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July 7, 2019  |  

Probiotic genomes: Sequencing and annotation in the past decade

Probiotics are live microorganisms that confer many health benefits to the host when administered in adequate quantities. These health benefits have garnered much attention towards Probiotics and have given an impetus to their use as dietary supplements for the improvement of general health and as adjuvant therapies for certain diseases. The increased demand for probiotic products in the recent times has provided the thrust for probiotic research applied to several areas of human biology. The advances in genomic technologies have further facilitated the sequencing of the genomes of such probiotic bacteria and their genomic analyses to identify the genes that endow the beneficial effects they are known to exert. This work reviews the application of genomic strategies on probiotic bacteria, while providing the details about the probiotic strains whose genome sequences are available. It also consolidates the Genomic tools used for the sequencing, assembly and annotation of the probiotic genes and how it has helped in comparative genomic analyses.

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July 7, 2019  |  

Thauera sinica sp. nov., a phenol derivative-degrading bacterium isolated from activated sludge.

A bacterial strain, K11T, capable of degrading phenol derivatives was isolated from activated sludge of a sewage treatment plant in China. This strain, which can degrade more than ten phenol derivatives, was identified as a Gram-stain negative, rod-shaped, asporogenous, facultative anaerobic bacterium with a polar flagellum. The strain was found to grow in tryptic soy broth in the presence of 0-2.5% (w/v) NaCl (optimum 0-1%), at 4-43 °C (optimum 30-35 °C) and pH 4.5-10.5 (optimum 7.5-8). Comparative analysis of nearly full-length 16S rRNA gene sequences showed that this strain belongs to the genus Thauera. The 16S rRNA gene sequence was found to show high similarity (97.5%) to that of Thauera chlorobenzoica 3CB-1T, with lesser similarity to other recognised Thauera strains. The G+C content of the DNA of the strain was determined to be 67.8 mol%. The DNA-DNA hybridization value between K11T and Thauera aromatica DSM6984T was 10.4 ± 4.5%. The genomic OrthoANI values of K11T with the other nine type strains of genus Thauera were less than 81.1%. Chemotaxonomic analysis of strain K11T revealed that Q-8 is the predominant quinone; the polar lipids contain phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and five uncharacterised lipids; the major cellular fatty acid was identified as summed feature 3 (C16:1 ?7c and/or iso-C15:0 2-OH; 45.9%), followed by C16:0 (20.5%) and C18:1 ?7c (15.8%). Based on the phenotypic and phylogenetic evidence, DNA-DNA hybridisation, OrthoANI, chemotaxonomic analysis and results of the physiological and biochemical tests, a new species named Thauera sinica sp. nov. is proposed with strain K11T (= CGMCC 1.15731T = KACC 19216T) designated as the type strain.

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July 7, 2019  |  

Complete genome of Pseudoalteromonas marina ECSMB14103, a mussel settlement-inducing bacterium isolated from the East China Sea

Pseudoalteromonas marina ECSMB14103, a strain isolated from natural multiple-species biofilms formed in the East China Sea, induces the settlement of larvae and plantigrades in Mytilus coruscus. Here, we report the complete genome of this strain; the genome is 3,441,076?bp in size, has a GC content of 39.90% and contains a total of 3200 predicted genes. These genomic data will provide significant datasets to help improve understanding of the physiological potential and molecular mechanisms of settlement induction by P. marina ECSMB14103.

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July 7, 2019  |  

Emerging mechanisms of antimicrobial resistance in bacteria and fungi: advances in the era of genomics.

Bacteria and fungi continue to develop new ways to adapt and survive the lethal or biostatic effects of antimicrobials through myriad mechanisms. Novel antibiotic resistance genes such as lsa(C), erm(44), VCC-1, mcr-1, mcr-2, mcr-3, mcr-4, bla KLUC-3 and bla KLUC-4 were discovered through comparative genomics and further functional studies. As well, mutations in genes that hitherto were unknown to confer resistance to antimicrobials, such as trm, PP2C, rpsJ, HSC82, FKS2 and Rv2887, were shown by genomics and transcomplementation assays to mediate antimicrobial resistance in Acinetobacter baumannii, Staphylococcus aureus, Enterococcus faecium, Saccharomyces cerevisae, Candida glabrata and Mycobacterium tuberculosis, respectively. Thus, genomics, transcriptomics and metagenomics, coupled with functional studies are the future of antimicrobial resistance research and novel drug discovery or design.

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July 7, 2019  |  

Evolution and comparative genomics of F33:A-:B- plasmids carrying blaCTX-M-55 or blaCTX-M-65 in Escherichia coli and Klebsiella pneumoniae isolated from animals.

