Genome analysis of Lactococcus taiwanensis strain K_LL001 with potential cellulose degrading functions

Lactococcus taiwanensis starin K_LL001 was isolated from the gut of grasshopper (Oxya chinensis sinuosa). In this study, we presented the complete genome sequence of L. taiwanensis stain K_LL001. The genome of K_LL001 genome was composed of 1 circular chromosome without plasmids. The length of the whole genome was 2,018,259bp, guanin + cytosine (G+C) content (%) was 38.75%, with 2,021 predicted protein-coding sequences (CDS). The most abundant CAZyme class in L. taiwanensis strain K_LL001 was glycoside hydrolases (GH) class. GHs is the key enzymes involved in carbohydrate metabolism, and they catalyze the hydrolysis of glycosidic bonds in complex carbohydrates such as cellulose, hemicellulose, and starch. Moreover, L. taiwanensis strain K_LL001 has genes encoding enzymes which can catalyze the transformation of one glycoside to another. Overall, this study will contribute to a further understanding of L. taiwanensis strain K_LL001 at the genomic level and provide a theoretical basis for its future application in swine industry.

Toxicity of cadmium on dynamic human gut microbiome cultures and the protective effect of cadmium-tolerant bacteria autochthonous to the gut

Cadmium (Cd) is a heavy metal toxic to the gut microbiome. In this study, we cultivated two human gut microbiomes (A and B) in bioreactors with Cd at 0 and 20 ppm for 7 days to investigate effects of Cd on the gut microbiome and to isolate Cd-tolerant bacteria autochthonous to the gut. Cd showed profound toxicity, abolishing butyrate production, depleting microbes in microbiome B, and simplifying microbiome A to a small Cd-tolerant community after 2 d of incubation. When spiked into the Cd-sensitive microbiome B, the Cd-tolerant community from microbiome A and isolates from that community worked synergistically with microbiome B to enhance butyrate production and maintained this synergism at Cd concentrations up to 5 ppm. Bacteria isolated from this Cd-tolerant community included Enterococcus faecium, Enterobacter cloacae, Lactococcus lactis, and Lactobacillus taiwanensis species. This work demonstrates a straightforward method for identifying Cd-tolerant bacteria autochthonous to the human gut that synergize with the microbiome to protect against Cd-related loss of butyrate production.

Towards the diversification of lactococcal starter and non-starter species in mesophilic dairy culture systems

Lactococcus is one of the earliest identified fermentative bacterial genera and among its member species, the dairy-associated Lactococcus lactis and Lactococcus cremoris are undoubtedly the best studied. These two species are believed to have evolved from plant-associated lactococci and through genome decay and acquisition of plasmids, have adapted to the dairy niche. The past decade has witnessed a surge of activity in novel lactococcal species identification from insect, plant and animal sources. Currently, 22 Lactococcus species are described and in this review, we summarise the genome characteristics of and phylogenetic relationships among these species. Furthermore, we explore the role of mobile elements including plasmids and bacteriophages in the diversification of lactococcal species. The pace of identification of novel lactococcal species suggests that the number of lactococcal species is likely to continue to grow. With additional sequence data for the emerging species, it will be possible to perform pathogenicity/virulence risk evaluations and generate extensive insights into the niche adaptation strategies through which they have evolved.

Lactococcus intestinalis sp. nov., a new lactic acid bacterium isolated from intestinal contents in Alzheimer's disease mice

A gram-positive, facultatively anaerobic, and coccoid or ovoid-shaped bacterium designated M2458^T was isolated from the intestinal contents of APP^swe/PS^ΔE9 mouse model of Alzheimer's disease. With the polyphasic approach, the taxonomic position of the novel isolate was confirmed. Strain M2458^T grew well at 37 °C on YCFA agar. Strain M2458^T belongs to the family Streptococcaceae and class Bacilli, and it is closed to Lactococcus formosensis NBRC 109475^T (97.59% sequence similarity) according to its 16S rRNA gene sequence. In a comparison of two housekeeping genes, rpoA and rpoB, strain M2458^T was found to be well separated from Lactococcus formosensis NBRC 109475^T. On the basis of whole genome sequences, the DNA G+C content was 38.29 mol%. The phylogentic analysis of the whole genome showed that a different branch was clearly formed in the phylogenetic tree of strain M2458^T compared to other strains in the genus Lactococcus. A total of eight genes in strain M2458^T are involved in the 'neurodegenerative disease' pathway, which involves an annotated protein (glyceraldehyde 3-phosphate dehydrogenase) involved in Alzheimer's disease. In terms of average nucleotide identity and digital DNA-DNA hybridization, strain M2458^T was identified as a novel species of the genus Lacococcus. The major fatty acids (> 10% of the total fatty acids) were C18:1ω9c (39.68%), C16:0 (13.26%) and C18:1ω7c (11.52%). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid. As a result of its genotypic and phenotypic characteristics, strain M2458^T was considered to be a new species within the genus Lactococcus; the name Lactococcus intestinalis sp. nov. has been proposed, with type strain M2458^T (=JCM 35706 = CGMCC 1.60066).

