínos/genética , Suínos/imunologia , Suínos/microbiologia , Fator de Necrose Tumoral alfa/genética , Fator de Necrose Tumoral alfa/imunologia , Desmame
5.
Microbes Environ ; 34(2): 219-222, 2019 Jun 27.
Artigo em Inglês | MEDLINE | ID: mdl-31167992

RESUMO

Insects of the heteropteran superfamilies Coreoidea and Lygaeoidea are consistently associated with symbionts of a specific group of the genus Burkholderia, called the "stinkbug-associated beneficial and environmental (SBE)" group. The symbiosis is maintained by the environmental transmission of symbionts. We investigated European and Japanese populations of the dock bug Coreus marginatus (Coreoidea: Coreidae). High nymphal mortality in reared aposymbiotic insects suggested an obligate host-symbiont association in this species. Molecular phylogenetic analyses based on 16S rRNA gene sequences revealed that all 173 individuals investigated were colonized by Burkholderia, which were further assigned to different subgroups of the SBE in a region-dependent pattern.


Assuntos
Burkholderia/fisiologia , Heterópteros/microbiologia , Simbiose , Animais , Burkholderia/classificação , Burkholderia/genética , Burkholderia/isolamento & purificação , DNA Bacteriano/genética , Europa (Continente) , Feminino , Trato Gastrointestinal/anatomia & histologia , Trato Gastrointestinal/microbiologia , Heterópteros/anatomia & histologia , Japão , Masculino , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
6.
Plant Foods Hum Nutr ; 74(3): 383-390, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31228035

RESUMO

Orange juice is an important source of flavanones in the Western diet. However, little is known of the variation in flavanone content of shop-bought orange juice with pulp (OJP) or without pulp (OJ), nor the impact of pulp on the fate of flavanones in the gut. Total phenols, total flavonoids, antioxidant capacity, hesperidin and narirutin, and dietary fibre were measured in six orange juice brands sold as OJP and OJ. The inclusion of pulp had little impact on fibre content. Apart from total phenols (OJ: 208.4 ± 10.7 µg gallic acid equivalents (GAE) ml-1; OJP: 225.9 ± 16.7 µg GAE ml-1, P < 0.05), there were no differences between OJ and OJP. The fate of flavanones in OJ and OJP (Tropicana) were further compared using in vitro gastrointestinal (GI) models. After in vitro upper GI digestion, recovery of hesperidin was higher in OJ compared with OJP (89 ± 6 vs. 68 ± 3%, P = 0.033). After 2 h colonic fermentation, hesperidin was 1.2 fold higher in OJP than OJ. However, after 24 h colonic fermentation there was no significant difference between juices in terms of hesperidin, hesperetin, narirutin, naringenin and catabolites. In conclusion, the amount of pulp included in these shop-bought orange juices had little impact on flavanone metabolism in models of the GI tract. The effects of greater amounts of orange pulp remain to be determined.


Assuntos
Antioxidantes/análise , Citrus sinensis/química , Flavanonas/análise , Flavonoides/análise , Sucos de Frutas e Vegetais/análise , Fenóis/análise , Bactérias/metabolismo , Fibras na Dieta/análise , Digestão , Dissacarídeos/análise , Fermentação , Flavanonas/metabolismo , Trato Gastrointestinal/metabolismo , Trato Gastrointestinal/microbiologia , Hesperidina/análise , Humanos
7.
Int J Syst Evol Microbiol ; 69(9): 2815-2822, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31251720