To understand the underlying evolution process of F33:A-:B- plasmids among Enterobacteriaceae isolates of various origins in China, the complete sequences of 17 blaCTX-M-harboring F33:A-:B- plasmids obtained from Escherichia coli and Klebsiella pneumoniae isolates from different sources (animals, animal-derived food, and human clinics) in China were determined. F33:A-:B- plasmids shared similar plasmid backbones comprising replication, leading, and conjugative transfer regions and differed by the numbers of repeats in yddA and traD and by the presence of group II intron, except that pHNAH9 lacked a large segment of the leading and transfer regions. The variable regions of F33:A-B- plasmids were distinct and were inserted downstream of the addiction system pemI/pemK, identified as the integration hot spot among F33:A-B- plasmids. The variable region contained resistance genes and mobile elements or contained segments from other types of plasmids, such as IncI1, IncN1, and IncX1. Three plasmids encoding CTX-M-65 were very similar to our previously described pHN7A8 plasmid. Four CTX-M-55-producing plasmids contained multidrug resistance regions related to that of F2:A-B- plasmid pHK23a from Hong Kong. Five plasmids with IncN and/or IncX replication regions and IncI1-backbone fragments had variable regions related to those of pE80 and p42-2. The remaining five plasmids with IncN replicons and an IncI1 segment also possessed closely related variable regions. The diversity in variable regions was presumably associated with rearrangements, insertions, and/or deletions mediated by mobile elements, such as IS26 and IS1294 IMPORTANCE Worldwide spread of antibiotic resistance genes among Enterobacteriaceae isolates is of great concern. F33:A-:B- plasmids are important vectors of resistance genes, such as blaCTX-M-55/-65, blaNDM-1, fosA3, and rmtB, among E. coli isolates from various sources in China. We determined and compared the complete sequences of 17 F33:A-:B- plasmids from various sources. These plasmids appear to have evolved from the same ancestor by mobile element-mediated rearrangement, acquisition, and/or loss of resistance modules and similar IncN1, IncI1, and/or IncX1 plasmid backbone segments. Our findings highlight the evolutionary potential of F33:A-:B- plasmids as efficient vectors to capture and diffuse clinically relevant resistance genes. Copyright © 2018 Wang et al.

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July 7, 2019  |  

Immunoglobulin gene analysis as a tool for investigating human immune responses.

The human immunoglobulin repertoire is a hugely diverse set of sequences that are formed by processes of gene rearrangement, heavy and light chain gene assortment, class switching and somatic hypermutation. Early B cell development produces diverse IgM and IgD B cell receptors on the B cell surface, resulting in a repertoire that can bind many foreign antigens but which has had self-reactive B cells removed. Later antigen-dependent development processes adjust the antigen affinity of the receptor by somatic hypermutation. The effector mechanism of the antibody is also adjusted, by switching the class of the antibody from IgM to one of seven other classes depending on the required function. There are many instances in human biology where positive and negative selection forces can act to shape the immunoglobulin repertoire and therefore repertoire analysis can provide useful information on infection control, vaccination efficacy, autoimmune diseases, and cancer. It can also be used to identify antigen-specific sequences that may be of use in therapeutics. The juxtaposition of lymphocyte development and numerical evaluation of immune repertoires has resulted in the growth of a new sub-speciality in immunology where immunologists and computer scientists/physicists collaborate to assess immune repertoires and develop models of immune action.© 2018 The Authors. Immunological Reviews Published by John Wiley & Sons Ltd.

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July 7, 2019  |  

Implementation of pharmacogenomics in everyday clinical settings.

Currently, germline pharmacogenomics (PGx) is successfully implemented within certain specialties in clinical care. With the integration of PGx in pharmacotherapy multiple stakeholders are involved, which are identified in this chapter. Clinically relevant pharmacogenes with their related PGx test are discussed, along with diagnostic test criteria to guide clinicians and policy makers in PGx test selection. The chapter further reviews the similarities and the differences between the guidelines of the Dutch Pharmacogenetics Working Group and the Clinical Pharmacogenetics Implementation Consortium which both support healthcare professionals in understanding PGx test results and help guiding pharmacotherapy by providing evidence-based dosing recommendations. Finally, clinical studies which provide scientific evidence and information on cost-effectiveness supporting clinical implementation of PGx in clinical care are discussed along with the remaining barriers for adoption of PGx testing by healthcare professionals.© 2018 Elsevier Inc. All rights reserved.

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July 7, 2019  |  

The complete genome sequence of Rhodobaca barguzinensis alga05 (DSM 19920) documents its adaptation for life in soda lakes.

