Bacteroides faecium sp. nov. isolated from human faeces.

A novel bacterial strain, CBA7301T, was isolated from human faeces and was characterised using a polyphasic taxonomic approach. A phylogenetic analysis based on 16S rRNA gene sequences revealed that CBA7301T represented a member of the genus Bacteroides, in the family Bacteroidaceae. The similarity between the 16S rRNA gene sequence of CBA7301T and that of its most closely related species, Bacteroides faecichinchillae JCM 17102T, was 96.2 %, and the average nucleotide identity between these two strains was 77.9 %. The genome size was 6 782 182 bp, and the DNA G+C content was 42.5 mol%. Cells of CBA7301T were Gram-stain-negative, strictly anaerobic and rod-shaped. The optimal growth of this organism occurred at 30-35 °C, pH 7.0 and 0.5 % (w/v) NaCl. The respiratory quinone was menaquinone 10. The predominant polar lipids were phosphatidylethanolamine, phospholipids and aminophospholipids. The major cellular fatty acid was anteiso-C15 : 0. According to the results of the polyphasic taxonomic analysis, CBA7301T represents a novel species of the genus Bacteroides, which we named Bacteroides faecium sp. nov. The type strain is CBA7301T (=KCCM 43355T=ATCC TSD-227T).

Brachybacterium kimchii sp. nov. and Brachybacterium halotolerans subsp. kimchii subsp. nov., isolated from the Korean fermented vegetables, kimchi, and description of Brachybacterium halotolerans subsp. halotolerans subsp. nov.

Two Gram-stain-positive, oxidase-negative, catalase-positive, and coccus-shaped bacterial strains, designated CBA3104T and CBA3105T, were isolated from kimchi. Strain CBA3104T and CBA3105T grew at 10-35°C (optimum, 25°C and 30°C, respectively), at pH 6.0-8.5 (optimum, pH 6.5), and in the presence of 0-15% (w/v) NaCl (optimum, 5%). A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CBA3104T formed a distinct phylogenetic lineage within the genus Brachybacterium whereas strain CBA3105T was closely positioned with Brachybacterium halotolerans MASK1Z-5T. The 16S rRNA gene sequence similarity between strains CBA3104T and CBA3105T was 99.9%, but ANI and dDDH values between strains CBA3104T and CBA3105T were 93.61% and 51.5%, respectively. Strain CBA3104T showed lower ANI and dDDH values than species delineation against three closely related strains and type species of the genus Brachybacterium, however, strain CBA3105T showed 96.63% ANI value and 69.6% dDDH value with Brachybacterium halotolerans MASK1Z-5T. Among biochemical analysis results, strain CBA3104T could uniquely utilize bromo-succinic acid whereas only strain CBA3105T was positive for alkaline phosphatase and α-fucosidase among two novel strains, closely related strains, and type species of the genus Brachybacterium. Compared with strain CBA3105T and Brachybacterium halotolerans JCM 34339T, strain CBA3105T was differentially positive for acid production of D-arabinose, D-adonitol, and potassium 5-ketogluconate and enzyme activity of ß-glucuronidase. Both strains contained menaquinone-7 as the dominant quinone. The cell-wall peptidoglycan of two novel strains contained meso-diaminopimelic acid. The major fatty acids of strains CBA3104T and CBA3105T were anteiso-C15:0, anteiso-C17:0, and iso-C16:0. The major polar lipids of both strains were phosphatidylglycerol and diphosphatidylglycerol. Strain CBA3104T possessed a uniquely higher abundance of tRNA (97 tRNAs) than four Brachybacterium strains used for comparative taxonomic analysis (54-62 tRNAs). Both the CBA3104T and CBA3105T strain harbored various oxidoreductase, transferase, hydrolase, and lyase as strain-specific functional genes compared to closely related strains and Brachybacterium type species. The results of biochemical/physiological, chemotaxonomic, and genomic analyses demonstrated that strains CBA3104T and CBA3105T represent a novel species of the genus Brachybacterium and a novel subspecies of B. halotolerans, respectively, for which the names Brachybacterium kimchii sp. nov. and B. halotolerans subsp. kimchii subsp. nov. are proposed. The type strains of the novel species and the novel subspecies are CBA3104T (= KCCM 43417T = JCM 34759T) and CBA3105T (= KCCM 43418T =JCM 34760T), respectively.

A qRT-PCR Method Capable of Quantifying Specific Microorganisms Compared to NGS-Based Metagenome Profiling Data.

