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Lactobacillus Genome

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https://www.readbyqxmd.com/read/30094916/how-lactobacillus-plantarum-shapes-its-transcriptome-in-response-to-contrasting-habitats
#1
Pasquale Filannino, Maria De Angelis, Raffaella Di Cagno, Giorgia Gozzi, Ylenia Riciputi, Marco Gobbetti
Triplets of Lactobacullus plantarum strains were isolated from nine contrasting habitats. Without any passage through other culture media, isolation and cultivation were on model media that strictly reproduced the chemical and physical conditions and stressors of the habitats of origin. Here, we demonstrated how L. plantarum regulates and shapes its transcriptome in response to contrasting habitats. Firstly, multivariate clustering analysis of transcriptional data (RNA-Seq), complemented with metabolomics and phenomics, grouped the strains according to the habitats of origin...
August 9, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/30086200/lactobacillus-rhamnosus-lrb-mediated-inhibition-of-oral-streptococci
#2
Saswati Biswas, Lance Turner, Indranil Biswas
Lactobacillus rhamnosus is a lactic acid bacterium with a diverse ecological habitat. We recently isolated a L. rhamnosus strain (LRB) from a healthy baby-tooth that had naturally fallen out. We determined the whole genome sequence of LRB and found that the isolate is closely genetically related to an intestinal isolate, L. rhamnosus GG (ATCC 53103). However, the LRB genome had lost about a 75-kb segment and undergone a genomic rearrangement. We assessed LRB's capacity to survive in the gut environment, at least temporarily...
August 7, 2018: Molecular Oral Microbiology
https://www.readbyqxmd.com/read/30078067/crispr-cas-system-history-and-prospects-as-a-genome-editing-tool-in-microorganisms
#3
REVIEW
Muhammad R Javed, Maria Sadaf, Temoor Ahmed, Amna Jamil, Marium Nawaz, Hira Abbas, Anam Ijaz
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR or more precisely CRISPR-Cas) system has proven to be a highly efficient and simple tool for achieving site-specific genome modifications in comparison to Zinc Finger Nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs). The discovery of bacterial defense system that uses RNA-guided DNA cleaving enzymes for producing double-strand breaks along CRISPR has provided an exciting alternative to ZFNs and TALENs for gene editing & regulation, as the CRISPR-associated (Cas) proteins remain the same for different gene targets and only the short sequence of the guide RNA needs to be changed to redirect the site-specific cleavage...
August 4, 2018: Current Microbiology
https://www.readbyqxmd.com/read/30061572/discovery-and-control-of-culturable-and-viable-but-non-culturable-cells-of-a-distinctive-lactobacillus-harbinensis-strain-from-spoiled-beer
#4
Junyan Liu, Yang Deng, Lin Li, Bing Li, Yanyan Li, Shishui Zhou, Mark E Shirtliff, Zhenbo Xu, Brian M Peters
Occasional beer spoilage incidents caused by false-negative isolation of lactic acid bacteria (LAB) in the viable but non-culturable (VBNC) state, result in significant profit loss and pose a major concern in the brewing industry. In this study, both culturable and VBNC cells of an individual Lactobacillus harbinensis strain BM-LH14723 were identified in one spoiled beer sample by genome sequencing, with the induction and resuscitation of VBNC state for this strain further investigated. Formation of the VBNC state was triggered by low-temperature storage in beer (175 ± 1...
