scholarly journals Evolution of the Bacterial Species Lactobacillus delbrueckii: A Partial Genomic Study with Reflections on Prokaryotic Species Concept

2003 ◽  
Vol 20 (1) ◽  
pp. 93-104 ◽  
Author(s):  
Jacques-Edouard Germond ◽  
Luciane Lapierre ◽  
Michèle Delley ◽  
Beat Mollet ◽  
Giovanna E. Felis ◽  
...  
Keyword(s):  
Species Concept ◽  
Bacterial Species ◽  
Lactobacillus Delbrueckii ◽  
Genomic Study ◽  
Prokaryotic Species

scholarly journals Heterozygous, Polyploid, Giant Bacterium, Achromatium, Possesses an Identical Functional Inventory Worldwide across Drastically Different Ecosystems

2020 ◽  
Author(s):  
Danny Ionescu ◽  
Luca Zoccarato ◽  
Artur Zaduryan ◽  
Sina Schorn ◽  
Mina Bizic ◽  
...  
Keyword(s):  
Species Concept ◽  
Single Cells ◽  
Bacterial Species ◽  
Expression Patterns ◽  
Allelic Diversity ◽  
Evolutionary Mechanisms ◽  
Genomic Features ◽  
Bacterial Speciation ◽  
Depth Ranges ◽  
Functional Versatility

Abstract Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain approximately 300 different chromosomes with allelic diversity far exceeding that typically harbored by single bacteria genera. Surveying all publicly available sediment sequence archives, we show that Achromatium is common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Although saline and freshwater Achromatium spp. appear phylogenetically separated, the genus Achromatium contains a globally identical, complete functional inventory regardless of habitat. Achromatium spp. cells from differing ecosystems (e.g., from freshwater to saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest that environmental adaptation occurs by increasing the copy number of relevant genes across the cell’s hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium and its genomic features reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.

scholarly journals The bacterial species dilemma and the genomic–phylogenetic species concept

2006 ◽  
Vol 361 (1475) ◽  
pp. 1899-1909 ◽  
Author(s):  
James T Staley
Keyword(s):  
New Species ◽  
Dna Hybridization ◽  
Species Concept ◽  
Bacterial Species ◽  
Ecological Niches ◽  
Phylogenetic Species ◽  
Bacterial Taxonomy ◽  
Species Definition ◽  
Phylogenetic Species Concept

The number of species of Bacteria and Archaea ( ca 5000) is surprisingly small considering their early evolution, genetic diversity and residence in all ecosystems. The bacterial species definition accounts in part for the small number of named species. The primary procedures required to identify new species of Bacteria and Archaea are DNA–DNA hybridization and phenotypic characterization. Recently, 16S rRNA gene sequencing and phylogenetic analysis have been applied to bacterial taxonomy. Although 16S phylogeny is arguably excellent for classification of Bacteria and Archaea from the Domain level down to the family or genus, it lacks resolution below that level. Newer approaches, including multilocus sequence analysis, and genome sequence and microarray analyses, promise to provide necessary information to better understand bacterial speciation. Indeed, recent data using these approaches, while meagre, support the view that speciation processes may occur at the subspecies level within ecological niches (ecovars) and owing to biogeography (geovars). A major dilemma for bacterial taxonomists is how to incorporate this new information into the present hierarchical system for classification of Bacteria and Archaea without causing undesirable confusion and contention. This author proposes the genomic–phylogenetic species concept (GPSC) for the taxonomy of prokaryotes. The aim is twofold. First, the GPSC would provide a conceptual and testable framework for bacterial taxonomy. Second, the GPSC would replace the burdensome requirement for DNA hybridization presently needed to describe new species. Furthermore, the GPSC is consistent with the present treatment at higher taxonomic levels.

scholarly journals Biodegradation of dairy wastewater using bacterial and fungal local isolates

2017 ◽  
Vol 76 (11) ◽  
pp. 3094-3100 ◽  
Author(s):  
Raed S. Al-Wasify ◽  
Mohamed N. Ali ◽  
Shimaa R. Hamed
Keyword(s):  
Activated Carbon ◽  
Rice Straw ◽  
Bacterial Species ◽  
Lactobacillus Delbrueckii ◽  
Dairy Wastewater ◽  
Scale Model ◽  
Dairy Effluent ◽  
Great Ability ◽  
Biodegradation Process ◽  
Bacteria And Fungi

