101
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Albert K, Rani A, Sela DA. The comparative genomics of Bifidobacterium callitrichos reflects dietary carbohydrate utilization within the common marmoset gut. Microb Genom 2018; 4. [PMID: 29906260 PMCID: PMC6096940 DOI: 10.1099/mgen.0.000183] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bifidobacterium is a diverse genus of anaerobic, saccharolytic bacteria that colonize many animals, notably humans and other mammals. The presence of these bacteria in the gastrointestinal tract represents a potential coevolution between the gut microbiome and its mammalian host mediated by diet. To study the relationship between bifidobacterial gut symbionts and host nutrition, we analyzed the genome of two bifidobacteria strains isolated from the feces of a common marmoset (Callithrix jacchus), a primate species studied for its ability to subsist on host-indigestible carbohydrates. Whole genome sequencing identified these isolates as unique strains of Bifidobacterium callitrichos. All three strains, including these isolates and the previously described type strain, contain genes that may enable utilization of marmoset dietary substrates. These include genes predicted to contribute to galactose, arabinose, and trehalose metabolic pathways. In addition, significant genomic differences between strains suggest that bifidobacteria possess distinct roles in carbohydrate metabolism within the same host. Thus, bifidobacteria utilize dietary components specific to their host, both humans and non-human primates alike. Comparative genomics suggests conservation of possible coevolutionary relationships within the primate clade.
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Affiliation(s)
- Korin Albert
- 1Department of Food Science, University of Massachusetts, Amherst, MA, USA.,2Molecular and Cellular Biology Program, University of Massachusetts, Amherst, MA, USA
| | - Asha Rani
- 1Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - David A Sela
- 1Department of Food Science, University of Massachusetts, Amherst, MA, USA.,2Molecular and Cellular Biology Program, University of Massachusetts, Amherst, MA, USA.,3Department of Microbiology, University of Massachusetts, Amherst, MA, USA.,4Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
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102
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UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280-285. [PMID: 29492869 DOI: 10.1007/s12275-018-8014-6] [Citation(s) in RCA: 907] [Impact Index Per Article: 151.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/27/2018] [Accepted: 01/28/2018] [Indexed: 10/17/2022]
Abstract
Genome-based phylogeny plays a central role in the future taxonomy and phylogenetics of Bacteria and Archaea by replacing 16S rRNA gene phylogeny. The concatenated core gene alignments are frequently used for such a purpose. The bacterial core genes are defined as single-copy, homologous genes that are present in most of the known bacterial species. There have been several studies describing such a gene set, but the number of species considered was rather small. Here we present the up-to-date bacterial core gene set, named UBCG, and software suites to accommodate necessary steps to generate and evaluate phylogenetic trees. The method was successfully used to infer phylogenomic relationship of Escherichia and related taxa and can be used for the set of genomes at any taxonomic ranks of Bacteria. The UBCG pipeline and file viewer are freely available at https://www.ezbiocloud.net/tools/ubcg and https://www.ezbiocloud.net/tools/ubcg_viewer , respectively.
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103
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Schmid M, Muri J, Melidis D, Varadarajan AR, Somerville V, Wicki A, Moser A, Bourqui M, Wenzel C, Eugster-Meier E, Frey JE, Irmler S, Ahrens CH. Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level. Front Microbiol 2018; 9:63. [PMID: 29441050 PMCID: PMC5797582 DOI: 10.3389/fmicb.2018.00063] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/10/2018] [Indexed: 11/20/2022] Open
Abstract
Although complete genome sequences hold particular value for an accurate description of core genomes, the identification of strain-specific genes, and as the optimal basis for functional genomics studies, they are still largely underrepresented in public repositories. Based on an assessment of the genome assembly complexity for all lactobacilli, we used Pacific Biosciences' long read technology to sequence and de novo assemble the genomes of three Lactobacillus helveticus starter strains, raising the number of completely sequenced strains to 12. The first comparative genomics study for L. helveticus—to our knowledge—identified a core genome of 988 genes and sets of unique, strain-specific genes ranging from about 30 to more than 200 genes. Importantly, the comparison of MiSeq- and PacBio-based assemblies uncovered that not only accessory but also core genes can be missed in incomplete genome assemblies based on short reads. Analysis of the three genomes revealed that a large number of pseudogenes were enriched for functional Gene Ontology categories such as amino acid transmembrane transport and carbohydrate metabolism, which is in line with a reductive genome evolution in the rich natural habitat of L. helveticus. Notably, the functional Clusters of Orthologous Groups of proteins categories “cell wall/membrane biogenesis” and “defense mechanisms” were found to be enriched among the strain-specific genes. A genome mining effort uncovered examples where an experimentally observed phenotype could be linked to the underlying genotype, such as for cell envelope proteinase PrtH3 of strain FAM8627. Another possible link identified for peptidoglycan hydrolases will require further experiments. Of note, strain FAM22155 did not harbor a CRISPR/Cas system; its loss was also observed in other L. helveticus strains and lactobacillus species, thus questioning the value of the CRISPR/Cas system for diagnostic purposes. Importantly, the complete genome sequences proved to be very useful for the analysis of natural whey starter cultures with metagenomics, as a larger percentage of the sequenced reads of these complex mixtures could be unambiguously assigned down to the strain level.
