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Holman DB, Gzyl KE, Kommadath A. The gut microbiome and resistome of conventionally vs. pasture-raised pigs. Microb Genom 2023; 9:mgen001061. [PMID: 37439777 PMCID: PMC10438820 DOI: 10.1099/mgen.0.001061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/12/2023] [Indexed: 07/14/2023] Open
Abstract
Conventional swine production typically houses pigs indoors and in large groups, whereas pasture-raised pigs are reared outdoors at lower stocking densities. Antimicrobial use also differs, with conventionally raised pigs often being exposed to antimicrobials directly or indirectly to control and prevent infectious disease. However, antimicrobial use can be associated with the development and persistence of antimicrobial resistance. In this study, we used shotgun metagenomic sequencing to compare the gut microbiomes and resistomes of pigs raised indoors on a conventional farm with those raised outdoors on pasture. The microbial compositions as well as the resistomes of both groups of pigs were significantly different from each other. Bacterial species such as Intestinibaculum porci, Pseudoscardovia radai and Sharpea azabuensis were relatively more abundant in the gut microbiomes of pasture-raised pigs and Hallella faecis and Limosilactobacillus reuteri in the conventionally raised swine. The abundance of antimicrobial resistance genes (ARGs) was significantly higher in the conventionally raised pigs for nearly all antimicrobial classes, including aminoglycosides, beta-lactams, macrolides-lincosamides-streptogramin B, and tetracyclines. Functionally, the gut microbiomes of the two group of pigs also differed significantly based on their carbohydrate-active enzyme (CAZyme) profiles, with certain CAZyme families associated with host mucin degradation enriched in the conventional pig microbiomes. We also recovered 1043 dereplicated strain-level metagenome-assembled genomes (≥90 % completeness and <5 % contamination) to provide taxonomic context for specific ARGs and metabolic functions. Overall, the study provides insights into the differences between the gut microbiomes and resistomes of pigs raised under two very different production systems.
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Affiliation(s)
- Devin B. Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Lacombe, AB, T4L1W1, Canada
| | - Katherine E. Gzyl
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Lacombe, AB, T4L1W1, Canada
| | - Arun Kommadath
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Lacombe, AB, T4L1W1, Canada
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2
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Bajagai YS, Petranyi F, J Yu S, Lobo E, Batacan R, Kayal A, Horyanto D, Ren X, M Whitton M, Stanley D. Phytogenic supplement containing menthol, carvacrol and carvone ameliorates gut microbiota and production performance of commercial layers. Sci Rep 2022; 12:11033. [PMID: 35773309 PMCID: PMC9246849 DOI: 10.1038/s41598-022-14925-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 06/15/2022] [Indexed: 11/17/2022] Open
Abstract
Consumer push towards open and free-range production systems makes biosecurity on farms challenging, leading to increased disease and animal welfare issues. Phytogenic products are increasingly becoming a viable alternative for the use of antibiotics in livestock production. Here we present a study of the effects of commercial phytogenic supplement containing menthol, carvacrol and carvone on intestinal microbiota of layer hens, microbial functional capacity, and intestinal morphology. A total of 40,000 pullets were randomly assigned to two sides of the experimental shed. Growth performance, mortality, egg production and egg quality parameters were recorded throughout the trial period (18–30 weeks of age). Microbial community was investigated using 16S amplicon sequencing and functional difference using metagenomic sequencing. Phytogen supplemented birds had lower mortality and number of dirty eggs, and their microbial communities showed reduced richness. Although phytogen showed the ability to control the range of poultry pathogens, its action was not restricted to pathogenic taxa, and it involved functional remodelling the intestinal community towards increased cofactor production, heterolactic fermentation and salvage and recycling of metabolites. The phytogen did not alter the antimicrobial resistance profile or the number of antibiotic resistance genes. The study indicates that phytogenic supplementation can mimic the action of antibiotics in altering the gut microbiota and be used as their alternative in industry-scale layer production.
