scholarly journals A Proposed New Strain of Avian Picornavirus in Broiler Chicken from Brazil

2018 ◽  
Vol 6 (12) ◽  
Author(s):  
Ceyla Maria Oeiras Castro ◽  
Elaine Hellen Nunes Chagas ◽  
Delana Andreza Melo Bezerra ◽  
Aline Farias Ribeiro ◽  
Sandro Patroca da Silva ◽  
...  
Keyword(s):  
Broiler Chickens ◽  
Broiler Chicken ◽  
Genomic Analysis ◽  
Nucleotide Identity ◽  
Fecal Samples ◽  
Content Type ◽  
Commercial Farm ◽  
The Family

ABSTRACT A new strain of avian picornavirus was identified in fecal samples from broiler chickens in a commercial farm in the municipality of Benevides, Pará, Brazil. Genomic analysis showed it to have a nucleotide identity of 78.4% with the family Picornaviridae , genus Avisivirus, and species Avisivirus A , suggesting that this is a possible new strain within this species.

scholarly journals First Whole-Genome Characterization of Avian Nephritis Virus 2 of Broiler Chicken from Pará, Brazil

2018 ◽  
Vol 6 (25) ◽  
Author(s):  
Ceyla Maria Oeiras Castro ◽  
Elaine Hellen Nunes Chagas ◽  
Delana Andreza Melo Bezerra ◽  
Sandro Patroca da Silva ◽  
Ana Cecília Ribeiro Cruz ◽  
...  
Keyword(s):  
Broiler Chickens ◽  
Broiler Chicken ◽  
Whole Genome ◽  
Full Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Genome Characterization ◽  
Avian Nephritis Virus ◽  
The Family

ABSTRACT Our results show the first full-genome characterization of avian nephritis virus 2 recovered from stools of broiler chickens at a commercial farm located in Benevides, Pará, Brazil. Nucleotide analyses of whole-genome sequences showed the isolate to be a strain of Avastrovirus 2 in the family Astroviridae.

scholarly journals Lichenicola cladoniae gen. nov., sp. nov., a member of the family Acetobacteraceae isolated from an Antarctic lichen

2020 ◽  
Vol 70 (11) ◽  
pp. 5918-5925 ◽  
Author(s):  
Hyun-Ju Noh ◽  
Seung Chul Shin ◽  
Yerin Park ◽  
Ahyoung Choi ◽  
Kiwoon Baek ◽  
...  
Keyword(s):  
Type Species ◽  
Genomic Analysis ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Nitrate And Nitrite

Two Gram-stain-negative, facultative anaerobic, chemoheterotrophic, pink-coloured, rod-shaped and non-motile bacterial strains, PAMC 26568 and PAMC 26569T, were isolated from an Antarctic lichen. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains PAMC 26568 and PAMC 26569T belong to the family Acetobacteraceae and the most closely related species are Gluconacetobacter takamatsuzukensis (96.1 %), Gluconacetobacter tumulisoli (95.9 %) and Gluconacetobacter sacchari (95.7 %). Phylogenomic and genomic relatedness analyses showed that strains PAMC 26568 and PAMC 26569T are clearly distinguished from other genera in the family Acetobacteraceae by average nucleotide identity values (<72.8 %) and the genome-to-genome distance values (<22.5 %). Genomic analysis revealed that strains PAMC 26568 and PAMC 26569T do not contain genes involved in atmospheric nitrogen fixation and utilization of sole carbon compounds such as methane and methanol. Instead, strains PAMC 26568 and PAMC 26569T possess genes to utilize nitrate and nitrite and certain monosaccharides and disaccharides. The major fatty acids (>10 %) are summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c; 40.3–40.4 %), C18 : 1 2OH (22.7–23.7 %) and summed feature 2 (C14 : 0 3OH and/or C16 : 1 iso I; 12.0 % in PAMC 26568). The major respiratory quinone is Q-10. The genomic DNA G+C content of PAMC 26568 and PAMC 26569T is 64.6 %. Their distinct phylogenetic position and some physiological characteristics distinguish strains PAMC 26568 and PAMC 26569T from other genera in the family Acetobacteraceae supporting the proposal of Lichenicola gen. nov., with the type species Lichenicola cladoniae sp. nov. (type strain, PAMC 26569T=KCCM 43315T=JCM 33604T).

scholarly journals Genome Sequences of Allochromatium palmeri and Allochromatium humboldtianum Expand the Allochromatium Family Tree of Purple Sulfur Photosynthetic Bacteria within the Gammaproteobacteria and Further Refine the Genus