The study of microbial diversity and volatile compounds in Tartary buckwheat sourdoughs

Microorganisms play an essential role in forming volatile compounds in traditional staple products. Tartary buckwheat, as a medicinal and food material, has high nutritional value but its development and utilization are seriously restricted due to its poor flavor. In this study, 16S rRNA and ITS rRNA sequencing were used to analyze the microbial diversity of Tartary buckwheat sourdoughs, while HS-SPME-GC/MS was used to identify volatile compounds during fermentation. The results showed that Lactococcus and Weissella were the dominant bacterial genus. Wickerhamomyces, Penicillium, and Aspergillus were the main fungal genera in the Tartary buckwheat sourdoughs. And the main volatile compounds in Tartary buckwheat sourdough were pyrazine compounds. After 12 h of fermentation, a large amount of alcohol and esters were produced, which endowed the sourdough with a good flavor. This suggests that sourdough fermentation could significantly improve the flavor of Tartary buckwheat.

Genome Characterization of Nocturne116, Novel Lactococcus lactis-Infecting Phage Isolated from Moth

While looking for novel insect-associated phages, a unique siphophage, Nocturne116, was isolated from a deceased local moth specimen along with its host, which was identified by 16S rRNA gene sequencing as a strain of Lactococcus lactis. Next-generation sequencing and the subsequent genome annotation elaborated on herein revealed that the genome of Nocturne116 is a 25,554 bp long dsDNA molecule with 10 bp long 3' cos overhangs and a GC content of 37.99%, comprising 52 predicted open reading frames. The complete nucleotide sequence of phage Nocturne116 genome is dissimilar to any of the already sequenced phages, save for a distant link with Lactococcus phage Q54. Functions for only 15/52 of Nocturne116 gene products could be reliably predicted using contemporary comparative genomics approaches, while 22 of its gene products do not yet have any homologous entries in the public biological sequence repositories. Despite the public availability of nearly 350 elucidated Lactococcus phage complete genomes as of now, Nocturne116 firmly stands out as a sole representative of novel phage genus.

Elevation of Lactococcus lactis subsp. cremoris to the species level as Lactococcus cremoris sp. nov. and transfer of Lactococcus lactis subsp. tructae to Lactococcus cremoris as Lactococcus cremoris subsp. tructae comb. nov

Currently, Lactococcus lactis contains four subspecies: L. lactis subsp. lactis, L. lactis subsp. hordniae, L. lactis subsp. cremoris and L. lactis subsp. tructae. In the study of Pérez et al., these four subspecies could be clearly divided into two groups based on recA sequence analysis: L. lactis subsp. lactis and L. lactis subsp. hordniae; L. lactis subsp. cremoris and L. lactis subsp. tructae. The two groups had a relatively low DNA-DNA hybridization value (about 60 %). In the present study, the taxonomic position of L. lactis subsp. cremoris and L. lactis subsp. tructae was re-examined based on sequence analyses of 16S rRNA, rpoB, recA and pheS genes, average nucleotide identity (ANI) values and digital DNA-DNA hybridization (dDDH) values. The result of 16S rRNA gene sequence analysis indicated that L. lactis subsp. cremoris NCDO 607^T and L. lactis subsp. tructae L105^T were phylogenetically related to the type strains of L. lactis subsp. hordniae, L. lactis subsp. lactis, Lactococcus taiwanensis, Lactococcus kimchii, Lactococcus allomyrinae, Lactococcus protaetiae, Lactococcus hircilactis, Lactococcus fujiensis and Lactococcus nasutitermitis. The 16S rRNA gene, rpoB, recA, pheS and concatenated rpoB, recA and pheS sequence similarities, ANI values, and dDDH values between the type strains of L. lactis subsp. cremoris, L. lactis subsp. tructae and phylogenetically related species were 93.5-99.4 %, 83.3-97.6 %, 80.6-92.4 %, 79.7-92.7 %, 83.5-94.3 %, 72.4-86.9 % and 21.4-32.5 %, respectively. Lower than 95-96 % ANI values and lower than 70 % dDDH values confirmed that the type strains of L. lactis subsp. cremoris and L. lactis subsp. tructae represent a novel species in the genus Lactococcus. Because L. lactis subsp. cremoris was proposed and validated before L. lactis subsp. tructae, L. lactis subsp. cremoris is elevated to the species level as Lactococcus cremoris sp. nov. and L. lactis subsp. tructae is transferred to L. cremoris as L. cremoris subsp. tructae comb. nov. The type strain of L. cremoris sp. nov. is NCDO 607^T (=ATCC 19257^T=DSM 20069^T=JCM 16167^T=LMG 6897^T=NBRC 100676^T). The type strain of L. cremoris subsp. tructae comb. nov. is L105^T (=NBRC 110453^T=DSM 21502^T=JCM 31125^T=LMG 24662^T).