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Affiliation(s)
- Michael Schmid
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Jonathan Muri
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | - Damianos Melidis
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | - Adithi R Varadarajan
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Vincent Somerville
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Adrian Wicki
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | - Aline Moser
- Agroscope, Research Group Biochemistry of Milk and Microorganisms, Bern, Switzerland
| | - Marc Bourqui
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Claudia Wenzel
- Agroscope, Research Group Biochemistry of Milk and Microorganisms, Bern, Switzerland
| | - Elisabeth Eugster-Meier
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Juerg E Frey
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | - Stefan Irmler
- Agroscope, Research Group Biochemistry of Milk and Microorganisms, Bern, Switzerland
| | - Christian H Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,Swiss Institute of Bioinformatics, Wädenswil, Switzerland
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104
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Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461-466. [PMID: 29292687 DOI: 10.1099/ijsem.0.002516] [Citation(s) in RCA: 2123] [Impact Index Per Article: 353.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Advancement of DNA sequencing technology allows the routine use of genome sequences in the various fields of microbiology. The information held in genome sequences proved to provide objective and reliable means in the taxonomy of prokaryotes. Here, we describe the minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes.
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Affiliation(s)
- Jongsik Chun
- Department of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Henrik Christensen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David Ruiz Arahal
- Departamento de Microbiología y Ecología, and Colección Española de Cultivos Tipo (CECT), Universitat de València, València, Spain
| | - Milton S da Costa
- Center for Neurosciences and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Alejandro P Rooney
- U.S. Department of Agriculture, Agricultural Research Service, Crop Bioprotection Research Unit, Peoria, IL 61604, USA
| | - Hana Yi
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea
| | - Xue-Wei Xu
- Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Sofie De Meyer
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA, Australia
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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105
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On SLW, Miller WG, Houf K, Fox JG, Vandamme P. Minimal standards for describing new species belonging to the families Campylobacteraceae and Helicobacteraceae: Campylobacter, Arcobacter, Helicobacter and Wolinella spp. Int J Syst Evol Microbiol 2017; 67:5296-5311. [PMID: 29034857 PMCID: PMC5845751 DOI: 10.1099/ijsem.0.002255] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/24/2017] [Indexed: 01/25/2023] Open
Abstract
Ongoing changes in taxonomic methods, and in the rapid development of the taxonomic structure of species assigned to the Epsilonproteobacteria have lead the International Committee of Systematic Bacteriology Subcommittee on the Taxonomy of Campylobacter and Related Bacteria to discuss significant updates to previous minimal standards for describing new species of Campylobacteraceae and Helicobacteraceae. This paper is the result of these discussions and proposes minimum requirements for the description of new species belonging to the families Campylobacteraceae and Helicobacteraceae, thus including species in Campylobacter, Arcobacter, Helicobacter, and Wolinella. The core underlying principle remains the use of appropriate phenotypic and genotypic methods to characterise strains sufficiently so as to effectively and unambiguously determine their taxonomic position in these families, and provide adequate means by which the new taxon can be distinguished from extant species and subspecies. This polyphasic taxonomic approach demands the use of appropriate reference data for comparison to ensure the novelty of proposed new taxa, and the recommended study of at least five strains to enable species diversity to be assessed. Methodological approaches for phenotypic and genotypic (including whole-genome sequence comparisons) characterisation are recommended.