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Affiliation(s)
- Yadav S Bajagai
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Friedrich Petranyi
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Sung J Yu
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Edina Lobo
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Romeo Batacan
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Advait Kayal
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Darwin Horyanto
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Xipeng Ren
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Maria M Whitton
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Dragana Stanley
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia.
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3
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Amin N, Schwarzkopf S, Kinoshita A, Tröscher-Mußotter J, Dänicke S, Camarinha-Silva A, Huber K, Frahm J, Seifert J. Evolution of rumen and oral microbiota in calves is influenced by age and time of weaning. Anim Microbiome 2021; 3:31. [PMID: 33883031 PMCID: PMC8059317 DOI: 10.1186/s42523-021-00095-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/04/2021] [Indexed: 01/04/2023] Open
Abstract
Background The rumen bacterial communities are changing dynamically throughout the first year of calf’s life including the weaning period as a critical event. Rumen microbiome analysis is often limited to invasive rumen sampling procedures but the oral cavity of ruminants is expected to harbour rumen microbes due to regurgitation activity. The present study used buccal swab samples to define the rumen core microbiome and characterize the shifts in rumen and oral microbial communities occurring as result of calf’s age as well as time of weaning. Results Buccal swab samples of 59 calves were collected along the first 140 days of life and compared to stomach tubing sample of the rumen at day 140. Animals were randomly divided into two weaning groups. Microbiota of saliva and rumen content was analysed by 16S rRNA gene amplicon sequencing. Our study showed that most rumen-specific bacterial taxa were equally observed in rumen samples as well as in the buccal swabs, though relative abundance varied. The occurrence of rumen-specific OTUs in buccal swab samples increased approximately 1.7 times from day 70 to day 140, indicating the gradual development of rumen as calf aged. The rumen-specific bacterial taxa diversity increased, and inter-animal variations decreased with age. Early weaning (7 weeks of age) rapidly increased the rumen microbial diversity from pre- to post-weaned state. Rumen microbiota of early-weaned calves seemed to have a suppressed growth of starch- and carbohydrate-utilizing bacteria and increased fibre degraders. Whereas, in late-weaned calves (17 weeks of age) no impact of dietary modifications on rumen microbiota composition was observed after weaning. Oral-specific bacterial community composition was significantly affected by calf’s age and time of weaning. Conclusions The present study showed the significant impact of calf’s age and weaning on the establishment of rumen- and oral-specific bacterial communities utilizing buccal swab samples. The results emphasize the possibility of using buccal swab samples as a replacement of complex stomach tube method for large-scale predictive studies on ruminants. For in-depth rumen microbiome studies, the time of sampling should be carefully considered using an active phase of regurgitation. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00095-3.
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Affiliation(s)
- Nida Amin
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany
| | - Sarah Schwarzkopf
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany
| | - Asako Kinoshita
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany.,Institute of Animal Nutrition, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Bundesallee 37, 38116, Braunschweig, Germany
| | - Johanna Tröscher-Mußotter
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany
| | - Sven Dänicke
- Institute of Animal Nutrition, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Bundesallee 37, 38116, Braunschweig, Germany
| | - Amélia Camarinha-Silva
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany
| | - Korinna Huber
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany
| | - Jana Frahm
- Institute of Animal Nutrition, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Bundesallee 37, 38116, Braunschweig, Germany
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany.
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4
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Killer J, Mekadim C, Bunešová V, Mrázek J, Hroncová Z, Vlková E. Glutamine synthetase type I (glnAI) represents a rewarding molecular marker in the classification of bifidobacteria and related genera. Folia Microbiol (Praha) 2019; 65:143-151. [PMID: 31069634 DOI: 10.1007/s12223-019-00716-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/29/2019] [Indexed: 01/01/2023]
Abstract
The family Bifidobacteriaceae constitutes an important phylogenetic group that particularly includes bifidobacterial taxa demonstrating proven or debated positive effects on host health. The increasingly widespread application of probiotic cultures in the twenty-first century requires detailed classification to the level of particular strains. This study aimed to apply the glutamine synthetase class I (glnAI) gene region (717 bp representing approximately 50% of the entire gene sequence) using specific PCR primers for the classification, typing, and phylogenetic analysis of bifidobacteria and closely related scardovial genera. In the family Bifidobacteriaceae, this is the first report on the use of this gene for such purposes. To achieve high-value results, almost all valid Bifidobacteriaceae type strains (75) and 15 strains isolated from various environments were evaluated. The threshold value of the glnAI gene identity among Bifidobacterium species (86.9%) was comparable to that of other phylogenetic/identification markers proposed for bifidobacteria and was much lower compared to the 16S rRNA gene. Further statistical and phylogenetic analyses suggest that the glnAI gene can be applied as a novel genetic marker in the classification, genotyping, and phylogenetic analysis of isolates belonging to the family Bifidobacteriaceae.
