The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

A strain, S-1T was isolated from rainbow trout (Oncorhynchus mykiss) exhibiting clinical symptoms of lens atrophy, inappetence, visual impairment and growth retardation. The strain was identified as representing a member of the genus Shewanella on the basis of the results of 16S rRNA gene sequence analysis. The neighbor-joining phylogenetic tree based on 16S rRNA gene sequences indicated that S-1T clustered with Shewanella putrefaciens JCM 20190T, Shewanella profunda DSM 15900T, and Shewanella hafniensis P010T, sharing 99.3, 98.8 and 87.7% 16S rRNA gene similarities, respectively. A polyphasic taxonomic approach including phenotypic, chemotaxonomic, and genomic characterization was employed to ascertain the taxonomic position of S-1T within the genus Shewanella. The overall genome relatedness indices (OGRI) for S-1T compared with the most closely related type strains S. hafniensis ATCC BAA-1207T, Shewanella baltica NCTC 10735T, S. putrefaciens ATCC 8071T and S. profunda DSM 15900T were calculated as 40.8, 40.1, 28.5 and 27.3% for digital DNA-DNA hybridization (dDDH), and 91.6, 91.0, 86.3 and 85.1% for average nucleotide identity (ANI), respectively. OGRI values between S-1T and its close neighbours confirmed that the strain represents a novel species in the genus Shewanella.The DNA G+C content of the strain is 45.2%. Major fatty acids were C17 : 1ω8c, C15 : 0iso, and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The predominant polar lipids were phosphatidylethanolamine, phospholipid, amino-phospholipid and unidentified lipids. The major respiratory quinones were ubiquinone-8, ubiquinone-7 and menaquinone-7. Chemotaxonomic and phylogenomic analyses of this isolate confirmed that the strain represents a novel species for which the name Shewanella oncorhynchi sp. nov. is proposed, with S-1T as the type strain (JCM 34183T= KCTC 82249T).

Shewanella oncorhynchi sp. nov., a novel member of the genus Shewanella, isolated from Rainbow Trout (Oncorhynchus mykiss).

This study is aimed at exploring the effects of Bacillus coagulans NRS 609 on the growth performance, intestinal health, antioxidant activity, and immune response in common carp (Cyprinus carpio L.) by colonizing the intestinal tract with the beneficial strain. Gavage B. coagulans with GFP-tag at 109 CFU/mL into common carp for 7 days. Results indicated that B. coagulans were maintained in the intestine for at least 14 days. Four groups fed B. coagulans at different levels of inclusion, including 0 (CK), 
 
 1
 ×
 
 
 10
 
 
 7
 
 
 
 (A), 
 
 1
 ×
 
 
 10
 
 
 8
 
 
 
 (B), and 
 
 1
 ×
 
 
 10
 
 
 9
 
 
 
 (C) CFU/g of feed for 8 weeks. Experimental groups showed significantly better growth performance than the control (
 
 P
 <
 0.05
 
 ). The treatment groups had higher digestive enzyme activity, villus height, and muscle thickness than the control (
 
 P
 <
 0.05
 
 ). Supplementation with B. coagulans also altered the composition of the intestinal flora. In addition, an enhancement of the antioxidant enzyme and a reduction of malondialdehyde in the liver were observed with the addition of B. coagulans (
 
 P
 <
 0.05
 
 ). Moreover, the cytokines of IL-1β and IL-12, IL-10, and TGF-β, significant upregulation in experimental groups (
 
 P
 <
 0.05
 
 ). Based on the results, the optimal level of B. coagulans was 107 CFU/g in diets for common carp.

/pdf/effect-of-beneficial-colonization-of-bacillus-coagulans-nrs-3corp539.pdf

Effect of Beneficial Colonization of Bacillus coagulans NRS 609 on Growth Performance, Intestinal Health, Antioxidant Capacity, and Immune Response of Common Carp (Cyprinus carpio L.)

