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1.
BMC Microbiol ; 20(1): 85, 2020 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-32276583

RESUMO

BACKGROUND: Koumiss is a naturally fermented mare's milk. Over recent decades, numerous studies have revealed the diversity of lactic acid bacteria in koumiss. However, there is limited information available regarding its secondary major component yeast profile. RESULTS: A total of 119 bacterial and 36 yeast species were identified among the 14 koumiss samples. The dominant bacterial species in koumiss were Lactobacillus helveticus, Lactobacillus kefiranofaciens, Lactococcus lactis, Lactococcus raffinolactis, and Citrobacter freundii. The main yeast species were Dekkera anomala, Kazachstania unispora, Meyerozyma caribbica, Pichia sp.BZ159, Kluyveromyces marxianus, and uncultured Guehomyces. The bacterial and yeast Shannon diversity of the Xilinhaote-urban group were higher than those of the Xilingol-rural group. The most dominant organic acids were lactic, acetic, tartaric, and malic acids. Lactic acid bacteria species were mostly responsible for the accumulation of those organic acids, although Kazachstania unispora, Dekkera anomala, and Meyerozyma caribbica may also have contributed. Redundancy analysis suggested that both bacteria and yeast respond to koumiss flavor, such as Lactobacillus helveticus and Dekkera anomala are associated with sourness, astringency, bitterness, and aftertaste, whereas Lactococcus lactis and Kazachstania unispora are associated with umami. CONCLUSIONS: Our results suggest that differences were observed in koumiss microbiota of Xilinhaote-urban and Xilingol-rural samples. The biodiversity of the former was higher than the latter group. Positive or negative correlations between bacteria and yeast species and taste also were found.

2.
Artigo em Inglês | MEDLINE | ID: mdl-32129738

RESUMO

A lactic acid bacterial strain, HBUAS57009T, isolated from traditionally fermented food (Zha-Chili) in China, was characterized to clarify its taxonomic status using a polyphasic approach. Strain HBUAS57009T was phylogenetically closely related to Lactobacillus koreensis DCY50T, Lactobacillus fujinensis 218-6T, Lactobacillus mulengensis 112-3T, Lactobacillus cerevisiae TUM BP 140423000-2250T, Lactobacillus tongjiangensis 218-10T and Lactobacillus yonginensis THK-V8T with sequence similarities of 98.6-99.3 %. The genome-to-genome distance and average nucleotide identity values between the genomes of strain HBUAS57009T and type strains of closely related Lactobacillus species were less than 32.0 and 86.0 %, respectively; this is below the threshold for species boundaries. The major cellular fatty acids (>10 %) were C16 : 0, C18 : 1 ω9c and iso-C19 : 0. The G+C content of the genomic DNA of strain HBUAS57009T was 47.8 mol%. Examination of the functional categories of the genome revealed that strain HBUAS57009T could perform both homolactic and heterolactic fermentation processes to produce lactic acid via complete glycolysis and the pentose phosphate pathway. The putative biosynthesis pathway of butane-2,3-diol and acetoin, two important flavour compounds in the food industry, were identified using kegg mapper analysis. Based on its genotypic and phenotypic features, strain HBUAS57009T (=GDMCC 1.1664T=KACC 21424T) is designated as the type strain of a novel species, for which the name Lactobacillus enshiensis sp. nov. is proposed.