Metagenome profiling research using next-generation sequencing (NGS), a technique widely used to analyze the diversity and composition of microorganisms living in the human body, especially the gastrointestinal tract, has been actively conducted, and there is a growing interest in the quantitative and diagnostic technology for specific microorganisms. According to recent trends, quantitative real-time PCR (qRT-PCR) is still a considerable technique in detecting and quantifying bacteria associated with the human oral and nasal cavities, due to the analytical cost and time burden of NGS technology. Here, based on NGS metagenome profiling data produced by utilizing 100 gut microbiota samples, we conducted a comparative analysis for the identification and quantification of five bacterial genera (Akkermansia, Bacteroides, Bifidobacterium, Phascolarctobacterium, and Roseburia) within same metagenomic DNA samples through qRT-PCR assay in parallel. Genus-specific primers, targeting the particular gene of each genus for qRT-PCR assay, allowed a statistically consistent quantification pattern with the metagenome profiling data. Furthermore, results of bacterial identification through Sanger validation demonstrated the high genus-specificity of each primer set. Therefore, our study suggests that an approach to quantifying specific microorganisms by applying the qRT-PCR method can compensate for the concerns (potential issues) of NGS while also providing efficient benefits to various microbial industries.

Genome-Wide Assessment of a Korean Composite Pig Breed, Woori-Heukdon.

A Korean synthetic pig breed, Woori-Heukdon (WRH; F3), was developed by crossing parental breeds (Korean native pig [KNP] and Korean Duroc [DUC]) with their crossbred populations (F1 and F2). This study in genome-wide assessed a total of 2,074 pigs which include the crossbred and the parental populations using the Illumina PorcineSNP60 BeadChip. After quality control of the initial datasets, we performed population structure, genetic diversity, and runs of homozygosity (ROH) analyses. Population structure analyses showed that crossbred populations were genetically influenced by the parental breeds according to their generation stage in the crossbreeding scheme. Moreover, principal component analysis showed the dispersed cluster of WRH, which might reflect introducing a new breeding group into the previous one. Expected heterozygosity values, which were used to assess genetic diversity, were .365, .349, .336, .330, and .211 for WRH, F2, F1, DUC, and KNP, respectively. The inbreeding coefficient based on ROH was the highest in KNP (.409), followed by WRH (.186), DUC (.178), F2 (.107), and F1 (.035). Moreover, the frequency of short ROH decreased according to the crossing stage (from F1 to WRH). Alternatively, the frequency of medium and long ROH increased, which indicated recent inbreeding in F2 and WRH. Furthermore, gene annotation of the ROH islands in WRH that might be inherited from their parental breeds revealed several interesting candidate genes that may be associated with adaptation, meat quality, production, and reproduction traits in pigs.

Human gut commensal bacterium Ruminococcus species FMB-CY1 completely degrades the granules of resistant starch.

Resistant starch (RS) in the diet reaches the large intestine and is fermented by the gut microbiota, providing beneficial effects on human health. The human gut bacterium FMB-CY1 was isolated and identified as a new species closest to Ruminococcus bromii. Ruminococcus sp. FMB-CY1 completely degraded RS including commercial RS types 2, 3, and 4, and generated glucose and maltose; however, it did not assimilate glucose. Genome analysis revealed 15 amylolytic enzymes (Amy) present in FMB-CY1. The evolutionary trees revealed that the Amys were well divided each other. All Amys (4, 9, 10, 12, and 16) containing cohesin and/or dockerin and scaffolding proteins known to be involved in constituting the amylosome, were identified. A new species of Ruminococcus, strain FMB-CY1, was considered to have the ability to form amylosomes for the degradation of RS. This new RS-degrading Ruminococcus species provides insights into the mechanism(s) underlying RS degradation in the human gut. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-021-01027-2.

Effect of Saengshik Supplementation on the Gut Microbial Composition of Healthy Korean Adults: A Single-Group Pilot Study.