Abstract Dairy wastewater contains high levels of organics and other pollutants. The present study was carried out to investigate the biodegradation process of dairy effluents using some locally isolated bacteria and fungi. Four different dairy effluent samples were collected from Obour and 6th October industrial cities, Egypt. Five bacterial species (Pseudomonas aeruginosa, Bacillus subtilis, Lactobacillus delbrueckii, Staphylococcus aureus and Enterococcus hirae) and three fungal strains (Alternaria sp., Fusarium sp. and Aspergillus sp.) were isolated from dairy wastewater samples, identified and used for biodegradation process. Bacterial and fungal consortia were prepared separately in the laboratory. Two-stages (aeration and filtration) laboratory scale model was designed. Rice straw and activated carbon layers were used as filtration media. Results indicated the great ability of both studied bacteria and fungi for removal of organics (biological oxygen demand removal percent were 78.7% and 74.7% for bacteria and fungi, respectively) and the improvement of the physicochemical quality (total suspended solids removal percent were 99.3% and 99.0% for bacteria and fungi, respectively) of the dairy effluent. The addition of rice straw and activated carbon increased removal efficiencies. Biodegradation of dairy wastewater depending on local microorganisms is an effective, cheap and eco-friendly technology.

scholarly journals Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures

2021 ◽  
Author(s):  
Vincent Somerville ◽  
Hélène Berthoud ◽  
Remo S. Schmidt ◽  
Hans-Peter Bachmann ◽  
Yi Hélène Meng ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Evolutionary Dynamics ◽  
Temporal Dynamics ◽  
Negative Impact ◽  
Bacterial Species ◽  
Starter Culture ◽  
Streptococcus Thermophilus ◽  
Starter Cultures ◽  
Lactobacillus Delbrueckii ◽  
Shotgun Metagenomics

AbstractUndefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly controlled environments over centuries. This makes them interesting for understanding eco-evolutionary dynamics governing microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to an important Swiss cheese starter culture and analyzed historical and experimental samples reflecting 82 years of starter culture propagation. We found that the bacterial community is highly stable and dominated by only a few coexisting strains of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Genome sequencing, metabolomics analysis, and co-culturing experiments of 43 isolates show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large and diverse repertoire of matching CRISPR spacers. Our findings show that functionally equivalent strains can coexist in domesticated microbial communities and highlight an important role of bacteria-phage interactions that are different from kill-the-winner dynamics.

scholarly journals Novel Phage Group Infecting Lactobacillus delbrueckii subsp. lactis, as Revealed by Genomic and Proteomic Analysis of Bacteriophage Ldl1

2014 ◽  
Vol 81 (4) ◽  
pp. 1319-1326 ◽  
Author(s):  
Eoghan Casey ◽  
Jennifer Mahony ◽  
Horst Neve ◽  
Jean-Paul Noben ◽  
Fabio Dal Bello ◽  
...  
Keyword(s):  
Burst Size ◽  
Bacterial Species ◽  
Lactobacillus Delbrueckii ◽  
Comparative Genomic ◽  
Phage Group ◽  
Content Type ◽  
Large Head ◽  
Electron Microscopy Analysis ◽  
Microscopy Analysis

ABSTRACTLdl1 is a virulent phage infecting the dairy starterLactobacillus delbrueckiisubsp.lactisLdlS. Electron microscopy analysis revealed that this phage exhibits a large head and a long tail and bears little resemblance to other characterized phages infectingLactobacillus delbrueckii.In vitropropagation of this phage revealed a latent period of 30 to 40 min and a burst size of 59.9 ± 1.9 phage particles. Comparative genomic and proteomic analyses showed remarkable similarity between the genome of Ldl1 and that ofLactobacillus plantarumphage ATCC 8014-B2. The genomic and proteomic characteristics of Ldl1 demonstrate that this phage does not belong to any of the four previously recognizedL. delbrueckiiphage groups, necessitating the creation of a new group, called group e, thus adding to the knowledge on the diversity of phages targeting strains of this industrially important lactic acid bacterial species.

scholarly journals Genome sequencing of Mycobacterium pinnipedii strains: genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens)

2019 ◽  
Author(s):  
Taiana Silva Pereira ◽  
Cássia Y. Ikuta ◽  
Cristina K. Zimpel ◽  
Naila C. S. Camargo ◽  
Antônio F. de Souza Filho ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Host Species ◽  
Bacterial Species ◽  
Gene Families ◽  
Comparative Genomic ◽  
South American ◽  
Nucleotide Polymorphisms ◽  
Sea Lion ◽  
South American Sea Lion ◽  
Genomic Study

