Comparative evaluation of spoilage-related bacterial diversity and metabolite profiles in chilled beef stored under air and vacuum packaging

Microbial spoilage is a complex event to which different bacterial populations and metabolites can contribute depending on the storage conditions. This study explored the evolution of spoilage and related volatile organic compounds (VOCs) in chilled beef under air and vacuum packaging (VP). The results suggested that different storage conditions affected changes in bacterial communities and metabolites in beef and consequently affected the odor properties of the stored beef, thereby leading to spoilage. Bacterial species belonging to Pseudomonadaceae (Pseudomonas spp.) and lactic acid bacteria (Lactobacillus sp.) dominated the bacterial communities in beef stored under air and VP, respectively, with several VOCs associated with off-odors of the stored beef and most likely produced by both bacteria. Our results suggested several microbial VOCs that could be used as potential spoilage indicators, including acetic acid, butanoic acid, and 2-butanone in VP-stored beef and 3-methylbutan-1-ol, ethyl acetate, acetoin, 2-butanone, and diacetyl in air-stored beef. These findings might provide valuable information regarding the quality monitoring of beef during storage.

Immune-Enhancing Effect of Nanometric Lactobacillus plantarum nF1 (nLp-nF1) in a Mouse Model of Cyclophosphamide-Induced Immunosuppression

Nanometric Lactobacillus plantarum nF1 (nLp-nF1) is a biogenics consisting of dead L. plantarum cells pretreated with heat and a nanodispersion process. In this study, we investigated the immune-enhancing effects of nLp-nF1 in vivo and in vitro. To evaluate the immunostimulatory effects of nLp-nF1, mice immunosuppressed by cyclophosphamide (CPP) treatment were administered with nLp-nF1. As expected, CPP restricted the immune response of mice, whereas oral administration of nLp-nF1 significantly increased the total IgG in the serum, and cytokine production (interleukin-12 (IL-12) and tumor necrosis factor alpha (TNF-α)) in bone marrow cells. Furthermore, nLp-nF1 enhanced the production of splenic cytokines such as IL-12, TNF-α, and interferon gamma (IFN-γ). In vitro, nLp-nF1 stimulated the immune response by enhancing the production of cytokines such as IL-12, TNF-α, and IFN-γ. Moreover, nLp-nF1 given a food additive enhanced the immune responses when combined with various food materials in vitro. These results suggest that nLp-nF1 could be used to strengthen the immune system and recover normal immunity in people with a weak immune system, such as children, the elderly, and patients.

Bacterial community analysis in three types of the fermented seafood, jeotgal, produced in South Korea

Jeotgal is a traditional Korean seafood fermented by indigenous microbes. The bacterial community in five myeolchi-jeot (Engraulis japonica), five meongge-jeot (Halocynthia roretzi), and six saeu-jeot (Acetes japonicas) produced in South Korea was analyzed by barcoded pyrosequencing targeting the V1/V2 hyper-variable regions of the 16S rRNA gene. All samples were dominated by the phyla Firmicutes, which represented 67.7% (SD = 27.2%) of the population. Tetragenococcus halophilus and Tetragenococcus muriaticus were the predominant species in myeolchi-jeot. The LABs, Lactobacillus sakei, Lactobacillus curvatus, and Weissella koreensis were the predominant species in meongge-jeot. In myeolchi-jeot and meongge-jeot, the bacterial communities within samples were consistent in their predominance, however each of saeu-jeot samples had inter-individual variety in the bacterial community leading to the difficulties of standardization for the commercial production of saeu-jeot. The results of this study will conclusively help to expand our basic knowledge of jeotgal and the related microorganisms involved in food fermentation.

Effects of bentonite Bgp35b-p on the gut microbiota of mice fed a high-fat diet

BACKGROUND

Bentonite is a natural clay mineral with health-promoting effects due to its high adsorption abilities with high cation-exchange capacity. Previously, we found an anti-obesity effect for Bgp35b-p bentonite produced in South Korea, where its high adsorbent ability of dietary lipids possibly partially removed the lipidic environment in the gut (unpublished). It is hypothesized that Bgp35b-p affects the intestinal microbial community, and thus the microbial changes were investigated via next-generation sequencing targeting the bacterial 16S rRNA gene and bioinformatics using QIIME (Quantitative Insights Into Microbial Ecology) were performed on feces of C57BL/6 male mice fed a high-fat diet (HFD) with the Bgp35b-p.