2020 ◽  
Vol 9 (33) ◽  
Author(s):  
John A. Kyndt ◽  
Terry E. Meyer
Keyword(s):  
Photosynthetic Bacteria ◽  
Nucleotide Identity ◽  
Whole Genome ◽  
Family Tree ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
Allochromatium Vinosum ◽  
Content Type ◽  
The Family ◽  
Identity Based

ABSTRACT New genomes of two Allochromatium strains were sequenced. Whole-genome and average nucleotide identity based on BLAST (ANIb) comparisons show that Allochromatium humboldtianum is the nearest relative of Allochromatium vinosum (ANIb, 91.5%), while both Allochromatium palmeri and Thermochromatium tepidum are more distantly related (ANIb, <87%). These new sequences firmly establish the position of Allochromatium on the family tree.

scholarly journals Galacto-Oligosaccharides Modulate the Juvenile Gut Microbiome and Innate Immunity To Improve Broiler Chicken Performance

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Philip J. Richards ◽  
Geraldine M. Flaujac Lafontaine ◽  
Phillippa L. Connerton ◽  
Lu Liang ◽  
Karishma Asiani ◽  
...  
Keyword(s):  
Growth Rate ◽  
Innate Immunity ◽  
Broiler Chickens ◽  
Broiler Chicken ◽  
Control Diet ◽  
Gut Health ◽  
Feed Conversion ◽  
Growth Promoters ◽  
Content Type ◽  
Key Species

ABSTRACT Improvements in growth performance and health are key goals in broiler chicken production. Inclusion of prebiotic galacto-oligosaccharides (GOS) in broiler feed enhanced the growth rate and feed conversion of chickens relative to those obtained with a calorie-matched control diet. Comparison of the cecal microbiota identified key differences in abundances of Lactobacillus spp. Increased levels of Lactobacillus johnsonii in GOS-fed juvenile birds at the expense of Lactobacillus crispatus were linked to improved performance (growth rate and market weight). Investigation of the innate immune responses highlighted increases of ileal and cecal interleukin-17A (IL-17A) gene expression counterposed to a decrease in IL-10. Quantification of the autochthonous Lactobacillus spp. revealed a correlation between bird performance and L. johnsonii abundance. Shifts in the cecal populations of key Lactobacillus spp. of juvenile birds primed intestinal innate immunity without harmful pathogen challenge. IMPORTANCE Improvements in the growth rate of broiler chickens can be achieved through dietary manipulation of the naturally occurring bacterial populations while mitigating the withdrawal of antibiotic growth promoters. Prebiotic galacto-oligosaccharides (GOS) are manufactured as a by-product of dairy cheese production and can be incorporated into the diets of juvenile chickens to improve their health and performance. This study investigated the key mechanisms behind this progression and pinpointed L. johnsonii as a key species that facilitates the enhancements in growth rate and gut health. The study identified the relationships between the GOS diet, L. johnsonii intestinal populations, and cytokine immune effectors to improve growth.

scholarly journals Parapseudoflavitalea muciniphila gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a human peritoneal tumour and reclassification of Pseudobacter ginsenosidimutans as Pseudoflavitalea ginsenosidimutans comb. nov.

2020 ◽  
Vol 70 (6) ◽  
pp. 3639-3646 ◽  
Author(s):  
Paul A. Lawson ◽  
Nisha B. Patel ◽  
Ahmed Mohammed ◽  
Edward R. B. Moore ◽  
Alexander S. Lo ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Nucleotide Identity ◽  
Rrna Gene ◽  
Average Nucleotide Identity ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-stain-negative, microaerophilic, non-motile, rod-shaped bacterium strain designated PMP191FT, was isolated from a human peritoneal tumour. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the organism formed a lineage within the family Chitinophagaceae that was distinct from members of the genus Pseudoflavitalea (95.1–95.2 % sequence similarity) and Pseudobacter ginsenosidimutans (94.4 % sequence similarity). The average nucleotide identity values between strain PMP191FT and Pseudoflavitalea rhizosphaerae T16R-265T and Pseudobacter ginsenosidimutans Gsoil 221T was 68.9 and 62.3% respectively. The only respiratory quinone of strain PMP191FT was MK-7 and the major fatty acids were iso-C15 : 0, iso-C15 : 1 G and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The polar lipids consisted of phosphatidylethanolamine and some unidentified amino and glycolipids. The G+C content of strain PMP191FT calculated from the genome sequence was 43.4 mol%. Based on phylogenetic, phenotypic and chemotaxonomic evidence, strain PMP191FT represents a novel species and genus for which the name Parapseudoflavitalea muciniphila gen. nov., sp. nov. is proposed. The type strain is PMP191FT (=DSM 104999T=ATCC BAA-2857T = CCUG 72691T). The phylogenetic analyses also revealed that Pseudobacter ginsenosidimutans shared over 98 % sequence similarly to members of the genus Pseudoflavitalea . However, the average nucleotide identity value between Pseudoflavitalea rhizosphaerae T16R-265T, the type species of the genus and Pseudobacter ginsenosidimutans Gsoil 221T was 86.8 %. Therefore, we also propose that Pseudobacter ginsenosidimutans be reclassified as Pseudoflavitalea ginsenosidimutans comb. nov.