July 30, 2018: Scientific Reports
https://www.readbyqxmd.com/read/30057579/efficient-exploitation-of-multiple-novel-bacteriocins-by-combination-of-complete-genome-and-peptidome
#5
Lanhua Yi, Lingli Luo, Xin Lü
Backgroud: The growing emergence of antibiotic-resistant pathogens including the most dangerous superbugs requires quick discovery of novel antibiotics/biopreservatives for human health and food safety. Bacteriocins, a subgroup of antimicrobial peptides, have been considered as promising alternatives to antibiotics. Abundant novel bacteriocins are stored in genome sequences of lactic acid bacteria. However, discovery of novel bacteriocins still mainly relies on dubious traditional purification with low efficiency...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/30038603/a-novel-plp-dependent-alanine-serine-racemase-from-the-hyperthermophilic-archaeon-pyrococcus-horikoshii-ot-3
#6
Ryushi Kawakami, Tatsuya Ohshida, Haruhiko Sakuraba, Toshihisa Ohshima
We recently identified and characterized a novel broad substrate specificity amino acid racemase (BAR) from the hyperthermophilic archaeon Pyrococcus horikoshii OT-3. Three genes, PH0782 , PH1423 , and PH1501 , encoding homologs exhibiting about 45% sequence identity with BAR were present in the P. horikoshii genome. In this study, we detected pyridoxal 5'-phosphate (PLP)-dependent amino acid racemase activity in the protein encoded by PH0782 . The enzyme showed activity toward Ala, Ser, Thr, and Val, but the catalytic efficiency with Thr or Val was much lower than with Ala or Ser...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/30033529/immune-synergistic-oligodeoxynucleotide-from-lactobacillus-rhamnosus-gg-enhances-the-immune-response-upon-co-stimulation-by-bacterial-and-fungal-cell-wall-components
#7
Shireen Nigar, Yoshinari Yamamoto, Takuma Okajima, Takashi Sato, Tasuku Ogita, Takeshi Shimosato
Bacterial genomic DNA has recently been shown to elicit a highly evolved immune defense. This response can be selectively triggered for a wide range of therapeutic applications, including use as a vaccine adjuvant to immunotherapies for allergy, cancer, and infectious diseases. Previously, we identified a low-concentration immune synergistic oligodeoxynucleotide (iSN-ODN, named iSN34) from Lactobacillus rhamnosus GG that has immunosynergistic activity upon costimulation of target cells with ligands of Toll-like receptor 9 (TLR9)...
July 23, 2018: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/30031987/comparative-genomics-of-lactobacillus-curvatus-enables-prediction-of-traits-relating-to-adaptation-and-strategies-of-assertiveness-in-sausage-fermentation
#8
Lara Eisenbach, Dorothee Janßen, Matthias A Ehrmann, Rudi F Vogel
Lactobacillus (L.) curvatus reaches high numbers in a variety of habitats, which suggests a high (genomic) diversity within this species. Empirically selected strains are used as starter cultures in sausage fermentation. Determinants for the assertiveness of a strain in this environment are assumed to be multifactorial. We used comparative genomics and in silico proteomics of 10 L. curvatus strains, which were representative of its genetic and physiological biodiversity, to possibly derive genetic determinants for strain or group specific assertiveness in sausage fermentation...
July 4, 2018: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/30026739/evaluation-of-the-potential-of-lactobacillus-paracasei-adjuncts-for-flavor-compounds-development-and-diversification-in-short-aged-cheddar-cheese
#9
Ewelina Stefanovic, Kieran N Kilcawley, Clara Roces, Mary C Rea, Maurice O'Sullivan, Jeremiah J Sheehan, Olivia McAuliffe
The non-starter microbiota of Cheddar cheese mostly comprises mesophilic lactobacilli, such as Lactobacillus casei, Lactobacillus paracasei, Lactobacillus rhamnosus , and Lactobacillus plantarum . These bacteria are recognized for their potential to improve Cheddar cheese flavor when used as adjunct cultures. In this study, three strains of L. paracasei (DPC2071, DPC4206, and DPC4536) were evaluated for their contribution to the enhancement and diversification of flavor in short-aged Cheddar cheese. The strains were selected based on their previously determined genomic diversity, variability in proteolytic enzyme activities and metabolic capability in cheese model systems...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/30024364/deletion-based-escape-of-crispr-cas9-targeting-in-lactobacillus-gasseri
#10
Emily A Stout, Rosemary Sanozky-Dawes, Yong Jun Goh, Alexandra B Crawley, Todd R Klaenhammer, Rodolphe Barrangou
Lactobacillus gasseri is a human commensal which carries CRISPR-Cas, an adaptive immune system that protects the cell from invasive mobile genetic elements (MGEs). However, MGEs occasionally escape CRISPR targeting due to DNA mutations that occur in sequences involved in CRISPR interference. To better understand CRISPR escape processes, a plasmid interference assay was used to screen for mutants that escape CRISPR-Cas targeting. Plasmids containing a target sequence and a protospacer adjacent motif (PAM) were transformed for targeting by the native CRISPR-Cas system...