Soda lakes, with their high salinity and high pH, pose a very challenging environment for life. Microorganisms living in these harsh conditions have had to adapt their physiology and gene inventory. Therefore, we analyzed the complete genome of the haloalkaliphilic photoheterotrophic bacterium Rhodobaca barguzinensis strain alga05. It consists of a 3,899,419 bp circular chromosome with 3624 predicted coding sequences. In contrast to most of Rhodobacterales, this strain lacks any extrachromosomal elements. To identify the genes responsible for adaptation to high pH, we compared the gene inventory in the alga05 genome with genomes of 17 reference strains belonging to order Rhodobacterales. We found that all haloalkaliphilic strains contain the mrpB gene coding for the B subunit of the MRP Na+/H+ antiporter, while this gene is absent in all non-alkaliphilic strains, which indicates its importance for adaptation to high pH. Further analysis showed that alga05 requires organic carbon sources for growth, but it also contains genes encoding the ethylmalonyl-CoA pathway for CO2 fixation. Remarkable is the genetic potential to utilize organophosphorus compounds as a source of phosphorus. In summary, its genetic inventory indicates a large flexibility of the alga05 metabolism, which is advantageous in rapidly changing environmental conditions in soda lakes.

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July 7, 2019  |  

Complete genome sequence of Clostridium kluyveri JZZ applied in Chinese strong-flavor liquor production.

Chinese strong-flavor liquor (CSFL), accounting for more than 70% of both Chinese liquor production and sales, was produced by complex fermentation with pit mud. Clostridium kluyveri, an important species coexisted with other microorganisms in fermentation pit mud (FPM), could produce caproic acid, which was subsequently converted to the key CSFL flavor substance ethyl caproate. In this study, we present the first complete genome sequence of C. kluyveri isolated from FPM. Clostridium kluyveri JZZ contains one circular chromosome and one circular plasmid with length of 4,454,353 and 58,581 bp, respectively. 4158 protein-coding genes were predicted and 2792 genes could be assigned with COG categories. It possesses the pathway predicted for biosynthesis of caproic acid with ethanol. Compared to other two C. kluyveri genomes, JZZ consists of longer chromosome with multiple gene rearrangements, and contains more genes involved in defense mechanisms, as well as DNA replication, recombination, and repair. Meanwhile, JZZ contains fewer genes involved in secondary metabolites biosynthesis, transport, and catabolism, including genes encoding Polyketide Synthases/Non-ribosomal Peptide Synthetases. Additionally, JZZ possesses 960 unique genes with relatively aggregating in defense mechanisms and transcription. Our study will be available for further research about C. kluyveri isolated from FPM, and will also facilitate the genetic engineering to increase biofuel production and improve fragrance flavor of CSFL.

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July 7, 2019  |  

Complete genome sequence of Rhodothermaceae bacterium RA with cellulolytic and xylanolytic activities.

Rhodothermaceae bacterium RA is a halo-thermophile isolated from a saline hot spring. Previously, the genome of this bacterium was sequenced using a HiSeq 2500 platform culminating in 91 contigs. In this report, we report on the resequencing of its complete genome using a PacBio RSII platform. The genome has a GC content of 68.3%, is 4,653,222 bp in size, and encodes 3711 genes. We are interested in understanding the carbohydrate metabolic pathway, in particular the lignocellulosic biomass degradation pathway. Strain RA harbors 57 glycosyl hydrolase (GH) genes that are affiliated with 30 families. The bacterium consists of cellulose-acting (GH 3, 5, 9, and 44) and hemicellulose-acting enzymes (GH 3, 10, and 43). A crude cell-free extract of the bacterium exhibited endoglucanase, xylanase, ß-glucosidase, and ß-xylosidase activities. The complete genome information coupled with biochemical assays confirms that strain RA is able to degrade cellulose and xylan. Therefore, strain RA is another excellent member of family Rhodothermaceae as a repository of novel and thermostable cellulolytic and hemicellulolytic enzymes.

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July 7, 2019  |  

Complete genome sequence of the halophile bacterium Kushneria konosiri X49T, isolated from salt-fermented Konosirus punctatus

Kushneria konosiri X49T is a member of the Halomonadaceae family within the order Oceanospirillales and can be isolated from salt-fermented larval gizzard shad. The genome of K. konosiri X49T reported here provides a genetic basis for its halophilic character. Diverse genes were involved in salt-in and -out strategies enabling adaptation of X49T to hypersaline environments. Due to resistance to high salt concentrations, genome research of K. konosiri X49T will contribute to the improvement of environmental and biotechnological usage by enhancing understanding of the osmotic equilibrium in the cytoplasm. Its genome consists of 3,584,631 bp, with an average Gthinspace+thinspaceC content of 59.1%, and 3261 coding sequences, 12 rRNAs, 66 tRNAs, and 8 miscRNAs.

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July 7, 2019  |  

Complete genome sequence of Agrobacterium pusense VsBac-Y9, a bacterial symbiont of the dark septate endophytic fungus Veronaeopsis simplex Y34 with potential for improving fungal colonization in roots.