Abstract Background: Mycobacterium pinnipedii , a member of the Mycobacterium tuberculosis Complex (MTBC), is capable of infecting several host species, including humans. Recently, ancient DNA from this organism was recovered from pre-Columbian mummies of Peru, sparking debate over the origin and frequency of tuberculosis in the Americas prior to European colonization. Results: We present the first comparative genomic study of this bacterial species, starting from the genome sequencing of two M. pinnipedii isolates (MP1 and MP2) obtained from different organs of a stranded South American sea lion. Our results indicate that MP1 and MP2 differ by 113 SNPs (single nucleotide polymorphisms) and 46 indels, constituting the first report of a mixed-strain infection in a sea lion. SNP annotation analyses indicate that genes of the VapBC family, a toxin-antitoxin system, and genes related to cell wall remodeling are under evolutionary pressure for protein sequence change in these strains. OrthoMCL analysis with seven modern isolates of M. pinnipedii shows that these strains have highly similar proteomes. Gene variations were only marginally associated with hypothetical proteins and PE/PPE (proline-glutamate and proline-proline-glutamate, respectively) gene families. We also detected large deletions in ancient and modern M. pinnipedii strains, including a few occurring only in modern strains, indicating a process of genome reduction occurring over the past one thousand years. Our phylogenomic analyses suggest the existence of two modern clusters of M. pinnipedii associated with geographic location, and possibly host species, and one basal node associated with the ancient M. pinnipedii strains. Previously described MiD3 and MiD4 deletions may have occurred independently, twice, over the evolutionary course of the MTBC. Conclusion: The presence of superinfection (i.e. mixed-strain infection) in this sea lion suggests that M. pinnipedii is highly endemic in this population. Mycobacterium pinnipedii proteomes of the studied isolates showed a high degree of conservation, despite being under genomic decay when compared to M. tuberculosis. This finding indicates that further genomes need to be sequenced and analyzed to increase the chances of finding variably present genes among strains or that M. pinnipedii genome remodeling occurred prior to bacterial speciation.

scholarly journals Genome sequencing of Mycobacterium pinnipedii strains: complete genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens)

2019 ◽  
Author(s):  
Taiana Silva Pereira ◽  
Cássia Y. Ikuta ◽  
Cristina K. Zimpel ◽  
Naila C. S. Camargo ◽  
Antônio F. de Souza Filho ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Host Species ◽  
Bacterial Species ◽  
Gene Families ◽  
Comparative Genomic ◽  
South American ◽  
Nucleotide Polymorphisms ◽  
Sea Lion ◽  
South American Sea Lion ◽  
Genomic Study

Abstract Background: Mycobacterium pinnipedii, a member of the Mycobacterium tuberculosis Complex (MTC), is capable of infecting several host species, including humans. Recently, ancient DNA from this organism was recovered from pre-Columbian mummies of Peru, sparkling debate over the origin and frequency of tuberculosis in the Americas prior to European colonization. Results: We present the first comparative genomic study of this bacterial species, building from the complete genome sequencing of two M. pinnipedii isolates (MP1 and MP2) obtained from different organs of a stranded South American sea lion. Our results indicate that MP1 and MP2 differ by 113 SNPs (single nucleotide polymorphisms) and 46 short deletions, constituting the first report of a mixed-strain infection in a sea lion. SNP annotation and protein networks indicate that genes of the VapBC family, a toxin-antitoxin system, are under evolutionary pressure for protein sequence change in these strains. OrthoMCL analysis with seven modern isolates of M. pinnipedii shows that these strains have highly similar proteomes. Gene variations was only marginally associated with hypothetical proteins and PE/PPE (proline-glutamate and proline-proline-glutamic, respectively) gene families. We also detected 28 large deletions in ancient and modern M. pinnipedii strains, including 21 never described and 15 occurring only in modern strains, indicating a process of genome reduction occurring over the past 1,000 years. Our phylogenomic analyses suggest the existence of two modern clusters of M. pinnipedii associated with geographic location, and possibly host species, and one basal node associated with the ancient M. pinnipedii strains. Previously described MiD3 and MiD4 or RD2Seal deletions may have occurred independently, twice, over evolutionary course of the MTC. Conclusion: The presence of superinfection (i.e. mixed-strain infection) in this sea lion suggests that M. pinnipedii is highly endemic in this population. In contrast to the human-adapted M. tuberculosis strains, M. pinnipedii proteomes of the studied isolate showed high degree of conservation, despite being under genomic decay when compared to M. tuberculosis. This finding indicates that further genomes need to be sequenced and analyzed to increase the chances of finding variably present genes among strains or that M. pinnipedii genome remodeling occurred prior to bacterial speciation.

scholarly journals STUDY OF ASSOCIATION OF INTESTINAL PREVOTELLA IN EARLY RHEUMATOID ARTHRITIS