July 19, 2018: Microbiology
https://www.readbyqxmd.com/read/30013519/reincarnation-of-bacteriocins-from-the-lactobacillus-pangenomic-graveyard
#11
Fergus W J Collins, Beatriz Mesa-Pereira, Paula M O'Connor, Mary C Rea, Colin Hill, R Paul Ross
Bacteria commonly produce narrow spectrum bacteriocins as a means of inhibiting closely related species competing for similar resources in an environment. The increasing availability of genomic data means that it is becoming easier to identify bacteriocins encoded within genomes. Often, however, the presence of bacteriocin genes in a strain does not always translate into biological antimicrobial activity. For example, when analysing the Lactobacillus pangenome we identified strains encoding ten pediocin-like bacteriocin structural genes which failed to display inhibitory activity...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/30013162/the-evolution-of-ecological-facilitation-within-mixed-species-biofilms-in-the-mouse-gastrointestinal-tract
#12
Xiaoxi B Lin, Tuo Wang, Paul Stothard, Jukka Corander, Jun Wang, John F Baines, Sarah C L Knowles, Laima Baltrūnaitė, Guergana Tasseva, Robert Schmaltz, Stephanie Tollenaar, Liz A Cody, Theodore Grenier, Wei Wu, Amanda E Ramer-Tait, Jens Walter
The eco-evolutionary interactions among members of the vertebrate gut microbiota that ultimately result in host-specific communities are poorly understood. Here we show that Lactobacillus reuteri coexists with  species that belong to the Lactobacillus johnsonii cluster (L. johnsonii, L. gasseri, and L taiwanensis) in a taxonomically wide range of rodents, suggesting cohabitation over evolutionary times. The two dominant Lactobacillus species found in wild mice establish a commensalistic relationship in gastric biofilms when introduced together into germ-free mice in which L...
July 16, 2018: ISME Journal
https://www.readbyqxmd.com/read/30010525/lactobacillus-terrae-sp-nov-a-novel-species-isolated-from-soil-samples-in-the-republic-of-korea
#13
Hyun-Joong Kim, Hye Jin Lee, Bora Lim, Eiseul Kim, Hae-Yeong Kim, Minhwan Suh, Moonsuk Hur
A novel strain, designated NIBRBAC000499792T , was isolated from a soil sample collected at Jukgye, Dongnam, Cheonan, Republic of Korea. Cells were Gram-positive, non-motile, non-spore-forming, rod-shaped, oxidase-negative and catalase-negative. Colonies grown on de Man, Rogosa and Sharpe agar were white, circular, raised and entire. Analysis of the 16S rRNA gene sequence analysis revealed that strain NIBRBAC000499792T belongs to the genus Lactobacillus (family Lactobacillaceae) and is most closely related to Lactobacillus nodensis DSM 19682T (96...
July 16, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/30006634/probiotics-in-human-gut-microbiota-can-degrade-host-glycosaminoglycans
#14
Keigo Kawai, Reiko Kamochi, Sayoko Oiki, Kousaku Murata, Wataru Hashimoto
Glycosaminoglycans (GAGs) (e.g. heparin, chondroitin sulfate, and hyaluronan) show various significant physiological functions as a major component of extracellular matrix in animals. Some bacteria target GAGs for adhesion and/or infection to host cells, although no probiotics have been known to degrade GAGs. Here, we show GAG degradation by probiotics from human gut microbiota and their adhesion to human intestinal cells through a GAG. GAG-degrading bacteria were isolated from human faeces and identified as Enterococcus faecium, and some typical probiotics such as Lactobacillus casei, Lactobacillus rhamnosus and Enterococcus faecalis were also found to degrade heparin...
