Altered gut microbiome in convalescent patients with coronavirus disease 2019.

Introduction: Coronavirus disease 2019 (COVID-19) alters the gut microbiome. This study aimed to assess the association between the disease severity of COVID-19 and changes in stool microbes through a seven-month follow-up of stool collection.

Methods: We conducted a multicentre, prospective longitudinal study of 58 COVID-19 patients and 116 uninfected controls.

Systemic multiomics evaluation of the therapeutic effect of species on liver cirrhosis in male mice.

The human gut microbiome mediates bidirectional interaction within the gut-liver axis, while liver diseases, including liver cirrhosis, are very closely related to the state of the gut environment. Thus, improving the health of the gut-liver axis by targeting the intestinal microbiota is a potential therapeutic approach in hepatic diseases. This study examines changes in metabolomics and microbiome composition by treating bacteria derived from the human gut in mice with liver cirrhosis.

Metagenomic data from surface seawater of the east coast of South Korea.

The East Sea, also known as the Sea of Japan, is a marginal sea located in the western Pacific Ocean, displaying comparable characteristics to Earth's oceans, thereby meriting its recognition as a "miniature ocean". The East Sea exhibits a range of annually-recurring biogeochemical features in accordance with seasonal fluctuations, such as phytoplankton blooms during the spring and autumn seasons. Despite ongoing monitoring efforts focused on water quality and physicochemical parameters, the investigation of prokaryotic assemblages in the East Sea, encompassing seasonal variations, has been infrequently pursued.

Lactobacillus lactis and Pediococcus pentosaceus-driven reprogramming of gut microbiome and metabolome ameliorates the progression of non-alcoholic fatty liver disease.

Background: Although microbioa-based therapies have shown putative effects on the treatment of non-alcoholic fatty liver disease (NAFLD), it is not clear how microbiota-derived metabolites contribute to the prevention of NAFLD. We explored the metabolomic signature of Lactobacillus lactis and Pediococcus pentosaceus in NAFLD mice and its association in NAFLD patients.

Methods: We used Western diet-induced NAFLD mice, and L.

sp. nov., isolated from faeces from a healthy human.

An obligately anaerobic, Gram-stain-positive, non-motile and coccoid- or oval-shaped bacterium, designated strain KGMB01111, was isolated from faeces from a healthy Korean. Comparative analysis of 16S rRNA gene sequences indicated that KGMB01111 was closely related to CCRI-16110 (93.9 %) and GAM6-1 (93.

sp. nov., isolated from human faeces.

A novel Gram-stain-negative and strictly anaerobic bacterial strain, designated KGMB02408, was isolated from faeces of a healthy human in the Republic of Korea. The isolate was characterized as non-motile, non-spore-forming and rod-shaped (variable in length). The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KGMB02408 belonged to the genus and was most closely related to JCM 17102 (=KCTC 15666; 96.

Olsenella faecalis sp. nov., an anaerobic actinobacterium isolated from human faeces.

A novel actinobacterial strain, designated KGMB04489, was isolated from the faeces of a healthy Korean. Cells of the strain were strictly anaerobic, Gram-stain-positive and short-rod-shaped. On the basis of 16S rRNA gene sequence similarity, strain KGMB04489 belonged to the genus Olsenella and was most closely related to Olsenella scatoligenes SK9K4 (94.

Mediterraneibacter butyricigenes sp. nov., a butyrate-producing bacterium isolated from human faeces.

A Gram-stain-positive, obligately anaerobic, non-motile, nonspore-forming, and rod-shaped bacterial strain, designated KGMB01110T, was isolated from a faecal sample of a healthy male in South Korea. Phylogenetic analysis based on 16S rRNA gene showed that strain KGMB01110 belonged to Clostridium cluster XIVa and was most closely related to Mediterraneibacter glycyrrhizinilyticus KCTC 5760T (95.9% 16S rRNA gene sequence similarity).

Blastococcus atacamensis sp. nov., a novel strain adapted to life in the Yungay core region of the Atacama Desert.

A polyphasic study was undertaken to establish the taxonomic status of a Blastococcus strain isolated from an extreme hyper-arid Atacama Desert soil. The isolate, strain P6, was found to have chemotaxonomic and morphological properties consistent with its classification in the genus Blastococcus. It was shown to form a well-supported branch in the Blastococcus 16S rRNA gene tree together with the type strains of Blastococcus capsensis and Blastococcus saxobsidens and was distinguished from the latter, its close phylogenetic neighbour, by a broad range of phenotypic properties.