3.
Gut Microbes ; : 1-20, 2020 Mar 21.
Artigo em Inglês | MEDLINE | ID: mdl-32200683

RESUMO

As an effective means to improve quality of life and prevent diseases, the demand for probiotics and related products has increased in recent years. However, it is still unclear whether a particular probiotic strain will have similar beneficial effects on healthy adults from different regions. In this study, the probiotic Lactobacillus casei Zhang (LCZ) was consumed by healthy adults from six different Asian regions and the changes in gut microbiota were compared using PacBio single molecule, real-time (SMRT) sequencing technology based on samples collected before, during and after consumption of LCZ. Our results reveal that the effect of LCZ consumption on individuals was closely related to the composition of that individual's basal gut microbiota. A Gut Microbiota Variability Index (GMVI) was proposed to quantitatively compare the effects of LCZ on human gut microecology. Subjects from Xinjiang and Singapore regions had the highest and lowest GMVI, respectively. In general, consumption of LCZ increased the relative abundance of certain beneficial bacteria such as Lactobacillus, Roseburia, Coprococcus and Eubacterium rectale, while it inhibited growth of certain harmful bacteria such as Blautia and Ralstonia pickettii. In addition, consumption of LCZ was responsible for the conversion of some participants from Prevotella copri/Faecalibacterium prausnitzii (PF) enterotype to Faecalibacterium prausnitzii/Bacteroides dorei (FB) enterotype and consistently increased the abundance of lactic acid bacteria in the gut. It also increased/enhanced phosphate metabolic modules, amino acid transport systems, and isoleucine biosynthesis, but conversely decreased lipopolysaccharide biosynthesis. These changes could have health benefits for healthy adults.

4.
J Anim Sci ; 98(2)2020 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-32017844

RESUMO

Fermented concentrated feed has been widely recognized as an ideal feed in the animal industry. In this study, we used a powerful method, coupling propidium monoazide (PMA) pretreatment with single-molecule real-time (SMRT) sequencing technology to compare the bacterial and fungal composition of feeds before and after fermentation with four added lactic acid bacteria (LAB) inoculants (one Lactobacillus casei strain and three L. plantarum strains). Five feed samples consisting of corn, soybean meal, and wheat bran were fermented with LAB additives for 3 d. Following anaerobic fermentation, the pH rapidly decreased, and the mean numbers of LAB increased from 106 to 109 colony-forming units (cfu)/g fresh matter. SMRT sequencing results showed that the abundance and diversity of bacteria and fungi in the feed were significantly higher before fermentation than after fermentation. Fifteen bacterial species and eight fungal genera were significantly altered following fermentation, and L. plantarum was the dominant species (relative abundance 88.94%) in the post-fermentation group. PMA treatment revealed that the bacteria Bacillus cereus, B. circulans, Alkaliphilus oremlandii, Cronobacter sakazakii, Paenibacillus barcinonensis, and P. amylolyticus (relative abundance >1%) were viable in the raw feed. After fermentation, their relative abundances decreased sharply to <0.2%; however, viable L. plantarum was still the dominant species post fermentation. We inferred that our LAB additives grew rapidly and inhibited harmful microorganisms and further improved feed quality. In addition, coupling PMA treatment with the Pacific Biosciences SMRT sequencing technology was a powerful tool for providing accurate live microbiota profiling data in this study.

5.
Bioresour Technol ; 297: 122456, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31786033

RESUMO

The addition of exogenous microorganisms is one approach with potential that may also overcome the problem in northern China of slow composting in autumn and winter due to low environmental temperatures. This study investigated the use of supplements of Lactobacillus plantarum (L. plantarum), strains P-8 and LP-10, on the efficiency of sheep manure composting and the quality of the final product. The composting process lasted eight weeks and, during this time, changes in multiple physical-chemical parameters and the compost microbiome were monitored. Microbiota-encoded functions, community structure and physical-chemical parameters were distinct between the two groups. 'Composting microbiota maturation index' was proposed to quantitatively compare the impact of maturation on composting microecology. The rapid improvement in composting rate (4 weeks) and quality of the final product suggest that this approach could provide both technological and economic benefits. This work reveals the tremendous potential of L. plantarum as a promoter in composting.


Assuntos
Compostagem , Lactobacillus plantarum , Animais , China , Esterco , Ovinos , Solo
6.
J Dairy Sci ; 103(2): 1238-1249, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31864732

RESUMO

Cheese is a fermented dairy product that is popular for its unique flavor and nutritional value. Recent studies have shown that microorganisms in cheese play an important role in the fermentation process and determine the quality of the cheese. We collected 12 cheese samples from different regions and studied the composition of their bacterial communities using PacBio small-molecule real-time sequencing (Pacific Biosciences, Menlo Park, CA). Our data revealed 144 bacterial genera (including Lactobacillus, Streptococcus, Lactococcus, and Staphylococcus) and 217 bacterial species (including Lactococcus lactis, Streptococcus thermophilus, Staphylococcus equorum, and Streptococcus uberis). We investigated the flavor quality of the cheese samples using an electronic nose system and we found differences in flavor-quality indices among samples from different regions. We found a clustering tendency based on flavor quality using principal component analysis. We found correlations between lactic acid bacteria and the flavor quality of the cheese samples. Biodegradation and metabolism of xenobiotics, and lipid-metabolism-related pathways, were predicted to contribute to differences in cheese flavor using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). This preliminary study explored the bacterial communities in cheeses collected from different regions and their potential genome functions from the perspective of flavor quality.