In the evolving biosphere, pathogenic microorganisms that cause disease may undergo phenotypic changes. While some of these changes result in new variants or mutants, others lead to the emergence of novel pathogens. Such phenotypic changes as well as advances in technology and analytical methods and the identification of genomic sequences of microbial DNA have brought about new methodological approaches in the diagnosis of bacterial diseases. Although bacterial identification was originally based on phenotypic characteristics, later researchers claimed that bacteria could be accurately identified by only gene sequencing and generally by the sequencing of the 16S ribosomal RNA gene region. Currently, there is still disagreement between classical microbiologists and those using new genomic sequence technology over the best method for identification. Fish are cold-blooded animals, and fish pathogens generally exhibit psychrophilic characteristics. Many bacterial identification systems that are used to identify mesophilic bacteria remain useless for identifying fish pathogens because the optimum incubation temperatures for mesophilic bacteria are 35–37°C. Bacteria that are pathogenic to piscine species require specific media for their cultivation at lower incubation temperatures (15–28°C), and this limits both their growth in culture and subsequent identification by phenotype-based methods. This review presents a comprehensive overview of the isolation and identification of bacterial fish pathogens by optimal culture conditions, biochemical tests, colorimetric methods for rapid identification systems, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and immunological and molecular methods, as well as an overview of the detection of uncultivable bacteria and the use of anamnesis. We conclude that the accurate identification of fish pathogens requires the use of different methods, including phenotype- and genotype-based tests, and the evaluation of anamnesis. 

General Assessment of Approaches to the Identification of Aquatic Bacterial Pathogens: A Methodological Review

Different species of Shewanella spp. widely inhabit freshwater and marine environments. Some of them are opportunistic fish pathogens. The application of high-throughput sequencing enabled the characterization and taxonomic reclassification of many Shewanella spp. species. Still, some strains collected from fish need to be better recognized. The aim of the present study was to classify and determine the phylogenetic relationships of Shewanella spp. collected from fish. The complete genomes of 94 strains of Shewanella spp. from different fish species were sequenced using Illumina platform (MiSeq). The 16S rRNA gene, genomic features and whole-genome relationships of those bacteria were comprehensively analysed in comparison to reference strains. Whole-genome analysis showed that the tested Shewanella spp. strains were clustered into six groups similar to reference strains of S. xiamenensis, S. oneidensis, S. glacialipiscicola, S. hafniensis, S. baltica and S. oncorhynchi. Our study indicates that the whole-genome sequence analysis enabled taxonomic classification and assessment of the diversity of the Shewanella spp. strains, as opposed to recently the gold standard method of 16S rRNA amplicon sequencing. The high genetic diversity and low similarity to the reference genome of S. oneidensis indicate that the group of strains may be a subspecies or even new species. Furthermore, we showed that the most frequent Shewanella spp. species occurring in freshwater fish in our study is the recently described species S. oncorhynchi.

Phylogenetic analysis of Shewanella spp. isolated from fish.

Description of lens atrophy caused by Shewanella sp. strain S-1, a putative novel species isolated from cultured rainbow trout

The Use of Acellular Matrices Obtained by the Esophagus, Intestine, and Trachea for Esophageal Wall Repair: an Experimental Study on a Rat Model

Anencephaly is a congenital disease manifesting with the absence of the brain due to the failure of the cranial part of the neural tube to close during the embryonic stage. The disease may be accompanied by other anomalies and usually results in premature death. A stillborn puppy of a 2-year-old female Pomeranian dog is examined in this case. The lack of brain tissue and accompanying abnormal skull formation was noted macroscopically. The eyes were protruding out of their normal position (exophthalmos), and a bifid tongue together with a secondary cleft palate was present. On serial sections stained with Haematoxylin-Eosin, only the medulla spinalis among the central nervous system structures could be inspected microscopically. Immunohistochemistry staining revealed GFAP immunoreactivity in the astrocytic glial cells. NeuN immunoreactivity was detected in the neurons in the medulla spinalis and spinal ganglions. Incomplete retinal layers were observed on the eye sections stained with Haematoxylin-Eosin and NeuN. The case was concluded to be coherent with skull and nervous system congenital malformations rarely observed in dogs. To the best of our knowledge, this represents the first description of a dog with anencephaly, bifid tongue and cleft palate.

Zehra Avci

Papers

Description of lens atrophy caused by Shewanella sp. strain S-1, a putative novel species isolated from cultured rainbow trout

The Use of Acellular Matrices Obtained by the Esophagus, Intestine, and Trachea for Esophageal Wall Repair: an Experimental Study on a Rat Model

Anencephaly, Bifid Tongue, and Cleft Palate in a Pomeranian Dog: GFAP and NeuN Immunoreactivities.