Saengshik is a type of meal-replacement product or dietary supplement comprising an uncooked and dried plant-based food mixture with various health-promoting properties, such as antidiabetic, anti-dyslipidemic, antioxidant, and anticancer properties. Although these properties are considered attributable to the various bioactive components absorbed through the intestine and its remolding effect on intestinal microorganisms, the effect of Saengshik supplementation on gut microbiota profiles has not yet been studied. In this study, we investigated the effect of Saengshik administration on the composition of gut microbiota. This single-group design trial was conducted on 102 healthy men and women who received 40 g/day of Saengshik powder for 8 weeks, during which stool samples were collected at two fixed time points (baseline and the endpoint) for gut microbiota-profiling analysis. We observed a significant decrease in the α-diversity of gut microbiota after Saengshik consumption (P < 0.05), with significant changes identified in the composition of major microbial taxa, such as Bacteroidetes (P < 0.0001), Proteobacteria, Actinobacteria, and Verrucomicrobia (P < 0.0001). Notably, the gut microbial response was related to the inter-individual variability of habitual dietary intake and enterotype at baseline. To the best of our knowledge, this is the first study investigating the effects of Saengshik intake on changes in gut microbiota, with the results suggesting that individual habitual diet patterns and gut microbial shapes should be considered key aspects in Saengshik-mediated health-promotion effects.

Amelioration of Hepatic Steatosis in Mice through Bacteroides uniformis CBA7346-Mediated Regulation of High-Fat Diet-Induced Insulin Resistance and Lipogenesis.

Dietary habits and gut microbiota play an essential role in non-alcoholic fatty liver disease (NAFLD) and related factors such as insulin resistance and de novo lipogenesis. In this study, we investigated the protective effects of Bacteroides uniformis CBA7346, isolated from the gut of healthy Koreans, on mice with high-fat diet (HFD)-induced NAFLD. Administration of B. uniformis CBA7346 reduced body and liver weight gain, serum alanine aminotransferase and aspartate aminotransferase levels, liver steatosis, and liver triglyceride levels in mice on an HFD; the strain also decreased homeostatic model assessment for insulin resistance values, as well as serum cholesterol, triglyceride, lipopolysaccharide, leptin, and adiponectin levels in mice on an HFD. Moreover, B. uniformis CBA7346 controlled fatty liver disease by attenuating steatosis and inflammation and regulating de novo lipogenesis-related proteins in mice on an HFD. Taken together, these findings suggest that B. uniformis CBA7346 ameliorates HFD-induced NAFLD by reducing insulin resistance and regulating de novo lipogenesis in obese mice.

Gut Microbiome Structure and Association with Host Factors in a Korean Population.

Characterizing the gut microbiome in the healthy population is the first step in elucidating its associations with host health conditions. Populations with different diet patterns, lifestyles, and genetic backgrounds harbor different gut microbes. In this study, we characterized the gut microbiome of 890 healthy Koreans using 16S rRNA sequencing. The Korean population harbored a relatively large fraction of the Prevotella enterotype and presented a distinctive gut microbiome, compared to that in the populations of other countries. Additionally, we determined the clusters of cooccurring microbes that were quantitatively correlated with each other. We found that microbe composition of the gut was strongly associated with age. We identified that the abundance of members of Bacteroidia and Clostridia differed with the host dietary patterns, body mass index, and stool frequency. The gut microbiome data obtained in this study would be an important resource for future studies addressing microbial contributions in health and disease. IMPORTANCE Comparing the gut microbiomes of healthy controls and disease patients showed that the composition of the gut microbiome is associated with various host health conditions. The gut microbiome in healthy Western populations is well characterized, while that of non-Western populations, with different diet patterns, lifestyles, and genetic backgrounds, is not clearly defined. In this study, we characterized the microbiome of 890 healthy Korean individuals using 16S rRNA sequencing and found that Koreans have a gut microbiome different from that in the individuals of neighboring countries. The members of Bacteroidetes and Firmicutes cooccurred and were quantitatively associated with each other. Additionally, we found that the gut microbial composition is strongly associated with the host's age. The microbiome data presented here represent the gut microbiome of a healthy Korean population and could be used to unveil gut microbiome-associated host conditions in this population.

The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology.

Characterizing the microbial communities inhabiting specimens is one of the primary objectives of microbiome studies. A short-read sequencing platform for reading partial regions of the 16S rRNA gene is most commonly used by reducing the cost burden of next-generation sequencing (NGS), but misclassification at the species level due to its length being too short to consider sequence similarity remains a challenge. Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S). We compared a 16S full-length-based synthetic long-read (sFL16S) and V3-V4 short-read (V3V4) methods using 24 human GUT microbiota samples. Our comparison analyses of sFL16S and V3V4 sequencing data showed that they were highly similar at all classification resolutions except the species level. At the species level, we confirmed that sFL16S showed better resolutions than V3V4 in analyses of alpha-diversity, relative abundance frequency and identification accuracy. Furthermore, we demonstrated that sFL16S could overcome the microbial misidentification caused by different sequence similarity in each 16S variable region through comparison the identification accuracy of Bifidobacterium, Bacteroides, and Alistipes strains classified from both methods. Therefore, this study suggests that the new sFL16S method is a suitable tool to overcome the weakness of the V3V4 method.