RESUMO

A novel bacterial isolate, designated as strain BM15T, was isolated from the gastrointestinal tract of a blood cockle, Tegillarca granosa, which was collected from the foreshore of Beolgyo-eup, Republic of Korea. Strain BM15T was Gram-stain-negative, non-motile, strictly aerobic and short-rod-shaped. Optimum growth of the isolate occurred at 20 °C, in the presence of 4 % (w/v) NaCl and at pH 6. The 16S rRNA gene sequence analysis showed that strain BM15T belonged to the genus Paracoccus and had more than 97 % 16S rRNA gene sequence similarity to 'Paracoccus zhejiangensis' J6 (97.40 % similarity) and Paracoccus lutimaris HDM-25T (97.04 %). The polar lipid profile of strain BM15T comprised phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified glycolipid and two unidentified lipids. The predominant respiratory quinone was ubiquinone-10. The major cellular fatty acid (>20 %) was summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The complete genome sequence of strain BM15T comprised 3,759,866 bp with 62.2 mol% G+C content. The results of the phylogenetic, phenotypic and genotypic analyses indicated that strain BM15T represents a novel species in the genus Paracoccus, for which the name Paracoccus tegillarcae is proposed. The type strain is BM15T (=KCTC 72032T=JCM 33289T).


Assuntos
Cardiidae/microbiologia , Trato Gastrointestinal/microbiologia , Paracoccus/classificação , Filogenia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Hibridização de Ácido Nucleico , Paracoccus/isolamento & purificação , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Ubiquinona/química
8.
Int J Syst Evol Microbiol ; 69(9): 2801-2806, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31246166

RESUMO

A taxonomic study of a Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, catalase-negative bacterium, isolated from the gut of an insect, Cryptocercus kyebangensis collected from the mountainous area of Seoraksan, Yangyang-gun, Republic of Korea, was conducted. Its 16S rRNA gene sequence showed high similarity values to Weissella ghanensis LMG 24286T (95.9 %), Weissella beninensis 2L24P13T (95.9 %), Weissella fabalis M75T (95.7 %) and Weissella fabaria 257T (95.7 %). The phylogenetic tree indicated that the novel organism formed a cluster with W. ghanensis LMG 24286T, W. beninensis 2L24P13T, W. fabalis M75T and W. fabaria 257T. The G+C content was 41.1 mol% on the basis of the whole-genome sequence. Polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, two unidentified aminophospholipids, one unidentified phospholipid and four unidentified lipids. The major cellular fatty acids were C18 : 1 ω9c, C16 : 0, C14 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and summed feature 8 (C16 : 1 ω7c and/or C16 : 1 ω6c). The cell-wall peptidoglycan was of A4α type with the interpeptide bridge of Gly-d-Glu. Based on these results, strain 26KH-42T could be classified as a novel species of the genus Weissella, for which the name Weissellacryptocerci sp. nov. is proposed. The type strain is 26KH-42T (=KACC 18423T=NBRC 113066T).


Assuntos
Baratas/microbiologia , Trato Gastrointestinal/microbiologia , Filogenia , Weissella/classificação , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Weissella/isolamento & purificação
9.
BMC Infect Dis ; 19(1): 361, 2019 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-31039738

RESUMO

BACKGROUND: Ulcerative colitis (UC) is an inflammatory bowel disease (IBD) that is widely identified worldwide. This study aimed to investigate the phenotypic characterization and molecular typing of Clostridium difficile isolates among patients with UC at an inflammatory bowel disease clinic in Iran. METHODS: In this cross-sectional study, conducted from April 2015 to December 2015, 85 UC patients were assessed for C.difficile infection (CDI). C. difficile isolates were characterized based on their toxin profile and antimicrobial resistance pattern. Multi-locus sequence typing analysis (MLST) and PCR ribotyping were performed to define the genetic relationships between different lineages of toxigenic strains. RESULTS: The prevalence of C. difficile isolates was 31.8% (27/85) in patients, of those 15 patients (17.6%) had CDI. Three different sequence types (STs) identified based on MLST among the toxigenic isolates, that is ST54 (33.3%), ST2 (53.3%), and ST37 (13.6%). C. difficile strains were divided into four different PCR-ribotypes (012, 014, 017 and IR1). The most common ribotype was 014 accounting for 48.3% (7/15) of all strains. The strains isolated during the first episode and recurrence of CDI usually belonged to PCR ribotype 014 (ST2). A high rate of CDI recurrence (14.1%, 12/85) experienced in UC patients. Colonization of the gastrointestinal tract with non-toxigenic C. difficile strains was frequent among patients with mild disease. All C. difficile isolates were susceptible to metronidazole, and vancomycin, 86 and 67% of isolates were resistant to clindamycin and erythromycin respectively. There was no correlation between the toxin type and antibiotic resistance (p > 0.05). CONCLUSION: Overall CDI is rather prevalent in UC patients. All patients with CDI experienced moderate to severe disease and exposed to different antimicrobial and anti-inflammatory agents. Close monitoring and appropriate management including early detection and fast treatment of CDI will improve UC outcomes.


