scholarly journals Bifidobacterium animalis subsp. lactis ATCC 27673 Is a Genomically Unique Strain within Its Conserved Subspecies

2013 ◽  
Vol 79 (22) ◽  
pp. 6903-6910 ◽  
Author(s):  
Joseph R. Loquasto ◽  
Rodolphe Barrangou ◽  
Edward G. Dudley ◽  
Buffy Stahl ◽  
Chun Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Open Reading Frames ◽  
Genomic Islands ◽  
Type I ◽  
Content Type ◽  
Bifidobacterium Animalis ◽  
Health Promoting ◽  
Short Palindromic Repeat ◽  
Unique Strain ◽  
Fermented Dairy

ABSTRACTMany strains ofBifidobacterium animalissubsp.lactisare considered health-promoting probiotic microorganisms and are commonly formulated into fermented dairy foods. Analyses of previously sequenced genomes ofB. animalissubsp.lactishave revealed little genetic diversity, suggesting that it is a monomorphic subspecies. However, during a multilocus sequence typing survey ofBifidobacterium, it was revealed thatB. animalissubsp.lactisATCC 27673 gave a profile distinct from that of the other strains of the subspecies. As part of an ongoing study designed to understand the genetic diversity of this subspecies, the genome of this strain was sequenced and compared to other sequenced genomes ofB. animalissubsp.lactisandB. animalissubsp.animalis. The complete genome of ATCC 27673 was 1,963,012 bp, contained 1,616 genes and 4 rRNA operons, and had a G+C content of 61.55%. Comparative analyses revealed that the genome of ATCC 27673 contained six distinct genomic islands encoding 83 open reading frames not found in other strains of the same subspecies. In four islands, either phage or mobile genetic elements were identified. In island 6, a novel clustered regularly interspaced short palindromic repeat (CRISPR) locus which contained 81 unique spacers was identified. This type I-E CRISPR-cassystem differs from the type I-C systems previously identified in this subspecies, representing the first identification of a different system inB. animalissubsp.lactis. This study revealed that ATCC 27673 is a strain ofB. animalissubsp.lactiswith novel genetic content and suggests that the lack of genetic variability observed is likely due to the repeated sequencing of a limited number of widely distributed commercial strains.

scholarly journals Complete Genome Sequence of Bifidobacterium animalis subsp. lactis BLC1

2011 ◽  
Vol 193 (22) ◽  
pp. 6387-6388 ◽  
Author(s):  
Francesca Bottacini ◽  
Fabio Dal Bello ◽  
Francesca Turroni ◽  
Christian Milani ◽  
Sabrina Duranti ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Functional Foods ◽  
Probiotic Bacterium ◽  
Content Type ◽  
Phylogenetic Relatedness ◽  
Food Industries ◽  
Bifidobacterium Animalis ◽  
Health Promoting

Bifidobacterium animalis subsp. lactis BLC1 is a probiotic bacterium that is widely exploited by food industries as the active ingredient of various functional foods. Here we report the complete genome sequence of B. animalis subsp. lactis BLC1, which is expected to provide insights into the biology of this health-promoting microorganism and improve our understanding of its phylogenetic relatedness with other members of the B. animalis subsp. lactis taxon.

scholarly journals Evolution of the U.S. Biological Select AgentRathayibacter toxicus

mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Edward W. Davis ◽  
Javier F. Tabima ◽  
Alexandra J. Weisberg ◽  
Lucas Dantas Lopes ◽  
Michele S. Wiseman ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Adaptive Immune System ◽  
The United States ◽  
Genomic Diversity ◽  
Data Set ◽  
Important Species ◽  
Content Type ◽  
Low Genetic Diversity ◽  
History Of ◽  
Short Palindromic Repeat