Rejection of reclassification of Lactobacillus kimchii and Lactobacillus bobalius as later subjective synonyms of Lactobacillus paralimentarius using comparative genomics.

Lactobacillus bobalius, Lactobacillus kimchii and Lactobacillus paralimentarius belong to the genus Lactobacillus and show close phylogenetic relationships. In a previous study, L. bobalius and L.

Expansion of Cultured Bacterial Diversity by Large-Scale Dilution-to-Extinction Culturing from a Single Seawater Sample.

High-throughput cultivation (HTC) based on a dilution-to-extinction method has been applied broadly to the cultivation of marine bacterial groups, which has often led to the repeated isolation of abundant lineages such as SAR11 and oligotrophic marine gammaproteobacteria (OMG). In this study, to expand the phylogenetic diversity of HTC isolates, we performed a large-scale HTC with a single surface seawater sample collected from the East Sea, the Western Pacific Ocean. Phylogenetic analyses of the 16S rRNA genes from 847 putative pure cultures demonstrated that some isolates were affiliated with not-yet-cultured clades, including the OPB35 and Puniceicoccaceae marine group of Verrucomicrobia and PS1 of Alphaproteobacteria.

Complete genome sequence of bacteriophage P8625, the first lytic phage that infects Verrucomicrobia.

Bacteriophage P8625 is a lytic bacteriophage that infects the verrucomicrobial strain IMCC8625, a marine bacterium affiliated with Verrucomicrobia subdivision 4. Both the bacteriophage and the host bacterial strain were isolated from surface seawater samples collected off the east coast of Korea. The phage particle has an icosahedral capsid with a diameter of ~47 nm and a long tail of ~75 nm in length, showing the distinctive morphology of the Siphoviridae family.

Lentisphaera marina sp. nov., and emended description of the genus Lentisphaera.

Two Gram-stain-negative, non-motile, non-pigmented cocci, designated IMCC11369(T) and IMCC11389, were isolated from surface seawater of the East Sea of Korea by high-throughput cultivation based on dilution to extinction. Strains IMCC11369(T) and IMCC11389 shared 99.9 % 16S rRNA gene sequence similarity and >86.

Lutibacter flavus sp. nov., a marine bacterium isolated from a tidal flat sediment.

A carotenoid-containing chemoheterotrophic bacterium, designated IMCC1507(T), was isolated from a tidal flat sediment of the Yellow Sea, Korea. Strain IMCC1507(T) was Gram-negative, yellow, obligately aerobic, non-motile and flexirubin-negative. 16S rRNA gene sequence analysis indicated that strain IMCC1507(T) belonged to the genus Lutibacter in the family Flavobacteriaceae and exhibited 96.

Complete genome sequence of strain HTCC2170, a novel member of the genus Maribacter in the family Flavobacteriaceae.

Strain HTCC2170 was isolated from surface waters off the Oregon coast using dilution-to-extinction culturing. Here, we present the finished genome sequence of a marine bacterium, Maribacter sp. strain HTCC2170.

Kordia periserrulae sp. nov., isolated from a marine polychaete Periserrula leucophryna, and emended description of the genus Kordia.

A Gram-negative, chemoheterotrophic, yellow-pigmented, non-motile, flexirubin-negative, facultatively anaerobic bacterium, designated strain IMCC1412(T), was isolated from a marine polychaete Periserrula leucophryna inhabiting a tidal flat of the Yellow Sea, Korea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain IMCC1412(T) was most closely related to Kordia algicida, with a sequence similarity of 96.7 %, but only distantly related to other species in the family Flavobacteriaceae (<92 % similarity).

Antarcticimonas flava gen. nov., sp. nov., isolated from Antarctic coastal seawater.

A marine bacterium, designated IMCC3175(T), was isolated from a seawater sample collected off the Antarctic coast. The strain was Gram-negative, obligately aerobic, carotenoid pigment-containing, and rod-shaped bacterium that divided by binary fission. As determined by 16S rRNA gene sequence comparisons, the most closely related genera were Formosa (92.