Assuntos
Infecções por Clostridium/diagnóstico , Colite Ulcerativa/diagnóstico , Fezes/microbiologia , Adulto , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Anti-Inflamatórios/uso terapêutico , Infecções por Clostridium/tratamento farmacológico , Infecções por Clostridium/microbiologia , Clostridium difficile/efeitos dos fármacos , Clostridium difficile/genética , Clostridium difficile/isolamento & purificação , Colite Ulcerativa/tratamento farmacológico , Colite Ulcerativa/microbiologia , Estudos Transversais , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , Farmacorresistência Bacteriana , Feminino , Trato Gastrointestinal/microbiologia , Humanos , Modelos Logísticos , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Tipagem de Sequências Multilocus , Recidiva , Ribotipagem
10.
mSphere ; 4(3)2019 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-31043514

RESUMO

Human beings have used large amounts of antibiotics, not only in medical contexts but also, for example, as growth factors in agriculture and livestock, resulting in the contamination of the environment. Even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are affected as well. Therefore, both pathogenic and nonpathogenic bacteria have gradually become resistant to antibiotics. We tested whether there is still cooccurrence of resistance and virulence determinants. We performed a comparative study of environmental and human gut metagenomes from different individuals and from distinct human populations across the world. We found a great diversity of antibiotic resistance determinants (AR diversity [ARd]) and virulence factors (VF diversity [VFd]) in metagenomes. Importantly there is a correlation between ARd and VFd, even after correcting for protein family richness. In the human gut, there are less ARd and VFd than in more diversified environments, and yet correlations between the ARd and VFd are stronger. They can vary from very high in Malawi, where antibiotic consumption is unattended, to nonexistent in the uncontacted Amerindian population. We conclude that there is cooccurrence of resistance and virulence determinants in human gut microbiomes, suggesting a possible coselective mechanism.IMPORTANCE Every year, thousands of tons of antibiotics are used, not only in human and animal health but also as growth promoters in livestock. Consequently, during the last 75 years, antibiotic-resistant bacterial strains have been selected in human and environmental microbial communities. This implies that, even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are also affected. Here, we performed a comparative study of environmental and human gut microbial communities issuing from different individuals and from distinct human populations across the world. We found that antibiotic resistance and pathogenicity are correlated and speculate that, by selecting for resistant bacteria, we may be selecting for more virulent strains as a side effect of antimicrobial therapy.


Assuntos
Resistência Microbiana a Medicamentos/genética , Microbiologia Ambiental , Microbioma Gastrointestinal/efeitos dos fármacos , Variação Genética , Microbiota/efeitos dos fármacos , Adolescente , Adulto , Antibacterianos/farmacologia , Bactérias/efeitos dos fármacos , Bactérias/genética , Criança , Pré-Escolar , Trato Gastrointestinal/microbiologia , Humanos , Lactente , Metagenoma , Metagenômica , Pessoa de Meia-Idade , RNA Ribossômico 16S/genética , Microbiologia do Solo , Virulência , Fatores de Virulência/genética , Adulto Jovem
11.
Int J Syst Evol Microbiol ; 69(7): 2101-2107, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31099733