Assuntos
Bactérias/isolamento & purificação , Queijo/microbiologia , Variação Genética , Bactérias/classificação , Bactérias/genética , Queijo/análise , DNA Bacteriano/análise , Microbiologia de Alimentos , Lactobacillales/genética , Lactobacillales/isolamento & purificação , Lactobacillus/genética , Lactobacillus/isolamento & purificação , Lactococcus lactis/genética , Lactococcus lactis/isolamento & purificação , Filogenia , Análise de Sequência de DNA , Streptococcus/genética , Streptococcus/isolamento & purificação , Streptococcus thermophilus/genética , Streptococcus thermophilus/isolamento & purificação
7.
BMC Genomics ; 20(1): 602, 2019 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-31331270

RESUMO

BACKGROUND: As an important nosocomial pathogen, Enterococcus faecium has received increasing attention in recent years. However, a large number of studies have focused on the hospital-associated isolates and ignored isolates originated from the natural environments. RESULTS: In this study, comparative genomic analysis was conducted on 161 isolates originated from human, animal, and naturally fermented dairy products. The results showed that the environment played an important role in shaping the genomes of Enterococcus faecium. The isolates from human had the largest average genome size, while the isolates from dairy products had the smallest average genome size and fewest antibiotic resistance genes. A phylogenetic tree was reconstructed based on the genomes of these isolates, which revealed new insights into the phylogenetic relationships among the dairy isolates and those from hospitals, communities, and animals. Furthermore, 202 environment-specific genes were identified, including 136 dairy-specific, 31 human blood-specific, and 35 human gastrointestinal-specific genes. Interestingly, five dairy-specific genes (namely lacF, lacA/B, lacD, lacG, and lacC) that constituted an integrated lactose metabolism pathway existed in almost all dairy isolates. The pathway conservation demonstrated an active role of the environment in shaping the genomes of Enterococcus faecium. CONCLUSIONS: This study shows that the Enterococcus faecium species has great genomic plasticity and high versatility to occupy broad ecological roles, dwelling as non-harmful dairy and animal gut commensals as well as significant nosocomial pathogens that disseminate antibiotic resistance genes.


Assuntos
Adaptação Fisiológica/genética , Enterococcus faecium/genética , Enterococcus faecium/fisiologia , Meio Ambiente , Genômica , Bases de Dados Genéticas , Resistência Microbiana a Medicamentos/genética , Enterococcus faecium/efeitos dos fármacos , Genes Bacterianos/genética , Filogenia , Fatores de Virulência/genética
8.
Eur J Nutr ; 2019 May 23.
Artigo em Inglês | MEDLINE | ID: mdl-31123864

RESUMO

PURPOSE: Human colon inflammation is associated with changes in the diverse and abundant microorganisms in the gut. As important beneficial microbes, Lactobacillus contributes to the immune responses and intestinal integrity that may alleviate experimental colitis. However, the mechanisms underlying probiotic benefits have not been fully elucidated. METHODS: Dextran sodium sulfate or rapamycin-challenged mice were used as model for colon inflammation evaluation. Histological scores of the colon, levels of colonic myeloperoxidase, serum tumor necrosis factor-α and interleukin-6 were assessed as inflammatory markers and the gut microbiota profiles of each mouse were studied. RESULTS: We found that Lactobacillus casei Zhang (LCZ) can prevent experimental colitis and rapamycin-induced inflammation in intestinal mucosa by improving histological scores, decreasing host inflammatory cytokines, modulating gut-dominated bacteria, enhancing cystic fibrosis transmembrane conductance regulator (CFTR) expression and downregulating the expression of p-STAT3 (phosphorylated signal transducer and activator of transcription 3) or Akt/NF-κB (AKT serine/threonine kinase and nuclear factor kappa B). CONCLUSION: Our results suggest that LCZ may provide effective prevention against colitis.