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Affiliation(s)
- Jiří Killer
- Institute of Animal Physiology and Genetics, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Krč, Czechia. .,Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague 6, Suchdol, Czechia.
| | - Chahrazed Mekadim
- Institute of Animal Physiology and Genetics, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Krč, Czechia.,Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague 6, Suchdol, Czechia
| | - Věra Bunešová
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague 6, Suchdol, Czechia
| | - Jakub Mrázek
- Institute of Animal Physiology and Genetics, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Krč, Czechia
| | - Zuzana Hroncová
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague 6, Suchdol, Czechia
| | - Eva Vlková
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague 6, Suchdol, Czechia
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5
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Killer J, Mekadim C, Pechar R, Bunešová V, Vlková E. The threonine-tRNA ligase gene region is applicable in classification, typing, and phylogenetic analysis of bifidobacteria. J Microbiol 2018; 56:713-721. [DOI: 10.1007/s12275-018-8167-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 11/27/2022]
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6
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Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M. Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 2018; 9:2007. [PMID: 30186281 PMCID: PMC6113628 DOI: 10.3389/fmicb.2018.02007] [Citation(s) in RCA: 414] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022] Open
Abstract
The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Rüdiger Pukall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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7
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Killer J, Mekadim C, Pechar R, Bunešová V, Mrázek J, Vlková E. Gene encoding the CTP synthetase as an appropriate molecular tool for identification and phylogenetic study of the family Bifidobacteriaceae. Microbiologyopen 2018; 7:e00579. [PMID: 29356451 PMCID: PMC6079163 DOI: 10.1002/mbo3.579] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/04/2017] [Accepted: 12/07/2017] [Indexed: 02/02/2023] Open
Abstract
An alternative molecular marker with respect to the 16S rRNA gene demonstrating better identification and phylogenetic parameters has not been designed for the whole Bifidobacteriaceae family, which includes the genus Bifidobacterium and scardovial genera. Therefore, the aim of the study was to find such a gene in available genomic sequences, suggest appropriate means and conditions for asmplification and sequencing of the desired region of the selected gene in various strains of the bacterial family and verify the importance in classification and phylogeny. Specific primers flanking the variable region (~800 pb) within the pyrG gene encoding the CTP synthetase were designed by means of gene sequences retrieved from the genomes of strains belonging to the family Bifidobacteriaceae. The functionality and specificity of the primers were subsequently tested on the wild (7) and type strains of bifidobacteria (36) and scardovia (7). Comparative and phylogenetic studies based on obtained sequences revealed actual significance in classification and phylogeny of the Bifidobacteriaceae family. Gene statistics (percentages of mean sequence similarities and identical sites, mean number of nucleotide differences, P- and K-distances) and phylogenetic analyses (congruence between tree topologies, percentages of bootstrap values >50 and 70%) indicate that the pyrG gene represents an alternative identification and phylogenetic marker exhibiting higher discriminatory power among strains, (sub)species, and genera than the 16S rRNA gene. Sequences of the particular gene fragment, simply achieved through specific primers, enable more precisely to classify and evaluate phylogeny of the family Bifidobacteriaceae including, with some exceptions, health-promoting probiotic bacteria.