ABSTRACTRathayibacter toxicusis a species of Gram-positive, corynetoxin-producing bacteria that causes annual ryegrass toxicity, a disease often fatal to grazing animals. A phylogenomic approach was employed to model the evolution ofR. toxicusto explain the low genetic diversity observed among isolates collected during a 30-year period of sampling in three regions of Australia, gain insight into the taxonomy ofRathayibacter, and provide a framework for studying these bacteria. Analyses of a data set of more than 100 sequencedRathayibactergenomes indicated thatRathayibacterforms nine species-level groups.R. toxicusis the most genetically distant, and evidence suggested that this species experienced a dramatic event in its evolution. Its genome is significantly reduced in size but is colinear to those of sister species. Moreover,R. toxicushas low intergroup genomic diversity and almost no intragroup genomic diversity between ecologically separated isolates.R. toxicusis the only species of the genus that encodes a clustered regularly interspaced short palindromic repeat (CRISPR) locus and that is known to host a bacteriophage parasite. The spacers, which represent a chronological history of infections, were characterized for information on past events. We propose a three-stage process that emphasizes the importance of the bacteriophage and CRISPR in the genome reduction and low genetic diversity of theR. toxicusspecies.IMPORTANCERathayibacter toxicusis a toxin-producing species found in Australia and is often fatal to grazing animals. The threat of introduction of the species into the United States led to its inclusion in the Federal Select Agent Program, which makesR. toxicusa highly regulated species. This work provides novel insights into the evolution ofR. toxicus.R. toxicusis the only species in the genus to have acquired a CRISPR adaptive immune system to protect against bacteriophages. Results suggest that coexistence with the bacteriophage NCPPB3778 led to the massive shrinkage of theR. toxicusgenome, species divergence, and the maintenance of low genetic diversity in extant bacterial groups. This work contributes to an understanding of the evolution and ecology of an agriculturally important species of bacteria.

scholarly journals Requirements for Pseudomonas aeruginosa Type I-F CRISPR-Cas Adaptation Determined Using a Biofilm Enrichment Assay

2016 ◽  
Vol 198 (22) ◽  
pp. 3080-3090 ◽  
Author(s):  
Gary E. Heussler ◽  
Jon L. Miller ◽  
Courtney E. Price ◽  
Alan J. Collins ◽  
George A. O'Toole
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Acquired Immunity ◽  
Type I ◽  
Lytic Bacteriophage ◽  
Content Type ◽  
Plasmid Loss ◽  
Short Palindromic Repeat ◽  
Adaptive Immune Systems ◽  
Specific Sequences ◽  
F System

ABSTRACTCRISPR (clustered regularly interspaced short palindromic repeat)-Cas (CRISPR-associated protein) systems are diverse and found in many archaea and bacteria. These systems have mainly been characterized as adaptive immune systems able to protect against invading mobile genetic elements, including viruses. The first step in this protection is acquisition of spacer sequences from the invader DNA and incorporation of those sequences into the CRISPR array, termed CRISPR adaptation. Progress in understanding the mechanisms and requirements of CRISPR adaptation has largely been accomplished using overexpression ofcasgenes or plasmid loss assays; little work has focused on endogenous CRISPR-acquired immunity from viral predation. Here, we developed a new biofilm-based assay system to enrich forPseudomonas aeruginosastrains with new spacer acquisition. We used this assay to demonstrate thatP. aeruginosarapidly acquires spacers protective against DMS3vir, an engineered lytic variant of the Mu-like bacteriophage DMS3, through primed CRISPR adaptation from spacers present in the native CRISPR2 array. We found that for theP. aeruginosatype I-F system, thecas1gene is required for CRISPR adaptation,recGcontributes to (but is not required for) primed CRISPR adaptation,recDis dispensable for primed CRISPR adaptation, and finally, the ability of a putative priming spacer to prime can vary considerably depending on the specific sequences of the spacer.IMPORTANCEOur understanding of CRISPR adaptation has expanded largely through experiments in type I CRISPR systems using plasmid loss assays, mutants ofEscherichia coli, orcas1-cas2overexpression systems, but there has been little focus on studying the adaptation of endogenous systems protecting against a lytic bacteriophage. Here we describe a biofilm system that allowsP. aeruginosato rapidly gain spacers protective against a lytic bacteriophage. This approach has allowed us to probe the requirements for CRISPR adaptation in the endogenous type I-F system ofP. aeruginosa. Our data suggest that CRISPR-acquired immunity in a biofilm may be one reason that manyP. aeruginosastrains maintain a CRISPR-Cas system.

scholarly journals Infection of Mice by Salmonella enterica Serovar Enteritidis Involves Additional Genes That Are Absent in the Genome of Serovar Typhimurium