9.
Front Immunol ; 10: 666, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31001271

RESUMO

Probiotics have been used successfully to promote human and animal health, but only limited studies have focused on using probiotics to improve the health of hosts of different age. Canine microbiome studies may be predictive of results in humans because of the high structural and functional similarity between dog and human microbiomes. A total of 90 dogs were divided into three groups based on dog age (elderly group, n = 30; young group, n = 24; and training group, n = 36). Each group was subdivided into two subgroups, with and without receiving daily probiotic feed additive. The probiotic feed additive contained three different bacterial strains, namely Lactobacillus casei Zhang, Lactobacillus plantarum P-8, and Bifdobacterium animalis subsp. lactis V9. Serum and fecal samples were collected and analyzed at four different time points, i.e., days 0, 30, and 60 of probiotic treatment, and 15 days after ceasing probiotic treatment. The results demonstrated that probiotics significantly promoted the average daily feed intake of the elderly dogs (P < 0.01) and the average daily weight gain of all dogs (P < 0.05), enhanced the level of serum IgG (P < 0.001), IFN-α (P < 0.05), and fecal SIgA (P < 0.001), while reduced the TNF-α (P < 0.05). Additionally, probiotics could change the gut microbial structure of elderly dogs and significantly increased beneficial bacteria (including some Lactobacillus species and Faecalibacterium prausnitzii) and decreased potentially harmful bacteria (including Escherichia coli and Sutterella stercoricanisin), and the elderly dogs showed the strongest response to the probiotics; the relative abundance of some of these species correlated with certain immune factors and physiological parameters, suggesting that the probiotic treatment improved the host health and enhanced the host immunity by stimulating antibody and cytokine secretion through regulating canine gut microbiota. Furthermore, the gut microbiota of the elderly dogs shifted toward a younger-like composition at day 60 of probiotic treatment. Our findings suggested that the probiotic treatment effects on canine health and immunity were age-related and have provided interesting insights into future development of probiotic-based strategies to improve animal and human health.

10.
Food Funct ; 10(5): 2618-2629, 2019 May 22.
Artigo em Inglês | MEDLINE | ID: mdl-31021333

RESUMO

The aim of the present study was to evaluate the effects of probiotics on the composition and function of the gut microbiota in dogs with diarrhoea. Forty dogs with diarrhoea were randomly allocated to the treatment group or control group. Probiotics, containing Lactobacillus casei Zhang, Lactobacillus plantarum P-8, and Bifidobacterium animalis subsp. lactis V9, were only fed to 20 treated dogs for 60 days. The faecal samples of all dogs at day 0 and day 60 were analyzed using a metagenomic approach. The results showed a significantly higher microbial diversity and an obvious change in the structure of the gut microbiota in the treatment group. There was also an increase in the abundance of some beneficial bacteria in differently aged dogs, such as Lactobacillus johnsonii (P < 0.05), Lactobacillus reuteri (P < 0.01), Lactobacillus acidophilus (P < 0.05) and Butyricicoccus pullicaecorum (P < 0.05), and a reduction in the abundance of many opportunistic pathogenic bacteria such as Clostridium perfringens (P < 0.05) and Stenotrophomonas maltophilia (P < 0.05) with the supplementation of probiotics. Intriguingly, the correlated networks among some pathogenic bacteria decreased following the administration of probiotics. Additionally, metagenomic analysis revealed the upregulation of pathways involved in the metabolism of amino acids and biosynthesis of secondary metabolites, accompanied by the downregulation of pathways associated with virulence of pathogenic bacteria and cell signaling, suggesting that probiotics could improve the health of dogs with diarrhoea through regulation of the gut microbiota. Our research provides new information relevant to the treatment of diarrhoea in animals and humans.