A Rhizobium-related bacterium (Rhizobium sp. VsBac-Y9) is a symbiont living with the dark septate endophytic (DSE) fungus Veronaeopsis simplex Y34. Co-inoculation of Rhizobium sp. VsBac-Y9 with V. simplex Y34 improves the fungal colonization of tomato roots, resulting in a significant increase in aboveground biomass. This study sequenced the complete genome of this V. simplex-helper bacterium using the PacBio and Illumina MiSeq platforms. Hybrid assembly using SPAdes outputted a circular chromosome, a linear chromid, and a circular plasmid for a total genome 5,321,211 bp in size with a G?+?C content of 59.2%. Analysis of concatenated housekeeping genes (atpD-dnaK-groEL-lepA-recA-rpoB-thrE) and calculation of average nucleotide identity, showed that VsBac-Y9 was affiliated with the species Agrobacterium pusense (syn. Rhizobium pusense). Genome analysis revealed that A. pusense VsBac-Y9 contains a series of genes responsible for the host interactions with both fungus and plant. Such genomic information will provide new insights into developing co-inoculants of endophytic fungus and its symbiotic bacterium in future agricultural innovation. Copyright © 2018 Elsevier B.V. All rights reserved.

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July 7, 2019  |  

Genome sequence of Halomonas hydrothermalis Y2, an efficient ectoine-producer isolated from pulp mill wastewater.

Halophilic microorganisms have great potentials towards biotechnological applications. Halomonas hydrothermalis Y2 is a halotolerant and alkaliphilic strain that isolated from the Na+-rich pulp mill wastewater. The strain is dominant in the bacterial community of pulp mill wastewater and exhibits metabolic diversity in utilizing various substrates. Here we present the genome sequence of this strain, which comprises a circular chromosome 3,933,432 bp in size and a GC content of 60.2%. Diverse genes that encoding proteins for compatible solutes synthesis and transport were identified from the genome. With a complete pathway for ectoine synthesis, the strain could produce ectoine from monosodium glutamate and further partially secreted into the medium. In addition, around 20% ectoine was increased by deleting the ectoine hydroxylase (EctD). The genome sequence we report here will provide genetic information regarding adaptive mechanisms of strain Y2 to its harsh habitat, as well as facilitate exploration of metabolic strategies for diverse compatible solutes, e.g., ectoine production. Copyright © 2018 Elsevier B.V. All rights reserved.

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July 7, 2019  |  

The molecular basis for the intramolecular migration (NIH shift) of the carboxyl group during para-hydroxybenzoate catabolism.

The NIH shift is a chemical rearrangement in which a substituent on an aromatic ring undergoes an intramolecular migration, primarily during an enzymatic hydroxylation reaction. The molecular mechanism for the NIH shift of a carboxyl group has remained a mystery for 40 years. Here, we elucidate the molecular mechanism of the reaction in the conversion of para-hydroxybenzoate (PHB) to gentisate (GA, 2, 5-dihydroxybenzoate). Three genes (phgABC) from the PHB utilizer Brevibacillus laterosporus PHB-7a encode enzymes (p-hydroxybenzoyl-CoA ligase, p-hydroxybenzoyl-CoA hydroxylase and gentisyl-CoA thioesterase, respectively) catalyzing the conversion of PHB to GA via a route involving CoA thioester formation, hydroxylation concomitant with a 1, 2-shift of the acetyl CoA moiety and thioester hydrolysis. The shift of the carboxyl group was established rigorously by stable isotopic experiments with heterologously expressed phgABC, converting 2, 3, 5, 6-tetradeutero-PHB and [carboxyl-13 C]-PHB to 3, 4, 6-trideutero-GA and [carboxyl-13 C]-GA respectively. This is distinct from the NIH shifts of hydrogen and aceto substituents, where a single oxygenase catalyzes the reaction without the involvement of a thioester. The discovery of this three-step strategy for carboxyl group migration reveals a novel role of the CoA thioester in biochemistry and also illustrates the diversity and complexity of microbial catabolism in the carbon cycle.© 2018 John Wiley & Sons Ltd.

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July 7, 2019  |  

Emergence of gyrovirus 3 in commercial broiler chickens with transmissible viral proventriculitis.

Gyrovirus 3 (GyV3) has been identified in faeces from children with acute gastroenteritis. However, whether GyV3 is prevalent in poultry has not been determined to date. To the best of our knowledge, this study is the first to isolate GyV3 from commercial broiler chickens with transmissible viral proventriculitis (TVP) in China. The complete genome of the virus shares 98.4% sequence identity with the FecGy strain that causes acute gastroenteritis in children. Epidemiological investigation from 2013 to 2017 revealed that the infection rate of GyV3 reached 12.5% (42/336) in commercial broiler chickens with TVP, indicating that the infection of GyV3 was ubiquitous in chickens. The emergence of GyV3 in commercial broiler chickens should be highly concerning for public health.© 2018 Blackwell Verlag GmbH.

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