RESULTS

The HFD caused microbial dysbiosis, characterized by a decrease in the relative abundance of Bacteroidetes and an increase in abundance of Firmicutes and Proteobacteria. It was found that HFD + Bgp35b-p led to significant changes in the microbial compositions of family-level bacteria known as short-chain fatty-acid-producing bacteria. The relative abundance of Ruminococcaceae was significantly increased, and the abundances of Clostridiaceae and Lachnospiraceae were decreased by HFD + Bgp35b-p, shifting close to that in mice fed a normal diet.

CONCLUSION

Bgp35b-p induced compositional changes in intestinal microbiota, which can be considered as a prebiotic effect, thus suggesting that bentonite may be a potential prebiotic functional supplement. © 2018 Society of Chemical Industry.

The influence of in vitro pectin fermentation on the human fecal microbiome

Pectin is a complex dietary fiber and a prebiotic. To investigate pectin-induced changes in the gut microbiome and their effects on the short chain fatty acids (SCFAs) production, we performed in vitro pectin fermentation using the feces of three Korean donors. The pectin degradations in all three donors were observed. While the donors displayed differences in baseline gut microbiota composition, commonly increased bacteria after pectin fermentation included Lachnospira, Dorea, Clostridium, and Sutterella. Regarding SCFAs, acetate levels rapidly increased with incubation with pectin, and butyrate levels also increased after 6 h of incubation. The results suggest that pectin fermentation increases bacterial species belonging to Clostridium cluster XIV (Lachnospira, Dorea, and Clostridium), with Lachnospira displaying the greatest increase. The results also confirm that pectin fermentation leads to the production of acetate and butyrate.

The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces

High-quality and high-throughput sequencing technologies are required for therapeutic and diagnostic analyses of human gut microbiota. Here, we evaluated the advantages and disadvantages of the various commercial sequencing platforms for studying human gut microbiota. We generated fecal bacterial sequences from 170 Korean subjects using the GS FLX+ (V1–4), Illumina MiSeq (V1–3, V3–4 and V4), and PacBio (V1–9) systems. Comparative analyses revealed that the PacBio data showed the weakest relationship with the reference whole-metagenome shotgun datasets. The PacBio system generated sequences with a significantly higher level of deletions than datasets generated by other platforms, with an abnormally high proportion of sequences assigned to the phylum Proteobacteria. Low sequencing accuracy and low coverage of terminal regions in public 16 S rRNA databases deteriorate the advantages of long read length, resulting in low taxonomic resolution in amplicon sequencing of human gut microbiota.

The effect of resistant starch (RS) on the bovine rumen microflora and isolation of RS-degrading bacteria

Resistant starch (RS) in the diet reaches the large intestine without degradation, where it is decomposed by the commensal microbiota. The fermentation of RS produces secondary metabolites including short-chain fatty acids (SCFAs), which have been linked to a variety of physiological and health effects. Therefore, the availability of RS as a prebiotic is a current issue. The objectives of this study were (1) to use metagenomics to observe microbial flora changes in Bos taurus coreanae rumen fluid in the presence of RS and (2) to isolate RS-degrading microorganisms. The major microbial genus in a general rumen fluid was Succiniclasticum sp., whereas Streptococcus sp. immediately predominated after the addition of RS into the culture medium and was then drastically replaced by Lactobacillus sp. The presence of Bifidobacterium sp. was also observed continuously. Several microorganisms with high RS granule-degrading activity were identified and isolated, including B. choerinum FMB-1 and B. pseudolongum FMB-2. B. choerinum FMB-1 showed the highest RS-hydrolyzing activity and degraded almost 60% of all substrates tested. Coculture experiments demonstrated that Lactobacillus brevis ATCC 14869, which was isolated from human feces, could grow using reducing sugars generated from RS by B. choerinum FMB-1. These results suggest that Bifidobacterium spp., especially B. choerinum FMB-1, are the putative primary degrader of RS in rumen microbial flora and could be further studied as probiotic candidates.

Expression and characterization of glutamate decarboxylase from Lactobacillus brevis HYE1 isolated from kimchi

A putative gene (gadlbhye1) encoding glutamate decarboxylase (GAD) was cloned from Lactobacillus brevis HYE1 isolated from kimchi, a traditional Korean fermented vegetable. The amino acid sequences of GADLbHYE1 showed 48% homology with the GadA family and 99% identity with the GadB family from L. brevis. The cloned GADLbHYE1 was functionally expressed in Escherichia coli using inducible expression vectors. The expressed recombinant GADLbHYE1 was successfully purified by Ni-NTA affinity chromatography, and had a molecular mass of 54 kDa with optimal hydrolysis activity at 55 °C and pH 4.0. Its thermal stability was determined to be higher than that of other GADs from L. brevis, based on its melting temperature (75.18 °C). Kinetic parameters including K_m and V_max values for GADLbHYE1 were 4.99 mmol/L and 0.224 mmol/L/min, respectively. In addition, the production of gamma-aminobutyric acid in E. coli BL21 harboring gadlbhye1/pET28a was increased by adding pyridoxine as a cheaper coenzyme.