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Affiliation(s)
- Jiří Killer
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Prague 4 - Krč, Czechia.,Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Prague 6 - Suchdol, Czechia
| | - Chahrazed Mekadim
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Prague 6 - Suchdol, Czechia
| | - Radko Pechar
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Prague 6 - Suchdol, Czechia
| | - Věra Bunešová
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Prague 6 - Suchdol, Czechia
| | - Jakub Mrázek
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Prague 4 - Krč, Czechia
| | - Eva Vlková
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Prague 6 - Suchdol, Czechia
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8
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Characterization of a xylanolytic bacterial strain C10 isolated from the rumen of a red deer (Cervus elaphus) closely related of the recently described species Actinomyces succiniciruminis, A. glycerinitolerans, and A. ruminicola. Folia Microbiol (Praha) 2017; 63:391-399. [DOI: 10.1007/s12223-017-0577-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 12/08/2017] [Indexed: 10/18/2022]
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9
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Sechovcová H, Killer J, Pechar R, Geigerová M, Švejstil R, Salmonová H, Mekadim C, Rada V, Vlková E, Kofroňová O, Benada O. Alloscardovia venturai sp. nov., a fructose 6-phosphate phosphoketolase-positive species isolated from the oral cavity of a guinea-pig (Cavia aperea f. porcellus). Int J Syst Evol Microbiol 2017; 67:2842-2847. [PMID: 28820091 DOI: 10.1099/ijsem.0.002031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A slightly irregular, short rod-shaped bacterial strain, MOZIV/2T, showing activity of fructose 6-phosphate phosphoketolase was isolated from the oral cavity of a home-bred guinea-pig. Based on comparative 16S rRNA gene sequence analyses, its closest relatives were Alloscardovia omnicolens DSM 21503T and Alloscardovia criceti DSM 17774T with 96.0 and 95.6 % pairwise similarities, respectively. Completeness of the compared sequences was 97.3 and 96.9 %, respectively. Growth was found only under anaerobic conditions. Activities of α- and β-gluco(galacto)sidases were detected in strain MOZIV/2T, which is characteristic for almost all members of the family Bifidobacteriaceae. Sequencing of other molecular markers (fusA, gyrB and xfp) revealed low gene sequence similarities to A. omnicolens DSM 21503T ranging from 72.7 to 87.5 %. Strain MOZIV/2T differed from other species within the genus Alloscardovia by the presence of C18 : 1ω9t. In addition, much higher proportions of C8 : 0, C11 : 0, C12 : 0, C14 : 1, C16 : 1 and C17 : 0 fatty acids were found in cells of strain MOZIV/2T. The peptidoglycan structure was of type A4α [l-Lys(l-Orn)-d-Asp], which is consistent with its classification within the genus Alloscardovia. The DNA G+C content (45.8 mol%) was lower than those found in other alloscardovia. Phylogenetic studies and evaluation of phenotypic characteristics including the results of biochemical, physiological and chemotaxonomic analyses confirmed the novel species status for strain MOZIV/2T, for which the name Alloscardovia venturai sp. nov. is proposed. The type strain is MOZIV/2T (=DSM 100237T=CCM 8604T=LMG 28781T).