RESUMO

A Gram-stain-positive, strictly aerobic, rod-shaped, non-spore-forming, non-motile bacterium, designated strain 2DFWR-13T, was isolated from gut of the larva of Protaetia brevitarsis seulensis, in the Republic of Korea. Strain 2DFWR-13T showed high sequence similarities to Lysinimonas kribbensis MSL-13T (97.7 %), Homoserinibacter gongjuensis 5GH26-15T (97.2 %), Microbacterium deminutum KV-483T (97.1 %) and Herbiconiux ginsengi CGMCC 4.3491T (97.1 %). The predominant fatty acids (>10 % of the total fatty acids) were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The major menaquinones were MK-13 and MK-12. The peptidoglycan type was type B2 with the diagnostic amino acid d-DAB. The N-acyl type of the murein was glycolyl. The polar lipids consisted of diphosphatidylglycerol, an unidentified glycolipid and an unidentified lipid. The DNA G+C content was 71.5 mol%. Based on its phylogenetic distinctiveness and distinguishing phenotypic characteristics, we conclude that strain 2DFWR-13T represents a novel genus and species of the family Microbacteriaceae, for which the name Protaetiibacter intestinalis gen. nov., sp. nov. is proposed. The type strain of Protaetiibacter intestinalis is 2DFWR-13T (=KACC 19321T=NBRC 113050T). In addition, an emended description of the genus LysinimonasJang et al. 2013 and the reclassification of Lysinimonas kribbensisJang et al. 2013 as Pseudolysinimonas kribbensis gen. nov., comb. nov. are proposed.


Assuntos
Actinobacteria/classificação , Besouros/microbiologia , Trato Gastrointestinal/microbiologia , Filogenia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Larva/microbiologia , Peptidoglicano/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/química
12.
mSphere ; 4(3)2019 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-31092601

RESUMO

Termites forage on a range of substrates, and it has been suggested that diet shapes the composition and function of termite gut bacterial communities. Through comparative analyses of gut metagenomes in nine termite species with distinct diets, we characterize bacterial community compositions and use peptide-based functional annotation method to determine biomass-degrading enzymes and the bacterial taxa that encode them. We find that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, while wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Interestingly, wood-feeding termite gut bacterial genes code for abundant chitinolytic enzymes, suggesting that fungal biomass within the decaying wood likely contributes to gut bacterial or termite host nutrition. Across diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community composition, with the most marked difference being the communities coding for the mycolytic capacity of the fungus-growing termite gut.IMPORTANCE Understanding functional capacities of gut microbiomes is important to improve our understanding of symbiotic associations. Here, we use peptide-based functional annotation to show that the gut microbiomes of fungus-farming termites code for a wealth of enzymes that likely target the fungal diet the termites eat. Comparisons to other termites showed that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, whereas wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Across termites with different diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community compositions.


Assuntos
Dieta , Fungos/crescimento & desenvolvimento , Microbioma Gastrointestinal , Isópteros/enzimologia , Isópteros/microbiologia , Animais , Bactérias/enzimologia , Bactérias/genética , Trato Gastrointestinal/enzimologia , Trato Gastrointestinal/microbiologia , Metagenoma , Filogenia , Células Vegetais/metabolismo , Análise de Sequência de DNA , Simbiose , Madeira/metabolismo
13.
J Appl Microbiol ; 127(2): 429-444, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31102430