Assuntos
Bactérias/genética , Diarreia/veterinária , Doenças do Cão/tratamento farmacológico , Microbioma Gastrointestinal/efeitos dos fármacos , Probióticos/administração & dosagem , Animais , Bactérias/classificação , Bactérias/efeitos dos fármacos , Bactérias/isolamento & purificação , Diarreia/tratamento farmacológico , Diarreia/microbiologia , Doenças do Cão/microbiologia , Cães , Fezes/microbiologia , Metagenômica , Filogenia
11.
J Dairy Sci ; 102(5): 3912-3923, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30852020

RESUMO

Traditional fermented dairy foods have been the major components of the Mongolian diet for millennia. In this study, we used propidium monoazide (PMA; binds to DNA of nonviable cells so that only viable cells are enumerated) and single-molecule real-time sequencing (SMRT) technology to investigate the total and viable bacterial compositions of 19 traditional fermented dairy foods, including koumiss from Inner Mongolia (KIM), koumiss from Mongolia (KM), and fermented cow milk from Mongolia (CM); sample groups treated with PMA were designated PKIM, PKM, and PCM. Full-length 16S rRNA sequencing identified 195 bacterial species in 121 genera and 13 phyla in PMA-treated and untreated samples. The PMA-treated and untreated samples differed significantly in their bacterial community composition and α-diversity values. The predominant species in KM, KIM, and CM were Lactobacillus helveticus, Streptococcus parauberis, and Lactobacillus delbrueckii, whereas the predominant species in PKM, PKIM, and PCM were Enterobacter xiangfangensis, Lactobacillus helveticus, and E. xiangfangensis, respectively. Weighted and unweighted principal coordinate analyses showed a clear clustering pattern with good separation and only minor overlapping. In addition, a pure culture method was performed to obtain lactic acid bacteria resources in dairy samples according to the results of SMRT sequencing. A total of 102 LAB strains were identified and Lb. helveticus (68.63%) was the most abundant, in agreement with SMRT sequencing results. Our results revealed that the bacterial communities of traditional dairy foods are complex and vary by type of fermented dairy product. The PMA treatment induced significant changes in bacterial community structure.


Assuntos
Azidas , Produtos Fermentados do Leite/microbiologia , Microbiota , Propídio/análogos & derivados , Análise de Sequência/métodos , Animais , Bactérias/classificação , Bovinos , China , DNA Bacteriano/análise , Feminino , Fermentação , Kumis , Lactobacillales/genética , Lactobacillus delbrueckii/genética , Lactobacillus helveticus/genética , Leite/microbiologia , Mongólia , RNA Bacteriano/análise , RNA Ribossômico 16S/análise , RNA Ribossômico 16S/química , RNA Ribossômico 16S/genética
12.
Int J Syst Evol Microbiol ; 69(8): 2196-2201, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-30900972

RESUMO

Strain HBUAS52074T is a Gram-positive staining, aerobic bacterium that was isolated from Zha-Chili, a traditional fermented food made in China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HBUAS52074T is a member of the genus Lactobacillus and closely related to Lactobacillus nantensis DSM 16982T (98.9 %), Lactobacillus heilongjiangensis DSM 28069T (98.8 %), Lactobacillus formosensis NBRC 1095009T (98.6 %), Lactobacillus futsaii JCM 17355T (98.5 %), Lactobacillus farciminis KCTC 3681T (98.5 %), Lactobacillus musae NBRC 112868T (98.5 %) and Lactobacillus crustorum LMG 23699T (98.4 %). The DNA G+C content is 36.3 mol%. The major cellular fatty acids are C16 : 0 (28.2 %), C18 : 1ω9c (30.5 %) and summed feature 7 (C19 : 1ω6c, and/or C19 : 1ω7c; 14.9 %). Average nucleotide identity and DNA-DNA hybridization (GGDC) values based on genomic comparisons between HBUAS52074T and related type species showed that the bacterium was significantly different from its closest relatives. Using polyphasic taxonomic analysis, we have shown that strain HBUAS52074T is a new species in the genus Lactobacillus, for which we propose the name Lactobacilluszhachilii sp. nov. The type strain is HBUAS52074T (=GDMCC 1.1417T=KCTC 21106T).