2011 ◽  
Vol 80 (2) ◽  
pp. 839-849 ◽  
Author(s):  
Cecilia A. Silva ◽  
Carlos J. Blondel ◽  
Carolina P. Quezada ◽  
Steffen Porwollik ◽  
Helene L. Andrews-Polymenis ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Phage Type ◽  
Pathogenicity Island ◽  
Genomic Islands ◽  
Enteric Infection ◽  
Type I ◽  
Modification System ◽  
Content Type

ABSTRACTSalmonella entericaserovar Enteritidis causes a systemic, typhoid-like infection in newly hatched poultry and mice. In the present study, a library of 54,000 transposon mutants ofS.Enteritidis phage type 4 (PT4) strain P125109 was screened for mutants deficient in thein vivocolonization of the BALB/c mouse model using a microarray-based negative-selection screening. Mutants in genes known to contribute to systemic infection (e.g.,Salmonellapathogenicity island 2 [SPI-2],aro,rfa,rfb,phoP, andphoQ) and enteric infection (e.g., SPI-1 and SPI-5) in this and otherSalmonellaserovars displayed colonization defects in our assay. In addition, a strong attenuation was observed for mutants in genes and genomic islands that are not present inS.Typhimurium or in most otherSalmonellaserovars. These genes include a type I restriction/modification system (SEN4290toSEN4292), thepegfimbrial operon (SEN2144AtoSEN2145B), a putative pathogenicity island (SEN1970 to SEN1999), and a type VI secretion system remnantSEN1001, encoding a hypothetical protein containing a lysin motif (LysM) domain associated with peptidoglycan binding. Proliferation defects for mutants in these individual genes and in exemplar genes for each of these clusters were confirmed in competitive infections with wild-typeS.Enteritidis. A ΔSEN1001mutant was defective for survival within RAW264.7 murine macrophagesin vitro. Complementation assays directly linked theSEN1001gene to phenotypes observedin vivoandin vitro. The genes identified here may perform novel virulence functions not characterized in previousSalmonellamodels.

scholarly journals Matrix Effects on the Delivery Efficacy of Bifidobacterium animalis subsp. lactis BB-12 on Fecal Microbiota, Gut Transit Time, and Short-Chain Fatty Acids in Healthy Young Adults

mSphere ◽  
2021 ◽  
Author(s):  
Zhaoyong Ba ◽  
Yujin Lee ◽  
Huicui Meng ◽  
Penny M. Kris-Etherton ◽  
Connie J. Rogers ◽  
...  
Keyword(s):  
Dairy Products ◽  
Matrix Effects ◽  
Probiotic Strain ◽  
Short Chain Fatty Acids ◽  
Fecal Microbiota ◽  
Gut Health ◽  
Content Type ◽  
Bifidobacterium Animalis ◽  
Fermented Dairy Products ◽  
Fermented Dairy

Bifidobacterium animalis subsp. lactis BB-12 is a probiotic strain that has been used worldwide since 1985. It has commonly been delivered in fermented dairy products for perceived benefits associated with gut health and enhanced immune function.

scholarly journals Genetic Diversity and Pathogenic Potential of Attaching and Effacing Escherichia coli O26:H11 Strains Recovered from Bovine Feces in the United States

2015 ◽  
Vol 81 (11) ◽  
pp. 3671-3678 ◽  
Author(s):  
Sarah A. Ison ◽  
Sabine Delannoy ◽  
Marie Bugarel ◽  
Kendra K. Nightingale ◽  
Hattie E. Webb ◽  
...  
Keyword(s):  
United States ◽  
Escherichia Coli ◽  
Genetic Diversity ◽  
The United States ◽  
Pathogenic Potential ◽  
Content Type ◽  
Genomic Plasticity ◽  
E Coli ◽  
Short Palindromic Repeat ◽  
Bovine Feces