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Affiliation(s)
- Hana Sechovcová
- Institute of Animal Physiology and Genetics v.v.i., Czech Academy of Sciences, v.v.i., Vídeňská 1083, Prague 4 - Krč, 142 20, Czech Republic
| | - Jiri Killer
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 - Suchdol, 16500, Czech Republic.,Institute of Animal Physiology and Genetics v.v.i., Czech Academy of Sciences, v.v.i., Vídeňská 1083, Prague 4 - Krč, 142 20, Czech Republic
| | - Radko Pechar
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 - Suchdol, 16500, Czech Republic
| | - Martina Geigerová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 - Suchdol, 16500, Czech Republic
| | - Roman Švejstil
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 - Suchdol, 16500, Czech Republic
| | - Hana Salmonová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 - Suchdol, 16500, Czech Republic
| | - Chahrazed Mekadim
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 - Suchdol, 16500, Czech Republic
| | - Vojtěch Rada
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 - Suchdol, 16500, Czech Republic
| | - Eva Vlková
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 - Suchdol, 16500, Czech Republic
| | - Olga Kofroňová
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Oldřich Benada
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic.,Department of Biology, Faculty of Science, J. E. Purkyně University in Ústí nad Labem, Za Válcovnou 1000/8, 400 96 Ústí nad Labem, Czech Republic
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10
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Killer J, Pechar R, Švec P, Salmonová H, Švejstil R, Geigerová M, Rada V, Vlková E, Mekadim C. Lactobacillus caviae sp. nov., an obligately heterofermentative bacterium isolated from the oral cavity of a guinea pig (Cavia aperea f. porcellus). Int J Syst Evol Microbiol 2017; 67:2903-2909. [DOI: 10.1099/ijsem.0.002044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Jiri Killer
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
- Institute of Animal Physiology and Genetics v.v.i., Czech Academy of Sciences, Vídeňská 1083, Prague 4 – Krč, 142 20, Czech Republic
| | - Radko Pechar
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
- Food Research Institute Prague, Radiová 1285/7, Prague 10 – Hostivař, 102 00, Czech Republic
| | - Pavel Švec
- Department of Experimental Biology, Czech Collection of Microorganisms, Masaryk University, Faculty of Science, Kamenice 5, 625 00 Brno, Czech Republic
| | - Hana Salmonová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - Roman Švejstil
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - Martina Geigerová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - Vojtěch Rada
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - Eva Vlková
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - Chahrazed Mekadim
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
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Pechar R, Killer J, Mekadim C, Geigerová M, Rada V. Classification of Culturable Bifidobacterial Population from Colonic Samples of Wild Pigs (Sus scrofa) Based on Three Molecular Genetic Methods. Curr Microbiol 2017; 74:1324-1331. [PMID: 28756573 DOI: 10.1007/s00284-017-1320-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/25/2017] [Indexed: 12/24/2022]
Abstract
Occurrence of bifidobacteria, known as health-promoting probiotic microorganisms, in the digestive tract of wild pigs (Sus scrofa) has not been examined yet. One hundred forty-nine fructose-6-phosphate phosphoketolase positive bacterial strains were isolated from colonic content of twenty-two individuals of wild pigs originated from four localities in the Czechia. Based on PCR-DGGE technique targeting the variable V3 region of the 16S rRNA genes, strains were initially differentiated into four groups represented by: (i) probably a new Bifidobacterium species (89 strains), (ii) B. boum/B. thermophilum/B. thermacidophilum subsp. porcinum/B. thermacidophilum subsp. thermacidophilum (sub)species (49 strains), (iii) Pseudoscardovia suis (7 strains), and (iv) B. pseudolongum subsp. globosum/B. pseudolongum subsp. pseudolongum (4 strains), respectively. Given the fact that DGGE technique did not allow to differentiate the representatives of thermophilic bifidobacteria and B. pseudolongum subspecies, strains were further classified by the 16S rRNA and thrS gene sequences. Primers targeting the variable regions of the latter gene were designed to be applicable in identification and phylogeny of Bifidobacteriaceae family. The 16S rRNA-derived phylogenetic study classified members of the first group into five subgroups in a separated cluster of thermophilic bifidobacteria. Comparable results were obtained by the thrS-derived phylogenetic analysis. Remarkably, variability among thrS sequences was higher compared with 16S rRNA gene sequences. Overall, molecular genetic techniques application allowed to identify a new Bifidobacterium phylotype which is predominant in the digestive tract of examined wild pigs.
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Affiliation(s)
- Radko Pechar
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic.,Food Research Institute Prague, Radiová 1285/7, Hostivař, 102 00, Prague 10, Czech Republic
| | - Jiří Killer
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic. .,Institute of Animal Physiology and Genetics v.v.i, Czech Academy of Sciences, Vídeňská 1083, Krč, 142 20, Prague 4, Czech Republic.