Genome analysis of 1-deoxynojirimycin (1-DNJ)-producing Bacillus velezensis K26 and distribution of Bacillus sp. harboring a 1-DNJ biosynthetic gene cluster.

1-Deoxynojirumycin (1-DNJ) is a representative iminosugar with α-glucosidase inhibition (AGI) activity. In this study, the full genome sequencing of 1-DNJ-producing Bacillus velezensis K26 was performed. The genome consists of a circular chromosome (4,047,350 bps) with two types of putative virulence factors, five antibiotic resistance genes, and seven secondary metabolite biosynthetic gene clusters. Genomic analysis of a wide range of Bacillus species revealed that a 1-DNJ biosynthetic gene cluster was commonly present in four Bacillus species (B. velezensis, B. pseudomycoides, B. amyloliquefaciens, and B. atrophaeus). In vitro experiments revealed that the increased mRNA expression levels of the three 1-DNJ biosynthetic genes were closely related to increased AGI activity. Genomic comparison and alignment of multiple gene sequences indicated the conservation of the 1-DNJ biosynthetic gene cluster in each Bacillus species. This genomic analysis of Bacillus species having a 1-DNJ biosynthetic gene cluster could provide a basis for further research on 1-DNJ-producing bacteria.

Beneficial Effects of Newly Isolated Akkermansia muciniphila Strains from the Human Gut on Obesity and Metabolic Dysregulation.

The identification of new probiotics with anti-obesity properties has attracted considerable interest. In the present study, the anti-obesity activities of Akkermansia muciniphila (A. muciniphila) strains isolated from human stool samples and their relationship with the gut microbiota were evaluated using a high fat-diet (HFD)-fed mice model. Three strains of A. muciniphila were chosen from 27 isolates selected based on their anti-lipogenic activity in 3T3-L1 cells. The anti-lipogenic, anti-adipogenic and anti-obesity properties of these three strains were evaluated further in HFD-induced obese mice. The animals were administered these strains six times per week for 12 weeks. The treatment improved the HFD-induced metabolic disorders in mice in terms of the prevention of body weight gain, caloric intake and reduction in the weights of the major adipose tissues and total fat. In addition, it improved glucose homeostasis and insulin sensitivity. These effects were also associated with the inhibition of low-grade intestinal inflammation and restoration of damaged gut integrity, prevention of liver steatosis and improvement of hepatic function. These results revealed a difference in the distribution pattern of the gut microbial communities between groups. Therefore, the gut microbial population modulation, at least in part, might contribute to the beneficial impact of the selected A. muciniphila strains against metabolic disorders.

The human gut archaeome: identification of diverse haloarchaea in Korean subjects.

BACKGROUND: Archaea are one of the least-studied members of the gut-dwelling autochthonous microbiota. Few studies have reported the dominance of methanogens in the archaeal microbiome (archaeome) of the human gut, although limited information regarding the diversity and abundance of other archaeal phylotypes is available. RESULTS: We surveyed the archaeome of faecal samples collected from 897 East Asian subjects living in South Korea. In total, 42.47% faecal samples were positive for archaeal colonisation; these were subsequently subjected to archaeal 16S rRNA gene deep sequencing and real-time quantitative polymerase chain reaction-based abundance estimation. The mean archaeal relative abundance was 10.24 ± 4.58% of the total bacterial and archaeal abundance. We observed extensive colonisation of haloarchaea (95.54%) in the archaea-positive faecal samples, with 9.63% mean relative abundance in archaeal communities. Haloarchaea were relatively more abundant than methanogens in some samples. The presence of haloarchaea was also verified by fluorescence in situ hybridisation analysis. Owing to large inter-individual variations, we categorised the human gut archaeome into four archaeal enterotypes. CONCLUSIONS: The study demonstrated that the human gut archaeome is indigenous, responsive, and functional, expanding our understanding of the archaeal signature in the gut of human individuals. Video Abstract.

The presence of resistant starch-degrading amylases in Bifidobacterium adolescentis of the human gut.