ABSTRACTEscherichia coliO26 has been identified as the most common non-O157 Shiga toxin-producingE. coli(STEC) serogroup to cause human illnesses in the United States and has been implicated in outbreaks around the world.E. colihas high genomic plasticity, which facilitates the loss or acquisition of virulence genes. Attaching and effacingE. coli(AEEC) O26 strains have frequently been isolated from bovine feces, and there is a need to better characterize the relatedness of these strains to defined molecular pathotypes and to describe the extent of their genetic diversity. High-throughput real-time PCR was used to screen 178E. coliO26 isolates from a single U.S. cattle feedlot, collected from May to July 2011, for the presence or absence of 25 O26 serogroup-specific and virulence-associated markers. The selected markers were capable of distinguishing these strains into molecularly defined groups (yielding 18 unique marker combinations). Analysis of the clustered regularly interspaced short palindromic repeat 1 (CRISPR1) and CRISPR2a loci further discriminated isolates into 24 CRISPR types. The combination of molecular markers and CRISPR typing provided 20.8% diversity. The recent CRISPR PCR target SP_O26-E, which was previously identified only instx2-positive O26:H11 human clinical strains, was identified in 96.4% (161/167 [95% confidence interval, 99.2 to 93.6%]) of thestx-negative AEEC O26:H11 bovine fecal strains. This supports that thesestx-negative strains may have previously contained a prophage carryingstxor could acquire this prophage, thus possibly giving them the potential to become pathogenic to humans. These results show that investigation of specific genetic markers may further elucidate our understanding of the genetic diversity of AEEC O26 strains in bovine feces.

scholarly journals Characterization of the Genome of the Dairy Lactobacillus helveticus Bacteriophage ΦAQ113

2013 ◽  
Vol 79 (15) ◽  
pp. 4712-4718 ◽  
Author(s):  
Miriam Zago ◽  
Erika Scaltriti ◽  
Lia Rossetti ◽  
Alessandro Guffanti ◽  
Angelarita Armiento ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Consensus Sequence ◽  
Genome Structure ◽  
Lactobacillus Helveticus ◽  
Open Reading Frames ◽  
Content Type ◽  
Double Stranded Dna ◽  
A Genome ◽  
Health Promoting ◽  
Contractile Tail

ABSTRACTThe complete genomic sequence of the dairyLactobacillus helveticusbacteriophage ΦAQ113 was determined. Phage ΦAQ113 is aMyoviridaebacteriophage with an isometric capsid and a contractile tail. The final assembled consensus sequence revealed a linear, circularly permuted, double-stranded DNA genome with a size of 36,566 bp and a G+C content of 37%. Fifty-six open reading frames (ORFs) were predicted, and a putative function was assigned to approximately 90% of them. The ΦAQ113 genome shows functionally related genes clustered together in a genome structure composed of modules for DNA replication/regulation, DNA packaging, head and tail morphogenesis, cell lysis, and lysogeny. The identification of genes involved in the establishment of lysogeny indicates that it may have originated as a temperate phage, even if it was isolated from natural cheese whey starters as a virulent phage, because it is able to propagate in a sensitive host strain. Additionally, we discovered that the ΦAQ113 phage genome is closely related toLactobacillus gasseriphage KC5a andLactobacillus johnsoniiphage Lj771 genomes. The phylogenetic similarities betweenL. helveticusphage ΦAQ113 and two phages that belong to gut species confirm a possible common ancestral origin and support the increasing consideration ofL. helveticusas a health-promoting organism.

scholarly journals Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) RNAs in the Porphyromonas gingivalis CRISPR-Cas I-C System

2017 ◽  
Vol 199 (23) ◽  
Author(s):  
Michal Burmistrz ◽  
Jose Ignacio Rodriguez Martinez ◽  
Daniel Krochmal ◽  
Dominika Staniec ◽  
Krzysztof Pyrc
Keyword(s):  
Rheumatoid Arthritis ◽  
Cardiovascular Disease ◽  
Porphyromonas Gingivalis ◽  
Aspiration Pneumonia ◽  
Repeat Sequence ◽  
Type I ◽  
Content Type ◽  
Short Palindromic Repeat ◽  
Cellular Defenses ◽  
Clinical Conditions

ABSTRACT The CRISPR-Cas (clustered regularly interspaced short palindromic repeat–CRISPR-associated protein) system is unique to prokaryotes and provides the majority of bacteria and archaea with immunity against nucleic acids of foreign origin. CRISPR RNAs (crRNAs) are the key element of this system, since they are responsible for its selectivity and effectiveness. Typical crRNAs consist of a spacer sequence flanked with 5′ and 3′ handles originating from repeat sequences that are important for recognition of these small RNAs by the Cas machinery. In this investigation, we studied the type I-C CRISPR-Cas system in Porphyromonas gingivalis, a human pathogen associated with periodontitis, rheumatoid arthritis, cardiovascular disease, and aspiration pneumonia. We demonstrated the importance of the 5′ handle for crRNA recognition by the effector complex and consequently activity, as well as secondary trimming of the 3′ handle, which was not affected by modifications of the repeat sequence. IMPORTANCE Porphyromonas gingivalis, a clinically relevant Gram-negative, anaerobic bacterium, is one of the major etiologic agents of periodontitis and has been linked with the development of other clinical conditions, including rheumatoid arthritis, cardiovascular disease, and aspiration pneumonia. The presented results on the biogenesis and functions of crRNAs expand our understanding of CRISPR-Cas cellular defenses in P. gingivalis and of horizontal gene transfer in bacteria.