RESUMO

AIMS: This study evaluated methods to sample and extract nucleic acids from Pacific oysters to accurately determine the microbiome associated with different tissues. METHODS AND RESULTS: Samples were collected from haemolymph, gill, gut and adductor muscle, using swabs and homogenates of solid tissues. Nucleic acids were extracted from fresh and frozen samples using three different commercial kits. The bacterial DNA yield varied between methods (P < 0·05) and each tissue harboured a unique microbiota, except for gill and muscle. Higher bacterial DNA yields were obtained by swabbing compared to tissue homogenates and from fresh tissues compared to frozen tissues, without impacting the bacterial community composition estimated by 16S rRNA gene (V1-V3 region) sequencing. Despite the higher bacterial DNA yields with QIAamp® DNA Microbiome Kit, the E.Z.N.A.® Mollusc DNA Kit identified twice as many operational taxonomic units (OTUs) and eliminated PCR inhibition from gut tissues. CONCLUSIONS: Sampling and nucleic acid purification substantially affected the quantity and diversity of bacteria identified in Pacific oyster microbiome studies and a fit-for-purpose strategy is recommended. SIGNIFICANCE AND IMPACT OF THE STUDY: Accurate identification of Pacific oyster microbial diversity is instrumental for understanding the polymicrobial aetiology of Pacific oyster mortality diseases which greatly impact oyster production.


Assuntos
Bactérias/isolamento & purificação , Crassostrea/microbiologia , DNA Bacteriano/isolamento & purificação , Microbiota/genética , Animais , Bactérias/genética , DNA Ribossômico/genética , Trato Gastrointestinal/microbiologia , Brânquias/microbiologia , Hemolinfa/microbiologia , Músculos/microbiologia , Reação em Cadeia da Polimerase , RNA Ribossômico 16S/genética
14.
J Anim Sci ; 97(7): 2889-2900, 2019 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-31136650

RESUMO

The importance of the microbiota in the gastrointestinal tract of animals is recognized as a critical player in host health. Recently, the significance of the mycobiome has been recognized, but culture-independent studies are limited, especially in swine. Weaning is a time of stress, dietary changes, and a predisposition to infections, making it a time point of interest to industry. In this pilot study, we sought to assess and characterize the mycobiome in the feces of swine from birth through the critical weaning transition to investigate the mycobiome population and its temporal dynamics in piglet feces. Cultured fecal samples demonstrate a significant increase in fungal burden following weaning that does not differ from adult levels, suggesting stable colonization. Culturable fungi were not found in any environmental samples tested, including water, food, sow milk or colostrum. To determine the fungal diversity present and to address the problem of unculturable fungi, we performed a pilot study utilizing ITS and 16S rRNA focused primers for high-throughput sequencing of fungal and bacterial species, respectively. Bacterial populations increase in diversity over the experimental timeline (days 1 to 35 postbirth), but the fungal populations do not demonstrate the same temporal trend. Following weaning, there is a dynamic shift in the feces to a Saccharomycetaceae-dominated population. The shift in fungal population was because of the dominance of Kazachstania slooffiae, a poorly characterized colonizer of animal gastrointestinal tracts. This study provides insights into the early colonization and subsequent establishment of fungi during the weaning transition in piglets. Future studies will investigate the effect of the mycobiome on piglet growth and health during the weaning transition.


Assuntos
Bactérias/classificação , Fungos/classificação , Microbioma Gastrointestinal , Micobioma , Suínos/microbiologia , Animais , Bactérias/genética , Colostro/microbiologia , Dieta/veterinária , Fezes/microbiologia , Feminino , Fungos/genética , Trato Gastrointestinal/microbiologia , Sequenciamento de Nucleotídeos em Larga Escala/veterinária , Leite/microbiologia , Projetos Piloto , Gravidez , RNA Ribossômico 16S/genética , Análise de Sequência de DNA/veterinária , Suínos/fisiologia , Desmame
15.
Vet Microbiol ; 232: 121-127, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31030835

