Genome of Bifidobacterium longum NCIM 5672 provides insights into its acid-tolerance mechanism and probiotic properties.

Bifidobacterium longum NCIM 5672 is a probiotic strain isolated from the Indian infant feces. The probiotic efficacy of Bifidobacteria is majorly affected by its acid tolerance. This study determined the probiotic properties and acid-tolerance mechanism of B. longum NCIM 5672 using whole-genome sequencing. The genome annotation is carried out using the RAST web server and NCBI PGAAP. The draft genome sequence of this strain, assembled in 63 contigs, consists of 22,46,978 base pairs, 1900 coding sequences and a GC content of 59.6%. The genome annotation revealed that seven candidate genes might be involved in regulating the acid tolerance of B. longum NCIM 5672. Furthermore, the presence of genes associated with immunomodulation and cell adhesion support the probiotic background of the strain. The analysis of candidate acid- tolerance-associated genes revealed three genes, argC, argH, and dapA, may play an essential role in high acid tolerance in B. longum NCIM 5672. The results of RT-qPCR supported this conclusion. Altogether, the results presented here supply an effective way to select acid-resistant strains for the food industry and provide new strategies to enhance this species' industrial applications and health-promoting properties.

Genome Sequence of Hymenobacter polaris RP-2-7T, Isolated from Arctic Soil.

Hymenobacter polaris RP-2-7T was isolated from soil from the Arctic region. This study presents the genome sequence of Hymenobacter polaris RP-2-7T, generated using the Illumina HiSeq platform. The genome size is 5,587,174 bp; it contains 4,721 genes and has 62.8 mol% DNA G+C content.

Role of probiotics to combat viral infections with emphasis on COVID-19.

Interspecies transmissions of viruses between animals and humans may result in unpredictable pathogenic potential and new transmissible diseases. This mechanism has recently been exemplified by the discovery of new pathogenic viruses, such as the novel severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) pandemic, Middle-East respiratory syndrome-coronavirus epidemic in Saudi Arabia, and the deadly outbreak of Ebola in West Africa. The. SARS-CoV-2 causes coronavirus disease-19 (COVID-19), which is having a massive global impact in terms of economic disruption, and, above all, human health. The disease is characterized by dry cough, fever, fatigue, myalgia, and dyspnea. Other symptoms include headache, sore throat, rhinorrhea, and gastrointestinal disorders. Pneumonia appears to be the most common and severe manifestation of the infection. Currently, there is no vaccine or specific drug for COVID-19. Further, the development of new antiviral requires a considerable length of time and effort for drug design and validation. Therefore, repurposing the use of natural compounds can provide alternatives and can support therapy against COVID-19. In this review, we comprehensively discuss the prophylactic and supportive therapeutic role of probiotics for the management of COVID-19. In addition, the unique role of probiotics to modulate the gut microbe and assert gut homeostasis and production of interferon as an antiviral mechanism is described. Further, the regulatory role of probiotics on gut-lung axis and mucosal immune system for the potential antiviral mechanisms is reviewed and discussed.Key points• Gut microbiota role in antiviral diseases• Factors influencing the antiviral mechanism• Probiotics and Covid-19.

Lentibacillus alimentarius sp. nov., isolated from Myeolchi-jeotgal, a traditional Korean high-salt fermented anchovy.

A Gram-positive, motile, endospore-forming, rod-shaped bacterium, designated strain M2024T, was isolated from Myeolchi-jeotgal, a traditional Korean high-salt fermented anchovy and was characterised using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain M2024T belongs to the genus Lentibacillus in the family Bacillaceae of the Firmicutes. The 16S rRNA gene sequence analysis showed that strain M2024T is closely related to Lentibacillus populi WD4L-1T (95.5%), Lentibacillus garicola SL-MJ1T (95.2%) and Virgibacillus siamensis MS3-4T (95.1%). The chemotaxonomic properties of strain M2024T are consistent with those of members of the genus Lentibacillus: the quinone system has MK-7 as the predominant menaquinone and anteiso-C15:0 and anteiso-C17:0 are the predominant cellular fatty acids. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genomic DNA was determined to be 36.2 mol%. Differential phenotypic properties compared with closely related type strains support the conclusion that strain M2024T can be separated from previously described members of the genus Lentibacillus. The strain thus represents a novel species in this genus, for which the name Lentibacillus alimentarius sp. nov. is proposed. The type strain is M2024T (= KEMB 9001-124T = JCM 16521T).

Vagococcus humatus sp. nov., isolated from soil beneath a decomposing pig carcass.

A Gram-stain-positive, non-motile, coccus-shaped bacterium, designated strain C25T, was isolated from the soil beneath a decomposing pig carcass in Korea and was characterized using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain C25T belongs to the genus Vagococcus in the family Enterococcaceae of the Lactobacillales. 16S rRNA gene sequence analysis showed that strain C25T was closely related to Vagococcus lutrae CCUG 39187T (96.5 % similarity) and Enterococcus termitis LMG 8895T (95.8 %). The chemotaxonomic properties of strain C25T were consistent with those of the genus Vagococcus; the major cellular fatty acids consisted of C16 : 0, C16 : 1ω9c and C18 : 1ω9c, and the cell-wall peptidoglycan type was based on meso-diaminopimelic acid. The G+C content of the genomic DNA was 44 mol%. On the basis of phylogenetic inference, fatty acid profile, and chemotaxonomic and other phenotypic properties, strain C25T is clearly differentiated from closely related type strains of the genus Vagococcus and represents a novel species in this genus, for which the name Vagococcus humatus sp. nov. is proposed. The type strain is C25T (=KEMB 562-002T=JCM 31581T).