scholarly journals Clinical and Microbiological Characteristics of Mycobacterium kansasii Pulmonary Infections in China

2022 ◽  
Author(s):  
Yinjuan Guo ◽  
Yanhua Cao ◽  
Haican Liu ◽  
Jinghui Yang ◽  
Weiping Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Detailed Analysis ◽  
Type I ◽  
Mycobacterium Kansasii ◽  
Genomic Evolution ◽  
Pulmonary Infections ◽  
Content Type ◽  
Microbiological Characteristics ◽  
Global Spread ◽  
History Of

M. kansasii type I is the main genotype spreading worldwide. The molecular history of the global spread of type I isolates remains largely unclear. We conducted a detailed analysis of genomic evolution of global M. kansasii isolates. Our results suggest that M. kansasii isolates exhibit greater genetic diversity globally.

scholarly journals Modulation of Chicken Intestinal Immune Gene Expression by Small Cationic Peptides as Feed Additives during the First Week Posthatch

2013 ◽  
Vol 20 (9) ◽  
pp. 1440-1448 ◽  
Author(s):  
Michael H. Kogut ◽  
Kenneth J. Genovese ◽  
Haiqi He ◽  
Christina L. Swaggerty ◽  
Yiwei Jiang
Keyword(s):  
Gene Expression ◽  
Proinflammatory Cytokines ◽  
Proinflammatory Cytokine ◽  
Feed Additives ◽  
Feed Additive ◽  
Cationic Peptides ◽  
Type I ◽  
Immune Gene ◽  
Content Type ◽  
Functional Efficiency

ABSTRACTWe have been investigating modulation strategies tailored around the selective stimulation of the host's immune system as an alternative to direct targeting of microbial pathogens by antibiotics. One such approach is the use of a group of small cationic peptides (BT) produced by a Gram-positive soil bacterium,Brevibacillus texasporus. These peptides have immune modulatory properties that enhance both leukocyte functional efficiency and leukocyte proinflammatory cytokine and chemokine mRNA transcription activitiesin vitro. In addition, when provided as a feed additive for just 4 days posthatch, BT peptides significantly induce a concentration-dependent protection against cecal and extraintestinal colonization bySalmonella entericaserovar Enteritidis. In the present studies, we assessed the effects of feeding BT peptides on transcriptional changes on proinflammatory cytokines, inflammatory chemokines, and Toll-like receptors (TLR) in the ceca of broiler chickens with and withoutS. Enteritidis infection. After feeding a BT peptide-supplemented diet for the first 4 days posthatch, chickens were then challenged withS. Enteritidis, and intestinal gene expression was measured at 1 or 7 days postinfection (p.i.) (5 or 11 days of age). Intestinal expression of innate immune mRNA transcripts was analyzed by quantitative real-time PCR (qRT-PCR). Analysis of relative mRNA expression showed that a BT peptide-supplemented diet did not directly induce the transcription of proinflammatory cytokine, inflammatory chemokine, type I/II interferon (IFN), or TLR mRNA in chicken cecum. However, feeding the BT peptide-supplemented diet primed cecal tissue for increased (P≤ 0.05) transcription of TLR4, TLR15, and TLR21 upon infection withS. Enteritidis on days 1 and 7 p.i. Likewise, feeding the BT peptides primed the cecal tissue for increased transcription of proinflammatory cytokines (interleukin 1β [IL-1β], IL-6, IL-18, type I and II IFNs) and inflammatory chemokine (CxCLi2) in response toS. Enteritidis infection 1 and 7 days p.i. compared to the chickens fed the basal diet. These small cationic peptides may prove useful as alternatives to antibiotics as local immune modulators in neonatal poultry by providing prophylactic protection againstSalmonellainfections.

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