| | - Chahrazed Mekadim
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
| | - Martina Geigerová
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
| | - Vojtěch Rada
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
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12
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Pechar R, Killer J, Švejstil R, Salmonová H, Geigerová M, Bunešová V, Rada V, Benada O. Galliscardovia ingluviei gen. nov., sp. nov., a thermophilic bacterium of the family Bifidobacteriaceae isolated from the crop of a laying hen (Gallus gallus f. domestica). Int J Syst Evol Microbiol 2017; 67:2403-2411. [DOI: 10.1099/ijsem.0.001972] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- R. Pechar
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - J. Killer
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 – Krč, 142 20, Czech Republic
| | - R. Švejstil
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - H. Salmonová
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - M. Geigerová
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - V. Bunešová
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - V. Rada
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - O. Benada
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
- Department of Biology, Faculty of Science, J. E. Purkyně University in Ústí nad Labem, Za Válcovnou 1000/8, 400 96 Ústí nad Labem, Czech Republic
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Pechar R, Killer J, Salmonová H, Geigerová M, Švejstil R, Švec P, Sedláček I, Rada V, Benada O. Bifidobacterium apri sp. nov., a thermophilic actinobacterium isolated from the digestive tract of wild pigs (Sus scrofa). Int J Syst Evol Microbiol 2017; 67:2349-2356. [DOI: 10.1099/ijsem.0.001956] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- R. Pechar
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - J. Killer
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 – Krč, 142 20, Czech Republic
| | - H. Salmonová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - M. Geigerová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - R. Švejstil
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - P. Švec
- Czech Collection of Microorganisms, Masaryk University, Faculty of Science, Kamenice 5, building A25, 625 00, Brno, Czech Republic
| | - I. Sedláček
- Czech Collection of Microorganisms, Masaryk University, Faculty of Science, Kamenice 5, building A25, 625 00, Brno, Czech Republic
| | - V. Rada
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - O. Benada
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
- Department of Biology, Faculty of Science, J. E. Purkyně University in Ústi nad Labem, Za Válcovnou 1000/8, 400 96 Ústí nad Labem, Czech Republic
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Modesto M, Michelini S, Stefanini I, Sandri C, Spiezio C, Pisi A, Filippini G, Biavati B, Mattarelli P. Bifidobacterium lemurum sp. nov., from faeces of the ring-tailed lemur (Lemur catta). Int J Syst Evol Microbiol 2015; 65:1726-1734. [PMID: 25736415 DOI: 10.1099/ijs.0.000162] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four Gram-positive-staining, microaerophilic, non-spore-forming, fructose-6-phosphate phosphoketolase-positive bacterial strains were isolated from a faecal sample of a 5-year-old ring-tailed lemur (Lemur catta). The strains showed a peculiar morphology, resembling a small coiled snake, a ring shape, or forming a little 'Y' shape. The isolated strains appeared identical, and LMC 13T was chosen as a representative strain and characterized further. Strain LMC 13T showed an A3β peptidoglycan type, similar to that found in Bifidobacterium longum. The DNA base composition was 57.2 mol% G+C. Almost-complete 16S rRNA, hsp60, rpoB, dnaJ, dnaG, purF, clpC and rpoC gene sequences were obtained, and phylogenetic relationships were determined. Comparative analysis of 16S rRNA gene sequences showed that strain LMC 13T showed the highest similarity to B. longum subsp. suis ATCC 27533T (96.65 %) and Bifidobacterium saguini DSM 23967T (96.64 %). Strain LMC 13T was located in an actinobacterial cluster and was more closely related to the genus Bifidobacteriumthan to other genera in the Bifidobacteriaceae. On the basis of these results, strain LMC 13T represents a novel species within the genus Bifidobacterium, for which the name Bifidobacterium lemurum sp. nov. is proposed; the type strain is LMC 13T ( = DSM 28807T = JCM 30168T).
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Affiliation(s)
- Monica Modesto
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Samanta Michelini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Ilaria Stefanini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Camillo Sandri
- Natura Viva Garda Zoological Park S.r.l, Bussolengo, Verona, Italy
| | - Caterina Spiezio
- Natura Viva Garda Zoological Park S.r.l, Bussolengo, Verona, Italy
| | - Annamaria Pisi
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | | | - Bruno Biavati
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Paola Mattarelli
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
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