Assuntos
/microbiologia , Lactobacillus/classificação , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Ácido Láctico , Lactobacillus/isolamento & purificação , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
13.
Food Sci Biotechnol ; 28(1): 139-145, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30815304

RESUMO

Chinese Tianshan tibico grains were collected from the rural area of Tianshan in Xinjiang province, China. Typical tibico grains are known to consist of polysaccharide matrix that embeds a variety of bacteria and yeasts. These grains are widely used in some rural regions to produce a beneficial sugary beverage that is slightly acidic and contains low level of alcohol. This work aimed to characterize the microbiota composition of Chinese Tianshan tibicos using the single molecule, real-time sequencing technology, which is advantageous in generating long reads. Our results revealed that the microbiota mainly comprised of the bacterial species of Lactobacillus hilgardii, Lactococcus raffinolactis, Leuconostoc mesenteroides, Zymomonas mobilis, together with a Guehomyces pullulans-dominating fungal community. The data generated in this work helps identify beneficial microbes in Chinese Tianshan tibico grains.

14.
Int J Syst Evol Microbiol ; 69(5): 1313-1319, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30801241

RESUMO

Strain HBUAS61001T was isolated from the pickling sauce used to make a traditional fermented food product, datoucai, in China. The strain belonged to the genus Vibrio, but was placed in a clade separate from any known Vibrio species based on the 16S rRNA gene and MLSA results. The genome consisted of two chromosomes: chromosome I was 2 901 449 bp long with a G+C content of 45.4 mol%; and chromosome II was 1 107 930 bp long with a G+C content of 45.5 mol%. The most abundant fatty acids were C16 : 0 (28.1 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 29.4 %) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 10.1 %). The isoprenoid quinones detected were Q7 and Q8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Strain HBUAS61001T could grow in the presence of up to 17 % NaCl. The calculated average nucleotide identity and in silico DNA-DNA hybridization (GGDC) values of the strain against the closest related type strains were all lower than 95 and 70 %, respectively. Putative genes in the genome associated with survival under high salinity stress were identified. Based on whole genome sequence analysis and phenotypic characteristics, strain HBUAS61001T is a new species in the genus Vibrio, and the name Vibrio zhugei (=GDMCC 1.1416T=KCTC 62784T) is proposed.


Assuntos
/microbiologia , Microbiologia de Alimentos , Filogenia , Vibrio/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vibrio/isolamento & purificação
15.
Int J Syst Evol Microbiol ; 69(1): 139-145, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30614783

RESUMO

In this study, we describe a new genus and species of yeast with high-salt tolerance. The strain was isolated from the pickling sauce used to make Datoucai, a traditional fermented food made from Brassica juncea in Xiangyang, China. Phylogenetic analysis of sequences from the D1/D2 region of the LSU rRNA gene and from the ITS region demonstrated that the strain, reference HBUAS51001T, was most closely related to members of the genera Occultifur and Cystobasidium. However, the greatest similarities between the D1/D2 and ITS nucleotide sequences of strain HBUAS51001T and the most closely related type strains from Occultifur and Cystobasidium were only 91 and 92 %, respectively. This suggests that strain HBUAS51001T does not belong to any currently described species. Strain HBUAS51001T grew readily on media in which xylose was the sole carbon source. The major ubiquinone was Q9. The genome of strain HBUAS51001T was 42.42 Mb with a G+C content of 53.93 mol%. Three candidate genes associated with xylose metabolism were identified. On the basis of genotypic and phenotypic data, strain HBUAS51001T can be considered as both a new species and a new genus, for which the name Halobasidium xiangyangense gen. nov., sp. nov. is proposed. The type strain is HBUAS51001T (=KCTC27810T=GDMCC 2.231T=CCTCC AY 2018002T).