scholarly journals Genomic Sequence of a Megrivirus Strain Identified in Laying Hens in Brazil

2019 ◽  
Vol 8 (4) ◽  
Author(s):  
Priscilla F. Gerber ◽  
Huigang Shen ◽  
Ying Zheng ◽  
Ganwu Li ◽  
Zélia I. P. Lobato ◽  
...  
Keyword(s):  
Laying Hens ◽  
Genomic Sequence ◽  
Minas Gerais ◽  
Nucleotide Identity ◽  
Fecal Samples ◽  
Commercial Flock ◽  
The Family ◽  
Layer Chickens

A new strain of chicken megrivirus was identified in fecal samples of layer chickens in a commercial flock in Minas Gerais, Brazil. It is most closely related to the family Picornaviridae, genus Megrivirus, species Melegrivirus A, and has an overall nucleotide identity of up to 85.1% with other megrivirus strains.

scholarly journals First Complete Genome Sequence of a Feline Alphacoronavirus 1 Strain from Brazil

2019 ◽  
Vol 8 (10) ◽  
Author(s):  
Bruno de Cássio Veloso de Barros ◽  
Ceyla Maria Oeiras de Castro ◽  
Diego Pereira ◽  
Laila Graziela Ribeiro ◽  
José Wandilson Barboza Duarte Júnior ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Rural Settlement ◽  
Nucleotide Identity ◽  
Domestic Cats ◽  
Santa Barbara ◽  
Fecal Samples ◽  
Content Type ◽  
Feline Coronavirus

We identified a strain of Alphacoronavirus 1, FCoV-SB22, from a pool of fecal samples from domestic cats from a rural settlement in the municipality of Santa Bárbara, Pará, Brazil. The nucleotide identity with feline coronavirus was 91.5%.

scholarly journals A NovelGlaesserellasp. Isolated from Pigs with Severe Respiratory Infections Has a Mosaic Genome with Virulence Factors Putatively Acquired by Horizontal Transfer

2018 ◽  
Vol 84 (11) ◽  
pp. e00092-18 ◽  
Author(s):  
Anne E. Watt ◽  
Glenn F. Browning ◽  
Alistair R. Legione ◽  
Rhys N. Bushell ◽  
Andrew Stent ◽  
...  
Keyword(s):  
Large Scale ◽  
Virulence Genes ◽  
Respiratory Infections ◽  
Genomic Structure ◽  
Genomic Analysis ◽  
Housekeeping Genes ◽  
Toxin Gene ◽  
Diverse Range ◽  
Content Type ◽  
The Family

ABSTRACTAn unknown member of the familyPasteurellaceaewas repeatedly isolated from 20- to 24-week-old pigs with severe pulmonary lesions reared on the same farm in Victoria, Australia. The etiological diagnosis of the disease was inconclusive. The complete genome sequence analysis of one strain, 15-184, revealed some phylogenic proximity toGlaesserella(Haemophilus)parasuis, the cause of Glasser's disease. However, the sequences of the 16S rRNA and housekeeping genes, as well as the average nucleotide identity scores, differed from those of all other known species in the familyPasteurellaceae. The protein content of 15-184 was composite, with 60% of coding sequences matching knownG. parasuisproducts, while more than 20% had a closer relative in the generaActinobacillus,Mannheimia,Pasteurella, andBibersteinia. Several putative virulence genes absent fromG. parasuisbut present in otherPasteurellaceaewere also found, including theapxIIIRTX toxin gene fromActinobacillus pleuropneumoniae, ABC transporters fromActinobacillus minor, and iron transporters from various species. Three prophages and one integrative conjugative element were present in the isolate. Horizontal gene transfers might explain the mosaic genomic structure and atypical metabolic and virulence characteristics of 15-184. This organism has not been assigned a taxonomic position in the family, but this study underlines the need for a large-scale epidemiological and clinical characterization of this novel pathogen in swine populations, as a genomic analysis suggests it could have a severe impact on pig health.IMPORTANCESeveral species ofPasteurellaceaecause a range of significant diseases in pigs. A novel member of this family was recently isolated from Australian pigs suffering from severe respiratory infections. Comparative whole-genome analyses suggest that this bacterium represents a new species, which possesses a number of virulence genes horizontally acquired from a diverse range of otherPasteurellaceae. While the possible contribution of other coinfecting noncultivable agents to the disease has not been ruled out in this study, the repertoire of virulence genes found in this organism may nevertheless explain some aspects of the associated pathology observed on the farm. The prevalence of this novel pathogen within pig populations is currently unknown. This finding is of particular importance for the pig industry, as this organism can have a serious impact on the health of these animals.