RESUMO

Enterotoxigenic and Shiga-toxigenic Escherichia coli (i.e., ETEC and STEC) are important causative agents of human and animal diseases. In humans, infections range from mild diarrhea to severe life-threating conditions, while infections of piglets result in lower weight gain and higher pig mortality with the accompanying significant economic losses. In this study, frequencies of four phylogenetic groups, fourteen virulence- and thirty bacteriocin determinants were analyzed in a set of 443 fecal E. coli isolates from diseased pigs and compared to a previously characterized set of 1283 human fecal E. coli isolates collected in the same geographical region. In addition, these characteristics were compared among ETEC, STEC, and non-toxigenic porcine E. coli isolates. Phylogenetic group A was prevalent among porcine pathogenic E. coli isolates, whereas the frequency of phylogroup B2, adhesion/invasion (fimA, pap, sfa, afaI, ial, ipaH, and pCVD432) and iron acquisition (aer and iucC) determinants were less frequent compared to human fecal isolates. Additionally, porcine isolates differed from human isolates relative to the spectrum of produced bacteriocins. While human fecal isolates encoded colicins and microcins with a similar prevalence, porcine pathogenic E. coli isolates produced predominantly colicins (94% of isolates); especially colicins B (42.6%), M (40.1%), and Ib (34.0%), which are encoded on large conjugative plasmids. The observed high prevalence of these colicin determinants suggests the importance of large colicinogenic plasmids and/or the importance of colicin production in intestinal inflammatory conditions.


Assuntos
Bacteriocinas/genética , Colicinas/genética , Escherichia coli Enterotoxigênica/patogenicidade , Escherichia coli Shiga Toxigênica/patogenicidade , Animais , Aderência Bacteriana , Proteínas de Transporte/genética , Diarreia/microbiologia , Escherichia coli Enterotoxigênica/genética , Proteínas de Escherichia coli/genética , Fezes/microbiologia , Proteínas de Fímbrias/genética , Trato Gastrointestinal/microbiologia , Humanos , Ferro/metabolismo , Filogenia , Plasmídeos , Reação em Cadeia da Polimerase , Escherichia coli Shiga Toxigênica/genética , Suínos , Simbiose , Fatores de Virulência/genética
16.
World J Gastroenterol ; 25(12): 1478-1491, 2019 Mar 28.
Artigo em Inglês | MEDLINE | ID: mdl-30948911

RESUMO

BACKGROUND: Recently, gut microbiota has been associated with various diseases other than intestinal disease. Thus, there has been rapid growth in the study of gut microbiota. Considering the numerous factors influencing gut microbiota such as age, diet, etc., area-based research is required. Indonesia has numerous different tribes and each of these tribes have different lifestyles. Hence, it is expected that each tribe has a specific gut microbiota. A deeper insight into the composition of gut microbiota can be used to determine the condition of gut microbiota in Indonesians and to consider which treatment may be suitable and effective to improve health status. AIM: To investigate the gut microbiota of Indonesian subjects represented by Javanese and Balinese tribes by analyzing fecal samples. METHODS: Fecal samples were collected from a total of 80 individuals with 20 in each of the young groups ranging from 25-45 years and the elderly group aged 70 years or more from two different regions, Yogyakarta and Bali. Fecal sample collection was performed at the end of the assessment period (day 14 ± 1 d) during which time the subjects were not allowed to consume probiotic or antibiotic products. The quantification of various Clostridium subgroups, Lactobacillus subgroups, Enterococcus, Streptococcus, Staphylococcus, Bacteroides fragilis group and Prevotella, Bifidobacterium and Atopobium cluster, Enterobacteriaceae and Pseudomonas was performed using the Yakult intestinal flora-scan (YIF-SCAN). RESULTS: The bacterial population in younger subjects' feces was higher than that in the elderly population, with a total of approximately 10.0 - 10.6 log10 bacterial cells/g feces. The most abundant bacteria in all groups were Clostridium, followed by Prevotella, Atopobium, Bifidobacterium and Bacteroides. In the elderly, an increase in Enterobacteriaceae, Coliform and Escherichia coli was found. In terms of bacterial counts in Yogyakarta, total bacteria, Clostridium coccoides (C. coccoides) group, Bifidobacterium, Prevotella, Lactobacillus plantarum subgroup, and Streptococcus were significantly higher (P < 0.05) in younger than elderly subjects, while the Lactobacillus gasseri subgroup, Lactobacillus casei subgroup, and Lactobacillus reuteri subgroup counts were significantly lower (P < 0.05) in younger subjects. In Balinese subjects, total bacteria, C. coccoides group, Clostridium leptum subgroup, Bacteroides fragilis group, and Prevotella were significantly higher (P < 0.05) in younger compared to elderly individuals, while the Lactobacillus ruminis subgroup, and Enterobacteriaceae were significantly lower (P < 0.05) in younger subjects. The results also revealed that, besides the C. coccoides group and Clostridium leptum group being the most abundant gut microbiota in both Yogyakarta and Balinese people, the latter was indicated by a higher Clostridium perfringens count, which was almost 10 times that of Yogyakarta subjects. This may be a response to different lifestyles in the different tribes; however, this phenomenon requires further extensive study. CONCLUSION: Bacterial populations were higher in younger than in elderly subjects. Most abundant bacterial groups were Clostridium, Prevotella, Atopobium, Bifidobacterium, and Bacteroides. The level of Clostridium perfringens in Yogyakarta subjects was lower than that in Balinese subjects.