Nutrikinetic study of genistein metabolites in ovariectomized mice

This study was designed to evaluate the effect of ovariectomy on nutrikinetics of genistein metabolites. To characterize the time-dependent changes in genistein metabolite concentrations, we identified 13 genistein metabolites using ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. The nutrikinetics of the individual metabolites at different time points were analyzed. Nutrikinetic analysis showed that genistein, genistein 4'-glucuronide, genistein 7-glucuronide, 3-hydroxygenistein, and hippuric acid showed relatively high bioavailability in the sham group compared to that in the ovariectomy group, suggesting that ovariectomy likely results in lower genistein bioavailability. These results may be related to alteration of gut microbiota by ovariectomy. The relative abundance of species of the Parabacteroides, Dorea, and Butyricimonas genera, and Desulfovibrionaceae_unclassified, Lachnospiraceae_unclassified, and Rikenellaceae_unclassified families increased in the ovariectomy group while the relative abundance of 523_7_unclassified and Y52_unclassified_unclassified increased in the sham group. These results suggest that gut microbiota alteration by ovariectomy may affect genistein bioavailability.

Flavimarina flava sp. nov., isolated from Salicornia herbacea

A Gram-stain-negative, motile-by-gliding, aerobic, non-spore-forming, rod-shaped and yellow-pigmented bacterium was isolated from Salicornia herbacea in the Yellow Sea and designated as strain MBLN091^T. It belonged to the family Flavobacteriaceae. The 16S rRNA gene sequence of this isolated strain was similar to that of Flavimarina pacifica IDSW-73^T with 94.8 % similarity, and with 92.3-92.8 % similarities to those of other closely related species of the genus Leeuwenhoekiella. The similarities of the RNA polymerase subunit B gene between this strain and F. pacifica KCTC 32466^T and Leeuwenhoekiella marinoflava DSM 3653^T were 80.5 and 80.2 %, respectively. Growth of strain MBLN091^T was observed in the presence of 0.5‒15.0 % (w/v) NaCl at 4‒35 °C and pH 6.0-8.0, with optimal growth in the presence of 2.5‒5.0 % (w/v) NaCl at 20‒25 °C and pH 7.0. This isolate was able to hydrolyse gelatin. The only respiratory quinone was MK-6. The major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and two unidentified lipids. Major fatty acids of the isolate were iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C17 : 0 3-OH and iso-C15 : 1 G. The genomic DNA G+C content was 39.6 mol%. The physiological features were closely related to F. pacifica. Therefore, strain MBLN091^T is considered to represent a novel species within the genus Flavimarina, for which the name Flavimarina flava sp. nov. is proposed. The type strain is MBLN091^T (=KCTC 52527^T=JCM 31731^T).

Complete genome sequence of a commensal bacterium, Hafnia alvei CBA7124, isolated from human feces

BACKGROUND

Members of the genus Hafnia have been isolated from the feces of mammals, birds, reptiles, and fish, as well as from soil, water, sewage, and foods. Hafnia alvei is an opportunistic pathogen that has been implicated in intestinal and extraintestinal infections in humans. However, its pathogenicity is still unclear. In this study, we isolated H. alvei from human feces and performed sequencing as well as comparative genomic analysis to better understand its pathogenicity.

RESULTS

The genome of H. alvei CBA7124 comprised a single circular chromosome with 4,585,298 bp and a GC content of 48.8%. The genome contained 25 rRNA genes (9 5S rRNA genes, 8 16S rRNA genes, and 8 23S rRNA genes), 88 tRNA genes, and 4043 protein-coding genes. Using comparative genomic analysis, the genome of this strain was found to have 72 strain-specific singletons. The genome also contained genes for antibiotic and antimicrobial resistance, as well as toxin-antitoxin systems.

CONCLUSIONS

We revealed the complete genome sequence of the opportunistic gut pathogen, H. alvei CBA7124. We also performed comparative genomic analysis of the sequences in the genome of H. alvei CBA7124, and found that it contained strain-specific singletons, antibiotic resistance genes, and toxin-antitoxin systems. These results could improve our understanding of the pathogenicity and the mechanism behind the antibiotic resistance of H. alvei strains.

Complete genome sequence of Clostridium perfringens CBA7123 isolated from a faecal sample from Korea

Background

Clostridium perfringens is an opportunistic human pathogen that causes necrotic enteritis, mild diarrhea, clostridial myonecrosis or gas gangrene, sepsis, etc. In this study, we aim to determine the pathogenesis of this bacterium at the genomic level. The genome of strain CBA7123 was sequenced, and a comparative genomic analysis between strain CBA7123 and four other related C. perfringens strains was performed.