scholarly journals Proposed New Strain of Canine Kobuvirus from Fecal Samples of Brazilian Domestic Dogs

2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Bruno de Cássio Veloso Barros ◽  
Ceyla Maria Oeiras Castro ◽  
Diego Pereira ◽  
Laila Graziela Ribeiro ◽  
José Wandilson Barboza Duarte Júnior ◽  
...  
Keyword(s):  
Rural Community ◽  
Domestic Dogs ◽  
Nucleotide Identity ◽  
Fecal Samples ◽  
The Family ◽  
Canine Kobuvirus

A proposed new strain of canine Kobuvirus was identified in fecal samples of domestic dogs from a rural community located in the municipality of Peixe-Boi, Pará, Brazil. The nucleotide identity was 92.3% similar to other representatives of the family Picornaviridae, genus Kobuvirus, and species Aichivirus A, which suggests that this is possibly a new strain within this species.

scholarly journals Genome Dynamics and Molecular Infection Epidemiology of Multidrug-Resistant Helicobacter pullorum Isolates Obtained from Broiler and Free-Range Chickens in India

2016 ◽  
Vol 83 (1) ◽  
Author(s):  
Shamsul Qumar ◽  
Mohammad Majid ◽  
Narender Kumar ◽  
Sumeet K. Tiwari ◽  
Torsten Semmler ◽  
...  
Keyword(s):  
Broiler Chicken ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Comparative Genomic Analysis ◽  
Resistant Bacteria ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Multidrug Resistant Bacteria ◽  
Content Type ◽  
Free Range

ABSTRACT Some life-threatening, foodborne, and zoonotic infections are transmitted through poultry birds. Inappropriate and indiscriminate use of antimicrobials in the livestock industry has led to an increased prevalence of multidrug-resistant bacteria with epidemic potential. Here, we present a functional molecular epidemiological analysis entailing the phenotypic and whole-genome sequence-based characterization of 11 H. pullorum isolates from broiler and free-range chickens sampled from retail wet markets in Hyderabad City, India. Antimicrobial susceptibility tests revealed all of the isolates to be resistant to multiple antibiotic classes such as fluoroquinolones, cephalosporins, sulfonamides, and macrolides. The isolates were also found to be extended-spectrum β-lactamase producers and were even resistant to clavulanic acid. Whole-genome sequencing and comparative genomic analysis of these isolates revealed the presence of five or six well-characterized antimicrobial resistance genes, including those encoding a resistance-nodulation-division efflux pump(s). Phylogenetic analysis combined with pan-genome analysis revealed a remarkable degree of genetic diversity among the isolates from free-range chickens; in contrast, a high degree of genetic similarity was observed among broiler chicken isolates. Comparative genomic analysis of all publicly available H. pullorum genomes, including our isolates (n = 16), together with the genomes of 17 other Helicobacter species, revealed a high number (8,560) of H. pullorum-specific protein-encoding genes, with an average of 535 such genes per isolate. In silico virulence screening identified 182 important virulence genes and also revealed high strain-specific gene content in isolates from free-range chickens (average, 34) compared to broiler chicken isolates. A significant prevalence of prophages (ranging from 1 to 9) and a significant presence of genomic islands (0 to 4) were observed in free-range and broiler chicken isolates. Taken together, these observations provide significant baseline data for functional molecular infection epidemiology of nonpyloric Helicobacter species such as H. pullorum by unraveling their evolution in chickens and their possible zoonotic transmission to humans. IMPORTANCE Globally, the poultry industry is expanding with an ever-growing consumer base for chicken meat. Given this, food-associated transmission of multidrug-resistant bacteria represents an important health care issue. Our study involves a critical baseline approach directed at genome sequence-based epidemiology and transmission dynamics of H. pullorum, a poultry pathogen having established zoonotic potential. We believe our studies would facilitate the development of surveillance systems that ensure the safety of food for humans and guide public health policies related to the use of antibiotics in animal feed in countries such as India. We sequenced 11 new genomes of H. pullorum as a part of this study. These genomes would provide much value in addition to the ongoing comparative genomic studies of helicobacters.

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