Assuntos
Bactérias/isolamento & purificação , Microbioma Gastrointestinal , Trato Gastrointestinal/microbiologia , Adulto , Fatores Etários , Idoso , Fezes/microbiologia , Feminino , Voluntários Saudáveis , Humanos , Indonésia , Masculino , Reação em Cadeia da Polimerase
17.
Artigo em Chinês | MEDLINE | ID: mdl-31016928

RESUMO

As the largest and most complex ecosystem in humans, gut microbiota resides in human or animal gastrointestinal tract with intestinal viruses and parasites. Previous studies have demonstrated that gut microbiotadysbiosis is strongly correlated with the development, progression and prognosis of multiple diseases. The parasites that are colonized in the host, may directly or indirectly affect gut microbiota and the gut microbiota-host homeostasis, and changes in the composition and diversity of gut microbiota may also affect parasitic infections and the development, progression and prognosis of parasitic diseases. This paper reviews the progress of research on the interplay between helminth and intestinal protozoa and gut microbiota.


Assuntos
Microbioma Gastrointestinal , Trato Gastrointestinal , Helmintos , Animais , Trato Gastrointestinal/microbiologia , Trato Gastrointestinal/parasitologia , Homeostase , Humanos , Intestinos/parasitologia , Pesquisa/tendências
18.
Aust Vet J ; 97(5): 166-170, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31025325

RESUMO

BACKGROUND: Koalas in the Mount Lofty Ranges, South Australia, have a high prevalence of oxalate nephrosis, or calcium oxalate kidney crystals. Gastrointestinal tract oxalate-degrading bacteria, particularly Oxalobacter formigenes, have been identified in other animal species and humans, and their absence or low abundance is postulated to increase the risk of renal oxalate diseases. This study aimed to identify oxalate-degrading bacteria in the gastrointestinal tract of koalas and determine their association with oxalate nephrosis. METHODS: Caecal and faecal samples were collected at necropsy from 22 Mount Lofty Ranges koalas that had been euthanased on welfare grounds, with 8 koalas found to have oxalate nephrosis by renal histopathology. Samples were analysed by PCR for the oxc gene, which encodes oxalyl-CoA decarboxylase, and also by Illumina sequencing of the V3-V4 region of the bacterial 16S rRNA gene. RESULTS: The oxc gene was detected in 100% of koala samples, regardless of oxalate nephrosis status. Oxalobacter formigenes was detected in all but one faecal sample, with no difference in abundance between koalas affected and unaffected by oxalate nephrosis. Other species of known oxalate-degrading bacteria were infrequently detected. CONCLUSION: This is the first study to identify Oxalobacter and other oxalate-degrading bacterial species in koalas, but an association with oxalate nephrosis and absence or low abundance of Oxalobacter was not found. This suggests other mechanisms underlie the risk of oxalate nephrosis in koalas.