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Restructured Lactococcus lactis strains with emergent properties constructed by a novel highly efficient screening system

Background

After 2.83% genome reduction in Lactococcus lactis NZ9000, a good candidate host for proteins production was obtained in our previous work. However, the gene deletion process was time consuming and laborious. Here, we proposed a convenient gene deletion method suitable for large-scale genome reduction in L. lactis NZ9000.

Results

Plasmid pNZ5417 containing a visually selectable marker P_nisZ-lacZ was constructed, which allowed more efficient and convenient screening of gene deletion mutants. Using this plasmid, two large nonessential DNA regions, L-4A and L-5A, accounting for 1.25% of the chromosome were deleted stepwise in L. lactis 9k-3. When compared with the parent strain, the mutant L. lactis 9k-5A showed better growth characteristics, transformability, carbon metabolic capacity, and amino acids biosynthesis.

Conclusions

Thus, this study provides a convenient and efficient system for large-scale genome deletion in L. lactis through application of visually selectable marker, which could be helpful for rapid genome streamlining and generation of restructured L. lactis strains that can be used as cell factories.

Symposium review: Lactococcus lactis from nondairy sources: Their genetic and metabolic diversity and potential applications in cheese

The widespread dissemination of species of the lactic acid bacteria (LAB) group in different environments testifies to their extraordinary niche adaptability. Members of the LAB are present on grass and other plant material, in dairy products, on human skin, and in the gastrointestinal and reproductive tracts. The selective pressure imparted by these specific environments is a key driver in the genomic diversity observed between strains of the same species deriving from distinct habitats. Strains that are exploited in the dairy industry for the production of fermented dairy products are often referred to as "domesticated" strains. These strains, which initially may have occupied a nondairy niche, have become specialized for growth in the milk environment. In fact, comparative genome analysis of multiple LAB species and strains has revealed a central trend in LAB evolution: the loss of ancestral genes and metabolic simplification toward adaptation to nutritionally rich environments. In contrast, "environmental" strains, or those from raw milk, plants, and animals, exhibit diverse metabolic capabilities and lifestyle characteristics compared with their domesticated counterparts. Because of the limited number of established dairy strains used in fermented food production today, demand is increasing for novel strains, with concerted efforts to mine the microbiota of natural environments for strains of technological interest. Many studies have concentrated on uncovering the genomic and metabolic potential of these organisms, facilitating comparative genome analysis of strains from diverse environments and providing insight into the natural diversity of the LAB, a group of organisms that is at the core of the dairy industry. The natural biodiversity that exists in these environments may be exploited in dairy fermentations to expand flavor profiles, to produce natural "clean label" ingredients, or to develop safer products.

Lactococcus piscium: a psychrotrophic lactic acid bacterium with bioprotective or spoilage activity in food-a review

The genus Lactococcus comprises 12 species, some known for decades and others more recently described. Lactococcus piscium, isolated in 1990 from rainbow trout, is a psychrotrophic lactic acid bacterium, probably disregarded because most of the strains are unable to grow at 30°C. During the last 10 years, this species has been isolated from a large variety of food: meat, seafood and vegetables, mostly packed under vacuum (VP) or modified atmosphere (MAP) and stored at chilled temperature. Recently, culture-independent techniques used for characterization of microbial ecosystems have highlighted the importance of Lc. piscium in food. Its role in food spoilage varies according to the strain and the food matrix. However, most studies have indicated that Lc. piscium spoils meat, whereas it does not degrade the sensory properties of seafood. Lactococcus piscium strains have a large antimicrobial spectrum, including Gram-positive and negative bacteria. In various seafoods, some strains have a protective effect against spoilage and can extend the sensory shelf-life of the products. They can also inhibit the growth of Listeria monocytogenes, by a cell-to-cell contact-dependent. This article reviews the physiological and genomic characteristics of Lc. piscium and discusses its spoilage or protective activities in food.