Assuntos
Basidiomycota/classificação , Filogenia , Xilose/metabolismo , Composição de Bases , Basidiomycota/genética , Basidiomycota/isolamento & purificação , China , DNA Fúngico/genética , DNA Espaçador Ribossômico/genética , Técnicas de Tipagem Micológica , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
16.
Front Microbiol ; 9: 2045, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30233530

RESUMO

Lactic acid bacteria (LAB) are important for human health. However, the relative abundance of LAB in complex samples, such as fecal samples, is low and their presence and diversity (at the species level) is understudied. Therefore, we designed LAB-specific primer pairs based on 16S rRNA gene consensus sequences from 443 species of LAB from seven genera. The LAB strains selected were genetically similar and known to play a role in human health. Prior to primer design, we obtained consistent sequences for the primer-binding sites by comparing the 16S rRNA gene sequences, manually identifying single-stranded primers and modifying these primers using degenerate bases. We assembled primer pairs with product sizes of >400 bp. Optimal LAB-specific primers were screened using three methods: PCR amplification, agarose gel electrophoresis and single-molecule real-time (SMRT) sequencing analysis. During the SMRT analysis procedure, we focused on sequence reads and diversity at the species level of target LAB in three fecal samples, using the universal bacterium primer 27f/1492r as a reference control. We created a phylogenetic tree to confirm the ability of the best candidate primer pair to differentiate amongst species. The results revealed that LAB-specific primer L5, with a product size of 750 bp, could generate 3222, 2552, and 3405 sequence reads from fecal Samples 1, 2, and 3. This represented 14, 13 and 10% of all target LAB sequence reads, respectively, compared with 2, 0.8, and 0.8% using the 27f/1492r primer. In addition, L5 detected LAB that were in low abundance and could not be detected using the 27f/1492r primer. The phylogenetic tree based on the alignments between the forward and reverse primer of L5 showed that species within the seven target LAB genera could be distinguished from each other, confirming L5 is a powerful tool for inferring phylogenetic relationships amongst LAB species. In conclusion, L5 is a LAB-specific primer that can be used for high-throughput sequencing and identification of taxa to the species level, especially in complex samples with relatively low LAB content. This enables further research on LAB population diversity in complex ecosystem, and on relationships between LAB and their hosts.

17.
BMC Genomics ; 19(1): 527, 2018 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-29996769

RESUMO

BACKGROUND: Enterococcus faecalis is widely studied as a common gut commensal and a nosocomial pathogen. In fact, Enterococcus faecalis is ubiquitous in nature, and it has been isolated from various niches, including the gastrointestinal tract, faeces, blood, urine, water, and fermented foods (such as dairy products). In order to elucidate the role of habitat in shaping the genome of Enterococcus faecalis, we performed a comparative genomic analysis of 78 strains of various origins. RESULTS: Although no correlation was found between the strain isolation habitat and the phylogeny of Enterococcus faecalis from our whole genome-based phylogenetic analysis, our results revealed some environment-associated features in the analysed Enterococcus faecalis genomes. Significant differences were found in the genome size and the number of predicted open reading frames (ORFs) between strains originated from different environments. In general, strains from water sources had the smallest genome size and the least number of predicted ORFs. We also identified 293 environment-specific genes, some of which might link to the adaptive strategies for survival in particular environments. In addition, the number of antibiotic resistance genes was significantly different between strains isolated from dairy products, water, and blood. Strains isolated from blood had the largest number of antibiotic resistance genes. CONCLUSION: These findings improve our understanding of the role of habitat in shaping the genomes of Enterococcus faecalis.


Assuntos
Enterococcus faecalis/genética , Genoma Bacteriano , Antibacterianos/farmacologia , Hibridização Genômica Comparativa , DNA Bacteriano/química , DNA Bacteriano/isolamento & purificação , DNA Bacteriano/metabolismo , Farmacorresistência Bacteriana/efeitos dos fármacos , Farmacorresistência Bacteriana/genética , Enterococcus faecalis/classificação , Filogenia , Análise de Sequência de DNA , Fatores de Virulência/genética
18.
Curr Microbiol ; 75(10): 1316-1323, 2018 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-29907938

RESUMO

BACKGROUND: The gut microbes of dairy cows are strongly associated with their health, but the relationship between milk production and the intestinal microbiota has seldom been studied. Thus, we explored the diversity of the intestinal microbiota during peak lactation of dairy cows. METHODS: The intestinal microbiota of nine dairy cows at peak lactation was evaluated using the Pacific Biosciences single-molecule real-time (PacBio SMRT) sequencing approach. RESULTS: A total of 32,670 high-quality 16S rRNA gene sequences were obtained, belonging to 12 phyla, 59 families, 107 genera, and 162 species. Firmicutes (83%) were the dominant phylum, while Bacteroides (6.16%) was the dominant genus. All samples showed a high microbial diversity, with numerous genera of short chain fatty acid (SCFA)-producers. The proportion of SCFA producers was relatively high in relation to the identified core intestinal microbiota. Moreover, the predicted functional metagenome was heavily involved in energy metabolism. CONCLUSIONS: This study provided novel insights into the link between the dairy cow gut microbiota and milk production.