July 13, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29976610/complete-genome-sequence-of-lactobacillus-paracasei-eg9-a-strain-accelerating-free-amino-acid-production-during-cheese-ripening
#15
Yui Asahina, Akino Shiroma, Kazuma Nakano, Hinako Tamotsu, Noriko Ashimine, Misuzu Shinzato, Maiko Minami, Makiko Shimoji, Tetsuhiro Nakanishi, Shun Ohki, Kuniko Teruya, Kazuhito Satou, Miho Kobayashi, Tatsuro Hagi, Naoko Moriya, Chise Suzuki, Atsushi Tajima, Masaru Nomura, Takashi Hirano
Lactobacillus paracasei EG9 is a strain isolated from well-ripened cheese and accelerates free amino acid production during cheese ripening. Its complete genome sequence was determined using the PacBio RS II platform, revealing a single circular chromosome of 2,927,257 bp, a G+C content of 46.59%, and three plasmids.
July 5, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29975997/pangenomics-of-lactobacillus-plantarum-revealed-group-specific-genomic-profiles-without-habitat-association
#16
Sukjung Choi, Gwi-Deuk Jin, Jongbin Park, Inhwan You, Eun Bae Kim
Lactobacillus plantarum is a lactic acid bacterium that promotes animal intestinal health as a probiotic and is found in a wide variety of habitats. Here, we investigated the genomic features of different clusters of L. plantarum strains via pan-genomic analysis. We compared the genomes of 108 L. plantarum strains that were available from the NCBI GenBank database. These genomes were 2.9-3.7 Mbp in size and 44-45% in G+C content. A total of 8,847 orthologs were collected, and 1,709 genes were identified to be shared as core genes by all the strains analyzed...
June 8, 2018: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29966337/in-vitro-transcriptome-response-to-a-mixture-of-lactobacilli-strains-in-intestinal-porcine-epithelial-cell-line
#17
Ionelia Taranu, Daniela Eliza Marin, Cornelia Braicu, Gina Cecilia Pistol, Ionut Sorescu, Lavinia Laura Pruteanu, Ioana Berindan Neagoe, Dan Cristian Vodnar
BACKGROUND: Food and feed supplements containing microorganisms with probiotic potential are of increasing interest due to their healthy promoting effect on human and animals. Their mechanism of action is still unknown. Using a microarray approach, the aim of this study was to investigate the differences in genome-wide gene expression induced by a mixture of three Lactobacillus strains ( L. rhamnosus , L. plantarum , and L. paracasei ) in intestinal porcine epithelial cells (IPEC-1) and to identify the genes and pathways involved in intestinal barrier functions...
June 30, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29963028/comparative-genomic-and-phenotypic-analysis-of-the-vaginal-probiotic-lactobacillus-rhamnosus-gr-1
#18
Mariya I Petrova, Jean M Macklaim, Sander Wuyts, Tine Verhoeven, Jos Vanderleyden, Gregory B Gloor, Sarah Lebeer, Gregor Reid
Lactobacillus represents a versatile bacterial genus, which can adapt to a wide variety of ecological niches, including human body sites such as the intestinal and urogenital tract. In this study, the complete genome sequence of the vaginal probiotic Lactobacillus rhamnosus GR-1 was determined and compared to other L. rhamnosus strains at genomic and phenotypic level. The strain GR-1 was originally isolated from a female urethra, and was assessed with L. rhamnosus GG from a feces sample of a healthy male, and L...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29954914/fifty-six-draft-genome-sequences-of-10-lactobacillus-species-from-22-commercial-dietary-supplements
#19
Jayanthi Gangiredla, Tammy J Barnaba, Mark K Mammel, David W Lacher, Christopher A Elkins, Keith A Lampel, Chris A Whitehouse, Carmen Tartera
Here, we present the genome sequences of 56 isolates of 10 species of the genus Lactobacillus that are considered beneficial components of the gut microbiota. The isolates examined were found in commercially available dietary supplements in the U.S. market.
June 28, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29954911/genome-sequences-of-five-lactobacillus-sp-isolates-from-traditional-turkish-sourdough
#20
Enes Dertli, Christopher D Skory, Ömer Şimşek
A high level of variation in microflora can be observed in profiles of lactic acid bacteria (LAB) from sourdoughs. Here, we present draft genome sequences of Lactobacillus reuteri E81, L. reuteri LR5A, L. rhamnosus LR2, L. plantarum PFC-311, and the novel Lactobacillus sp. strain PFC-70, isolated from traditional Turkish backslopped wheat sourdoughs.
June 28, 2018: Genome Announcements
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