Tessaracoccus defluvii sp. nov., isolated from an aeration tank of a sewage treatment plant.

A Gram-positive, non-motile, aerobic, coccus-shaped bacterium, designated strain LNB-140T, was isolated from a sewage treatment plant in the Republic of Korea and was characterised using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain LNB-140T belongs to genus Tessaracoccus in the family Propionibacteriaceae of the phylum Actinobacteria. The 16S rRNA gene sequence similarities between strain LNB-140T and type strains of the genus, Tessaracoccus flavescens SST-39T and Tessaracoccus rhinocerotis YIM101269T are 97.8 and 97.4 %, respectively. The chemotaxonomic properties of strain LNB-140T are consistent with those of members of the genus Tessaracoccus: a quinone system with MK-9(H4) as the predominant menaquinone; anteiso-C15:0 and iso C15:0 as the predominant cellular fatty acids; and LL-2,6-diaminopimelic acid as the diagnostic peptidoglycan diamino acid. The major polar lipids were identified as diphosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genomic DNA was determined to be 67.1 mol%. Differential phenotypic properties along with low DNA-DNA relatedness (<30 ± 3.2 %) with closely related type strains show that strain LNB-140T is distinct from previously described members of the genus Tessaracoccus and represents a novel species in this genus, for which the name Tessaracoccus defluvii sp. nov. is proposed. The type strain is LNB-140T (=KEMB 5401-076T = JCM 17540T).

Lutibacter oceani sp. nov., isolated from marine sediment in South Korea.

A novel Gram-negative, non-motile, non-spore forming, facultatively anaerobic and short-rod shaped bacterial strain, designated as 325-5T, was isolated from marine sediment obtained from a coastal region in South Korea. Phylogenetic analysis based on the 16S rRNA gene sequence of strain 325-5T showed close similarity to Lutibacter crassostreae (97.8 %). The novel isolate was found to grow optimally at 25 °C and pH 7.0. The major fatty acids identified in the strain were iso C15:0 and iso C15:0 3OH, which supports the affiliation of strain 325-5T to the genus Lutibacter. Menaquinone (MK-6) was identified as the respiratory quinone component. The polar lipid profile was found to contain phosphatidylethanolamine and two unidentified lipids. The G+C molar content of strain 325-5T was determined to be 33.1 mol%. DNA-DNA hybridization of strain 325-5T exhibited less than 40 % relatedness to L. crassostreae KCTC 42461T. Pigment analysis showed the presence of carotenoid pigments. Based on this polyphasic analysis, we propose that strain 325-5T represents a novel species of the genus Lutibacter, for which the name Lutibacter oceani sp. nov. (type strain 325-5T = JCM 30924T = KEMB 7306-529T) is proposed.

Virgibacillus jeotgali sp. nov., isolated from Myeolchi-jeotgal, a traditional Korean high-salt-fermented anchovy.

A Gram-staining-positive, motile, endospore-forming, rod-shaped bacterium, designated NS3012T, was isolated from Myeolchi-jeotgal, a traditional Korean high-salt-fermented anchovy and was characterized using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain NS3012T belongs to the genus Virgibacillus in the family Bacillaceae of the phylum Firmicutes. The 16S rRNA gene sequence analysis showed that strain NS3012T was closely related to Virgibacillus halotolerans WS-4627T (98.1 %), Virgibacillus oceani MY11T (96.6 %) and Virgibacillus byunsanensis ISL-24T (96.5 %). The chemotaxonomic properties of strain NS3012T were consistent with those of the genus Virgibacillus: the quinone system with MK-7 as the predominant menaquinone and anteiso-C15 : 0 and anteiso C17 : 0 as the major cellular fatty acids; the cell-wall peptidoglycan type was based on meso-diaminopimelic acid. The major polar lipid was diphosphatidylglycerol. The G+C content of the genomic DNA was 36.8 mol%. On the basis of phylogenetic inference, and chemotaxonomic and other phenotypic properties, strain NS3012T is clearly differentiated from closely related species of the genus Virgibacillus and represents a novel species in this genus, for which the name Virgibacillus jeotgali sp. nov. is proposed. The type strain is NS3012T (=KEMB 9001-125T=JCM 16522T).

Noviherbaspirillum humi sp. nov., isolated from soil.

Two novel Gram-stain negative, motile, non-spore forming, facultative aerobic and short rod shaped bacterial strains, designated U15(T) and U32, were isolated from soil obtained from Ukraine. The sequence similarity of the 16S rRNA gene between strains U15(T) and U32 was found to be 99.5 %. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that new bacteria belong to the genus Noviherbaspirillum. The closest member of the genus was found to be Noviherbaspirillum malthae (97.0 %) followed by Noviherbaspirillum suwonensis (96.3 %). The novel isolates was observed to grow optimally at 30 °C and pH 7.0. The major fatty acids present in the two strains were identified as summed feature 3 (C16:1 ω7c/C16:1 ω6c), C16:0, and summed feature 8 (C18:1 ω7c/C18:1 ω6c). Ubiquinone 8 was identified as the respiratory quinone component for both the strains. The polar lipid (L) profile contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid, unidentified aminolipid and unidentified Ls, and putrescine and 2-hydroxyputrescine as major polyamines. The G+C content of the DNA for the strain U15(T) was found to be 61.2 mol%. The DNA-DNA relatedness between U15(T) and U32 and closely related species was less than 40 %. Based on the polyphasic taxonomic analysis, a new species, Noviherbaspirillum humi sp. nov., is proposed. The type strain is strain U15(T) = JCM 19873(T) = KEMB 7305-102(T).