Results

The genome of strain CBA7123 consisted of one circular chromosome and one plasmid that were 3,088,370 and 46,640 bp long with 28.5 and 27.1 mol% G+C content, respectively. The genomic DNA was predicted to contain 2798 open reading frames (ORFs), 10 rRNA genes, and 94 tRNA genes. The genomic comparison analysis between the five strains revealed the distinctive virulence properties of strain CBA7123 by highlighting certain strain-specific genes.

Conclusions

In this study, the C. perfringens CBA7123 genome was sequenced and compared with other C. perfringens genomes. Among the various genes sequenced, the detection of antimicrobial resistance genes and those encoding various virulence factors may extend the understanding of the pathogenesis of C. perfringens strains.

Electronic supplementary material

The online version of this article (doi:10.1186/s13099-017-0181-1) contains supplementary material, which is available to authorized users.

Next-Generation Sequencing Analyses of Bacterial Community Structures in Soybean Pastes Produced in Northeast China

Fermented soybean foods contain nutritional components including easily digestible peptides, cholesterol-free oils, minerals, and vitamins. Various fermented soybean foods have been developed and are consumed as flavoring condiments in Asian regions. While the quality of fermented soybean foods is largely affected by microorganisms that participate in the fermentation process, our knowledge about the microorganisms in soybean pastes manufactured in Northeast China is limited. The current study used a culture-independent barcoded pyrosequencing method targeting hypervariable V1/V2 regions of the 16S rRNA gene to evaluate Korean doenjang and soybean pastes prepared by the Hun Chinese (SPHC) and Korean minority (SPKM) populations in Northeast China. In total, 63399 high-quality sequences were derived from 16 soybean paste samples collected in Northeast China. Each bacterial species-level taxon of SPHC, SPKM, and Korean doenjang was clustered separately. Each paste contained representative bacterial species that could be distinguished from each other: Bacillus subtilis in SPKM, Tetragenococcus halophilus in SPHC, and Enterococcus durans in Korean doenjang. This is the 1st massive sequencing-based study analyzing microbial communities in soybean pastes manufactured in Northeast China, compared to Korean doenjang. Our results clearly showed that each soybean paste contained unique microbial communities that varied depending on the manufacturing process and location.

Genomic Analysis of the Extremely Halophilic Archaeon Halobacterium noricense CBA1132 Isolated from Solar Salt That Is an Essential Material for Fermented Foods

The extremely halophilic archaeon Halobacterium noricense is a member of the genus Halobacterium. Strain CBA1132 (= KCCM 43183, JCM 31150) was isolated from solar salt. The genome of strain CBA1132 assembled with 4 contigs, including three rRNA genes, 44 tRNA genes, and 3,208 open reading frames. Strain CBA1132 had nine putative CRISPRs and the genome contained genes encoding metal resistance determinants: copper-translocating P-type ATPase (CtpA), arsenical pump-driving ATPase (ArsA), arsenate reductase (ArsC), and arsenical resistance operon repressor (ArsR). Strain CBA1132 was related to Halobacterium noricense, with 99.2% 16S rRNA gene sequence similarity. Based on the comparative genomic analysis, strain CBA1132 has distinctly evolved; moreover, essential genes related to nitrogen metabolism were only detected in the genome of strain CBA1132 among the reported genomes in the genus Halobacterium. This genome sequence of Halobacterium noricense CBA1132 may be of use in future molecular biological studies.

Furan, phenolic, and heptelidic acid derivatives produced by Aspergillus oryzae

Eleven compounds, including a new sesquiterpene, were isolated from the culture medium of Aspergillus oryzae incubated with capsaicin. The structure of the new compound was determined to be 1,3,5a,6,7,8,9,9a-octahydro-9-hydroxy-9-(hydroxymethyl)-6-isopropyl-1-oxobenzo[c]oxepine-4- carboxylic acid, a heptelidic acid derivative. In addition, 10 known compounds were identified, namely 5-(hydroxymethyl)-3-furancarboxylic acid (flufuran), 3-hydroxypropanoic acid, 5-(hydroxymethyl)-2- furancarboxylic acid, 2-(4-hydroxyphenyl)-ethanol, 4-hydroxybenzoic acid, vanillic acid, 3,4-dihydroxybenzoic acid, 2-furanol, hydroheptelidic acid, and trichoderonic acid A, using spectroscopic data from nuclear magnetic resonance and electrospray ionization-mass spectroscopy.