Lactococcus hircilactis sp. nov. and Lactococcus laudensis sp. nov., isolated from milk

Two strains of lactic acid bacteria, designated 117(T) and 4195(T), were isolated from goat milk in Valtellina, Italy and from cow milk in Valle Trompia, Italy, respectively, and characterized taxonomically by a polyphasic approach. The strains were Gram-stain-positive, coccoid, non-spore-forming and catalase-negative bacteria. Morphological, physiological and phylogenetic data indicated that these isolates belonged to the genus Lactococcus. Strain 117(T) was closely related to Lactococcus fujiensis, Lactococcus lactis subsp. lactis, L. lactis subsp. cremoris, L. lactis subsp. hordniae, L. lactis subsp. tructae and Lactococcus taiwanensis, showing 93-94% and 82-89% 16S rRNA and rpoB gene sequence similarities, respectively. Strain 4195(T) was closely related to Lactococcus chungangensis, Lactococcus raffinolactis, Lactococcus plantarum and Lactococcus piscium, showing 92-98% and 86-99% 16S rRNA and rpoB gene sequence similarities, respectively. Based on this evidence and the data obtained in the present study, the milk isolates represent two novel species of the genus Lactococcus, for which the names Lactococcushircilactis sp. nov., and Lactococcuslaudensis sp. nov. are proposed. The respective type strains are 117(T) ( = LMG 28352(T) = DSM 28960(T)) and 4195(T )( = LMG 28353(T) = DSM 28961(T)).

Lactobacillus formosensis sp. nov., a lactic acid bacterium isolated from fermented soybean meal

A Gram-reaction-positive, catalase-negative, facultatively anaerobic, rod-shaped lactic acid bacterium, designated strain S215(T), was isolated from fermented soybean meal. The organism produced d-lactic acid from glucose without gas formation. 16S rRNA gene sequencing results showed that strain S215(T) had 98.74-99.60 % sequence similarity to the type strains of three species of the genus Lactobacillus (Lactobacillus farciminis BCRC 14043(T), Lactobacillus futsaii BCRC 80278(T) and Lactobacillus crustorum JCM 15951(T)). A comparison of two housekeeping genes, rpoA and pheS, revealed that strain S215(T) was well separated from the reference strains of species of the genus Lactobacillus. DNA-DNA hybridization results indicated that strain S215(T) had DNA related to the three type strains of species of the genus Lactobacillus (33-66 % relatedness). The DNA G+C content of strain S215(T) was 36.2 mol%. The cell walls contained peptidoglycan of the d-meso-diaminopimelic acid type and the major fatty acids were C18 : 1ω9c, C16 : 0 and C19 : 0 cyclo ω10c/C19 : 1ω6c. Phenotypic and genotypic features demonstrated that the isolate represents a novel species of the genus Lactobacillus, for which the name Lactobacillus formosensis sp. nov. is proposed. The type strain is S215(T) ( = NBRC 109509(T) = BCRC 80582(T)).

From field to fermentation: the origins of Lactococcus lactis and its domestication to the dairy environment

Lactococcus lactis is an organism of substantial economic importance, used extensively in the production of fermented foods and widely held to have evolved from plant strains. The domestication of this organism to the milk environment is associated with genome reduction and gene decay, and the acquisition of specific genes involved in protein and lactose utilisation by horizontal gene transfer. In recent years, numerous studies have focused on uncovering the physiology and molecular biology of lactococcal strains from the wider environment for exploitation in the dairy industry. This in turn has facilitated comparative genome analysis of lactococci from different environments and provided insight into the natural phenotypic and genetic diversity of L. lactis. This diversity may be exploited in dairy fermentations to develop products with improved quality and sensory attributes. In this review, we discuss the classification of L. lactis and the problems that arise with phenotype/genotype designation. We also discuss the adaptation of non-dairy lactococci to milk, the traits associated with this adaptation and the potential application of non-dairy lactococci to dairy fermentations.

Lactococcus formosensis sp. nov., a lactic acid bacterium isolated from yan-tsai-shin (fermented broccoli stems)

A coccal-shaped organism, designated 516T, was isolated from yan-tsai-shin (fermented broccoli stems), a traditional fermented food in Taiwan. 16S rRNA gene sequencing results showed that strain 516T had 98.9 % sequence similarity to that of the type strain Lactococcus garvieae NBRC 100934T. Comparison of three housekeeping genes, rpoA, rpoB and pheS, revealed that strain 516T was well separated from Lactococcus garvieae NBRC 100934T. DNA–DNA hybridization studies indicated that strain 516T had low DNA relatedness with Lactococcus garvieae NBRC 100934T (46.1 %). The DNA G+C content of strain 516T was 38.1 mol% and the major fatty acids were C16 : 0 (22.7 %), C19 : 0 cyclo ω8c (17.9 %) and summed feature 7 (29.0 %). Based on the evidence, strain 516T represents a novel species of the genus Lactococcus , for which the name Lactococcus formosensis sp. nov. is proposed. The type strain is 516T ( = NBRC 109475T = BCRC 80576T).