Resistant starch (RS) is a complex prebiotic carbohydrate beneficial to the human gut. In the present study, four genes encoding for putative amylolytic enzymes, likely to be responsible for RS-degradation, were identified in the genome of Bifidobacterium adolescentis P2P3 by comparative genomic analysis. Our results showed that only three enzymes (RSD1, RSD2, and RSD3) exhibited non-gelatinized high amylose corn starch (HACS)-degrading activity in addition to typical α-amylase activity. These three RS-degrading enzymes (RSD) were composed of multiple domains, including signal peptide, catalytic domain, carbohydrate binding domains, and putative cell wall-anchoring domains. Typical catalytic domains were conserved by exhibiting seven typical conserved regions (I-VII) found mostly in α-amylases. Analysis of enzymatic activity revealed that RSD2 displayed stronger activity toward HACS-granules than RSD1 and RSD3. Comparative genomics in combination with enzymatic experiments confirmed that RSDs might be the key enzymes used by RS-degrading bifidobacteria to degrade RS in a particular ecological niche, such as the human gut.

Genome analysis of Lactobacillus plantarum subsp. plantarum KCCP11226 reveals a well-conserved C30 carotenoid biosynthetic pathway.

Carotenoids are group of colored terpenoids with antioxidant properties and widespread in nature including in microorganisms. Lactobacillus plantarum subsp. plantarum KCCP11226 was previously isolated from kimchi, while exhibiting the production of 4,4'-diaponeurosporene as a C30 carotenoid. In this study, full genome sequencing of the strain KCCP11226 was performed. Genome analysis revealed that the dehydrosqualene synthase (crtM) and dehydrosqualene desaturase (crtN) genes, which are major genes for biosynthesis of 4,4'-diaponeurosporene, were shown to act as an operon in most L. plantarum strains, but they were uncommon in other Lactobacillus species. In vitro experiments revealed that the production of 4,4'-diaponeurosporene was greatly increased by oxidative stress. In this situation, mRNA expressions of crtN and crtM were also significantly increased. In conclusion, genome analysis of L. plantarum subsp. plantarum KCCP11226 suggested the presence of a well-conserved C30 carotenoid biosynthetic pathway that includes the crtM-crtN operon. The genomic information on L. plantarum subsp. plantarum KCCP11226 could further elucidate the functions of genes involved in isoprenoid biosynthetic pathway, especially in C30 carotenoid biosynthesis.

Genome Analysis of Enterococcus mundtii Pe103, a Human Gut-Originated Pectinolytic Bacterium.

Pectin exists in significant amounts in vegetables and fruits as a component of the plant cell wall. In human diet, pectin is not degraded by the human digestive enzymes due to its complex structure; only gut bacteria degrade pectin in the large intestine. To date, although pectin is one of the most important sources of dietary fiber in human diet, there have been only few reports on human gut-originated pectinolytic bacteria. In this study, the strain Enterococcus mundtii Pe103, a bacterium with pectin-degrading activity, was isolated from the feces of a healthy Korean adult female. Culture experiments revealed that it could grow on pectin as the sole carbon source by degrading pectin to approximately 35% within 13 h. We report the complete genome data of human gut E. mundtii Pe103. It consists of a circular chromosome (3,084,146 bps) and two plasmids (63,713 and 56,223 bps). Genomic analysis suggested that at least nine putative enzymes related to pectin degradation are present in E. mundtii Pe103. These enzymes may be involved in the degradation of pectin. The whole genome information of E. mundtii Pe103 could improve the understanding of the mechanism underlying the degradation of pectin by human gut microbiota.

Complete genome sequence of Bifidobacterium adolescentis P2P3, a human gut bacterium possessing strong resistant starch-degrading activity.

Resistant starch (RS) is an important food source from which gut bacteria produce short chain fatty acids, which have beneficial effects for human health. The Bifidobacterium adolescentis P2P3, a human gut bacterium possessing a strong RS-degrading activity, was isolated from a healthy Korean adult male. In vitro experiments showed that this bacterium could utilize approximately 63% of high amylose corn starch after forming RS granule clusters. Here we provide the first complete set of genomic information on RS-degrading B. adolescentis P2P3. The genome of B. adolescentis P2P3 consists of one chromosome (2,202,982 bp) with high GC content (59.4%). Analysis of the protein-coding genes revealed that at least nineteen of the starch degradation-related enzymes were present in the genome. Among those, five genes evidently possess carbohydrate-binding domains, which are presumed to be involved in efficient RS decomposition. The complete set of genomic information on B. adolescentis P2P3 could provide an understanding of the role of RS-degrading gut bacteria and its RS degradation mechanism.