Assuntos
Trato Gastrointestinal/microbiologia , Nefrose/veterinária , Oxalobacter formigenes/genética , Phascolarctidae/genética , Phascolarctidae/microbiologia , Acil Coenzima A/genética , Animais , Autopsia/veterinária , Ceco/microbiologia , Fezes , Feminino , Masculino , Nefrose/genética , Nefrose/microbiologia , Oxalatos , Reação em Cadeia da Polimerase/veterinária , RNA Ribossômico 16S , Austrália do Sul
19.
Nat Commun ; 10(1): 1517, 2019 04 03.
Artigo em Inglês | MEDLINE | ID: mdl-30944304

RESUMO

Perinatal factors impact gut microbiota development in early life, however, little is known on the effects of these factors on microbes in later life. Here we sequence DNA from faecal samples of children over the first four years and reveal a perpetual evolution of the gut microbiota during this period. The significant impact of gestational age at birth and delivery mode on gut microbiota progression is evident in the first four years of life, while no measurable effects of antibiotics are found in the first year. Microbiota profiles are also characteristic in children dependant on gestational age and maturity. Full term delivery is characterised by Bacteroides (year one), Parabacteroides (year two) and Christensenellaceae (year four). Preterm delivery is characterised by Lactobacillus (year one), Streptococcus (year two) and Carnobacterium (year four). This study reveals that the gut retains distinct microbial profiles of perinatal factors up to four years of age.


Assuntos
Microbioma Gastrointestinal/fisiologia , Trato Gastrointestinal/microbiologia , Microbiota/fisiologia , Gravidez/fisiologia , Antibacterianos/farmacologia , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Pré-Escolar , Fezes/microbiologia , Feminino , Microbioma Gastrointestinal/efeitos dos fármacos , Microbioma Gastrointestinal/genética , Humanos , Lactente , Recém-Nascido , Masculino , Gravidez/efeitos dos fármacos , Nascimento Prematuro , RNA Ribossômico 16S/genética
20.
Int J Mol Sci ; 20(7)2019 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-30986907

RESUMO

Weaning is a crucial period when piglets have to cope with sudden dietary, social, and environmental stressors that often lead to serious intestinal dysbiosis and mortality. In this study, five mucosal and five digesta samples from each proximate jejunum, distal jejunum, and mid-colon were collected from 7- and 27-day post-weaned pigs and subjected to microbiota analysis using 16S rRNA gene profiling. Taxonomic analysis at phylum level revealed that Proteobacteria was significantly higher at 7 days (13.54%), while Bacteriodetes was higher at 27 days (30.72%) post weaning. Genera such as Campylobacter, Veillonella, Helicobacter, and Blautia that were previously reported in intestinal dysbiosis were significantly enriched in seven-day post-weaned pigs. However, microbial communities shifted as post weaning age increased with a significant increase in alpha diversity, and genera such as Moryella, Dialister, Clostridium, Streptococcus, Prevotella, and Bacteroides become significantly abundant in 27-day post-weaned pigs. Interestingly, the genus Campylobacter was significantly abundant on seven-day post-weaning in two piglets with diarrhea, implicating its role in post-weaning diarrhea. The results of this study suggest that gut microbiota in pigs with dysbiosis on 7-day post weaning undergoes significant changes toward a more normal state as the post-weaning age reaches 27 days.


Assuntos
Trato Gastrointestinal/microbiologia , Mucosa Intestinal/microbiologia , Microbiota , Suínos/microbiologia , Animais , Bactérias/classificação , Bactérias/genética , Biodiversidade , Análise por Conglomerados , Diarreia/microbiologia , Genes Bacterianos , Filogenia , Análise de Componente Principal , Desmame
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