Assuntos
Bactérias/isolamento & purificação , Biodiversidade , Bovinos/microbiologia , Microbioma Gastrointestinal , Intestinos/microbiologia , Animais , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Bovinos/fisiologia , DNA Bacteriano/genética , Ácidos Graxos Voláteis/metabolismo , Feminino , Lactação , Metagenoma , Leite/metabolismo , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
19.
J Sci Food Agric ; 98(9): 3234-3245, 2018 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-29417994

RESUMO

BACKGROUND: Traditional Chongqing radish paocai fermented with aged brine is considered to have the most intense flavor and authentic taste. Eight 'Yanzhi' (red, RRPB group) and 'Chunbulao' (white, WRPB) radish paocai brine samples were collected from Chongqing peasant households, and the diversity and community structures of bacteria present in these brines were determined using PacBio single-molecule real-time sequencing of their full-length 16S rRNA genes. RESULTS: In total, 30 phyla, 218 genera, and 306 species were identified from the RRPB group, with 20 phyla, 261 genera, and 420 species present in the WRPB group. Obvious differences in bacterial profiles between the RRPB and WRPB groups were found, with the bacterial diversity of the WRPB group shown to be greater than that of the RRPB group. This study revealed several characteristics of the bacteria composition, including the predominance of heterofermentative lactic acid bacteria, the species diversity of genus Pseudomonas, and the presence of three opportunistic pathogenic species. CONCLUSION: This study provides detailed information on the bacterial diversity and community structure of Chongqing radish paocai brine samples, and suggests it may be necessary to analyze paocai brine for potential sources of bacterial contamination and take appropriate measures to exclude any pathogenic species. © 2018 Society of Chemical Industry.


Assuntos
Bactérias/classificação , Microbiologia de Alimentos , Raphanus/microbiologia , Sais , Bactérias/genética , China , DNA Bacteriano/análise , DNA Bacteriano/química , Fermentação , Lactobacillus , Tubérculos/microbiologia , Reação em Cadeia da Polimerase , Pseudomonas , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
20.
Front Microbiol ; 8: 484, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28377764

RESUMO

Gut microbiota is a determining factor in human physiological functions and health. It is commonly accepted that diet has a major influence on the gut microbial community, however, the effects of diet is not fully understood. The typical Mongolian diet is characterized by high and frequent consumption of fermented dairy products and red meat, and low level of carbohydrates. In this study, the gut microbiota profile of 26 Mongolians whom consumed wheat, rice and oat as the sole carbohydrate staple food for a week each consecutively was determined. It was observed that changes in staple carbohydrate rapidly (within a week) altered gut microbial community structure and metabolic pathway of the subjects. Wheat and oat favored bifidobacteria (Bifidobacterium catenulatum, Bifodobacteriumbifidum, Bifidobacterium adolescentis); whereas rice suppressed bifidobacteria (Bifidobacterium longum, Bifidobacterium adolescentis) and wheat suppresses Lactobaciilus, Ruminococcus and Bacteroides. The study exhibited two gut microbial clustering patterns with the preference of fucosyllactose utilization linking to fucosidase genes (glycoside hydrolase family classifications: GH95 and GH29) encoded by Bifidobacterium, and xylan and arabinoxylan utilization linking to xylanase and arabinoxylanase genes encoded by Bacteroides. There was also a correlation between Lactobacillus ruminis and sialidase, as well as Butyrivibrio crossotus and xylanase/xylosidase. Meanwhile, a strong concordance was found between the gastrointestinal bacterial microbiome and the intestinal virome. Present research will contribute to understanding the impacts of the dietary carbohydrate on human gut microbiome, which will ultimately help understand relationships between dietary factor, microbial populations, and the health of global humans.

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