2019 ◽  
pp. 1-3
Author(s):  
Sabarish Vs
Keyword(s):  
Rheumatoid Arthritis ◽  
Gut Microbiota ◽  
Bacterial Species ◽  
Bacterial Genome ◽  
P Value ◽  
Anaerobic Culture ◽  
Genomic Study ◽  
16S Rna ◽  
Prevotella Species ◽  
Stool Samples

BACKGROUND: - Despite being highly prevalent and highly studied autoimmune disease, the etiology for the autoimmunity in Rheumatoid arthritis is not known. One of the recent advances being the role of gut microbiota. The primary objective of this study is to explore the association of Prevotella copri species in the gut microbiota in untreated Rheumatoid arthritis patients. AIMS AND OBJECTIVES:-To study the association of Prevotella copri in the gut microbiota in untreated Rheumatoid Arthritis patients MATERIALAND METHODS: Stool samples were collected from controls and new onset, untreated Rheumatoid arthritis patients in reduced transport fluid (RTF) and were subjected to anaerobic culture in Kanamycin-Vancomycin blood agar to identify Prevotella species based on colony morphology and biochemical tests. Inoculated plates were incubated anaerobically by gas pak method for 72 hours. Also, broadband PCR was run on stool samples collected in RTF for detection of 16S RNA of Prevotella species and the samples which test positive were further subjected to specific PCR with another set of internal primers to detect 16S RNA of Prevotella copri. HiPurATM Stool DNA Purification Kit (#MB544 HIMEDIA) was used for extraction of bacterial genome. Separation of genomic DNAwas done using agarose gel electrophoresis. 2 sets of primers were used among which one is universal primer for bacterial species i.e., 16S rDNA to validate the sample or DNA for bacterial genomic study. Another primer mix specific to Prevotella copri was procured from Helini Biosciences along with positive control for Prevotella copri to identify samples positive for Prevotella copri. RESULTS:- Stool samples were collected from 30 cases and 25 healthy controls and were subjected to PCR and culture. Anaerobic culture showed no growth of Prevotella. PCR studies showed 19(63%) cases being positive for Prevotella copri nucleic acid whereas only 7(28%) samples were positive in controls. CONCLUSION: - Intestinal Prevotella copri was found in significant number of cases of Rheumatoid arthritis compared to controls (p value: 0.009) indicating the alteration in gut microbiota in cases, which could be the reason for priming of autoimmunity in Rheumatoid arthritis

scholarly journals Comparative Genomics of Wolbachia and the Bacterial Species Concept

PLoS Genetics ◽  
2013 ◽  
Vol 9 (4) ◽  
pp. e1003381 ◽  
Author(s):  
Kirsten Maren Ellegaard ◽  
Lisa Klasson ◽  
Kristina Näslund ◽  
Kostas Bourtzis ◽  
Siv G. E. Andersson
Keyword(s):  
Comparative Genomics ◽  
Species Concept ◽  
Bacterial Species

scholarly journals Effects of Electrospinning on the Viability of Ten Species of Lactic Acid Bacteria in Poly(Ethylene Oxide) Nanofibers

Pharmaceutics ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 483 ◽  
Author(s):  
Špela Zupančič ◽  
Katja Škrlec ◽  
Petra Kocbek ◽  
Julijana Kristl ◽  
Aleš Berlec
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Ethylene Oxide ◽  
Bacterial Species ◽  
Cell Mass ◽  
Delivery Systems ◽  
Lactobacillus Delbrueckii ◽  
Average Cell ◽  
Poly Ethylene Oxide ◽  
Poly Ethylene

Lactic acid bacteria can have beneficial health effects and be used for the treatment of various diseases. However, there remains the challenge of encapsulating probiotics into delivery systems with a high viability and encapsulation efficacy. The electrospinning of bacteria is a novel and little-studied method, and further investigation of its promising potential is needed. Here, the morphology, zeta potential, hydrophobicity, average cell mass, and growth characteristics of nine different species of Lactobacillus and one of Lactococcus are characterized. The electrospinning of polymer solutions containing ~10 log colony forming units (CFU)/mL lactic acid bacteria enabled the successful incorporation of all bacterial species tested, from the smallest (0.74 µm; Lactococcus lactis) to the largest (10.82 µm; Lactobacillus delbrueckii ssp. bulgaricus), into poly(ethylene oxide) nanofibers with an average diameter of ~100 nm. All of these lactobacilli were viable after incorporation into nanofibers, with 0 to 3 log CFU/mg loss in viability, depending on the species. Viability correlated with the hydrophobicity and extreme length of lactic acid bacteria, whereas a horizonal or vertical electrospinning set-up did not have any role. Therefore, electrospinning represents a promising method for the incorporation of lactic acid bacteria into solid delivery systems, while drying the bacterial dispersion at the same time.

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