Whole-genome resequencing analysis of 20 Micro-pigs.

BACKGROUND: Miniature pigs have been increasingly used as mammalian model animals for biomedical research because of their similarity to human beings in terms of their metabolic features and proportional organ sizes. However, despite their importance, there is a severe lack of genome-wide studies on miniature pigs. OBJECTIVE: In this study, we performed whole-genome sequencing analysis of 20 Micro-pigs obtained from Medi Kinetics to elucidate their genomic characteristics. RESULTS: Approximately 595 gigabase pairs (Gb) of sequence reads were generated to be mapped to the swine reference genome assembly (Sus scrofa 10.2); on average, the sequence reads covered 99.15% of the reference genome at an average of 9.6-fold coverage. We detected a total of 19,518,548 SNPs, of which 8.7% were found to be novel. With further annotation of all of the SNPs, we retrieved 144,507 nonsynonymous SNPs (nsSNPs); of these, 5968 were found in all 20 individuals used in this study. SIFT prediction for these SNPs identified that 812 nsSNPs in 402 genes were deleterious. Among these 402 genes, we identified some genes that could potentially affect traits of interest in Micro-pigs, such as RHEB and FRAS1. Furthermore, we performed runs of homozygosity analysis to locate potential selection signatures in the genome, detecting several loci that might be involved in phenotypic characteristics in Micro-pigs, such as MSTN, GDF5, and GDF11. CONCLUSION: In this study, we identified numerous nsSNPs that could be used as candidate genetic markers with involvement in traits of interest. Furthermore, we detected putative selection footprints that might be associated with recent selection applied to miniature pigs.

Whole genome sequencing analysis of horse populations inhabiting the Korean Peninsula and Przewalski's horse.

BACKGROUND: The Jeju horse is an indigenous horse breed in Korea. However, there is a severe lack of genomic studies on Korean horse breeds. OBJECTIVE: The objective of this study was to report genomic characteristics of domestic horse populations that inhabit South Korea (Jeju, Jeju crossbred, and Thoroughbred) and a wild horse breed (Przewalski's horse). RESULTS: Using the equine reference genome assembly (EquCab 2.0), more than ~ 6.5 billion sequence reads were successfully mapped, which generated an average of 40.87-fold coverage throughout the genome. Using these data, we detected a total of 12.88 million SNPs, of which 73.7% were found to be novel. All the detected SNPs were deeply annotated to retrieve SNPs in gene regions using the RefSeq and Ensemble gene sets. Approximately 27% of the total SNPs were located within genes, whereas the remaining 73% were found in intergenic regions. Using 129,776 coding SNPs, we retrieved a total of 49,171 nonsynonymous SNPs in 12,351 genes. Furthermore, we identified a total of 10,770 deleterious nonsynonymous SNPs which are predicted to affect protein structure or function. CONCLUSION: We showed numerous genomic variants from domestic and wild horse breeds. These results provide a valuable resource for further studies on functions of SNP-containing genes, and can aid in determining the molecular basis underlying variation in economically important traits of horses.

Complete genome sequence of acetate-producing Klebsiella pneumoniae L5-2 isolated from infant feces.

Acetate is an important metabolite in infants as it can affect metabolism as well as immune and inflammatory responses. However, there have been no studies on acetate production by Klebsiella pneumoniae isolated from infant feces. In this study, we isolated a K. pneumoniae strain, L5-2, from infant feces, and we found it produces acetate. The genome of L5-2 consisted of a 5,237,123-bp single chromosome and a 139,211-bp single plasmid. The G + C content was 57.27%. By whole-genome analysis of K. pneumoniae L5-2, we identified seven genes related to acetate production (poxA, pta, eutD, ackA, eutP, eutQ, and adhE). We confirmed acetate production by K. pneumoniae L5-2 by ion chromatography. The aldehyde/alcohol dehydrogenase (adhE) activity of K. pneumoniae L5-2 was significantly higher than that of the K. pneumoniae subsp. ozaenae ATCC 11296. Thus, the acetate-producing ability of K. pneumoniae L5-2 was influenced by the adhE gene. In addition, K. pneumoniae L5-2 had significantly less virulence factor-encoding genes than other K. pneumoniae strains isolated from humans. In conclusion, K. pneumoniae L5-2 isolated from infant feces has less virulence factors and higher adhE activity than other K. pneumoniae strains.