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Affiliation(s)
- Stephen L. W. On
- Department of Wine, Food and Molecular Biosciences, Lincoln University, PO Box 85084, Lincoln, New Zealand
| | - William G. Miller
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Albany, CA, USA
| | - Kurt Houf
- Department of Veterinary Public Health, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- Department of Biochemistry and Microbiology, Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - James G. Fox
- Department of Comparative Medicine, Massachusetts Institute of Technology, 77, Massachusetts Avenue, Cambiridge, MA 02139, USA
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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106
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Wurdack M, Polidori C, Keller A, Feldhaar H, Schmitt T. Release from prey preservation behavior via prey switch allowed diversification of cuticular hydrocarbon profiles in digger wasps. Evolution 2017; 71:2562-2571. [PMID: 28791674 DOI: 10.1111/evo.13322] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 07/22/2017] [Accepted: 07/26/2017] [Indexed: 11/30/2022]
Abstract
The cuticle of insects is covered by a layer of hydrocarbons (CHC), whose original function is the protection from desiccation and pathogens. However, in most insects CHC profiles are species specific. While this variability among species was largely linked to communication and recognition functions, additional selective forces may shape insect CHC profiles. Here, we show that in Philanthinae digger wasps (Crabronidae) the CHC profile coevolved with a peculiar brood-care strategy. In particular, we found that the behavior to embalm prey stored in the nest with hydrocarbons is adaptive to protect larval food from fungi in those species hunting for Hymenoptera. The prey embalming secretion is identical in composition to the alkene-dominated CHC profile in these species, suggesting that their profile is adaptively conserved for this purpose. In contrast, prey embalming is not required in those species that switched to Coleoptera as prey. Released from this chemical brood-care strategy, Coleoptera-hunting species considerably diversified their CHC profiles. Differential needs to successfully protect prey types used as larval food have thus driven the diversification of CHCs profiles of female Philanthinae wasps. To the best of our knowledge, this is the first evidence of a direct link between selection pressure for food preservation and CHC diversity.
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Affiliation(s)
- Mareike Wurdack
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany.,Department of Evolutionary Biology and Animal Ecology, University of Freiburg, Hauptstrasse 1, D-79114 Freiburg, Germany
| | - Carlo Polidori
- Institute of Environmental Sciences (ICAM), University of Castilla-La Mancha, Avenida Carlos III, s/n; E-45071 Toledo, Spain
| | - Alexander Keller
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany.,Center for Computational and Theoretical Biology, Campus Nord, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Heike Feldhaar
- Department of Animal Ecology I, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, D-95440 Bayreuth, Germany
| | - Thomas Schmitt
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
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107
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Sablok G, Rosselli R, Seeman T, van Velzen R, Polone E, Giacomini A, La Porta N, Geurts R, Muresu R, Squartini A. Draft Genome Sequence of the Nitrogen-Fixing Rhizobium sullae Type Strain IS123 T Focusing on the Key Genes for Symbiosis with its Host Hedysarum coronarium L. Front Microbiol 2017; 8:1348. [PMID: 28798728 PMCID: PMC5526965 DOI: 10.3389/fmicb.2017.01348] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/03/2017] [Indexed: 11/24/2022] Open
Abstract
The prominent feature of rhizobia is their molecular dialogue with plant hosts. Such interaction is enabled by the presence of a series of symbiotic genes encoding for the synthesis and export of signals triggering organogenetic and physiological responses in the plant. The genome of the Rhizobium sullae type strain IS123T nodulating the legume Hedysarum coronarium, was sequenced and resulted in 317 scaffolds for a total assembled size of 7,889,576 bp. Its features were compared with those of genomes from rhizobia representing an increasing gradient of taxonomical distance, from a conspecific isolate (Rhizobium sullae WSM1592), to two congeneric cases (Rhizobium leguminosarum bv. viciae and Rhizobium etli) and up to different genera within the legume-nodulating taxa. The host plant is of agricultural importance, but, unlike the majority of other domesticated plant species, it is able to survive quite well in the wild. Data showed that that the type strain of R. sullae, isolated from a wild host specimen, is endowed with a richer array of symbiotic genes in comparison to other strains, species or genera of rhizobia that were rescued from domesticated plant ecotypes. The analysis revealed that the bacterium by itself is incapable of surviving in the extreme conditions that its host plant can tolerate. When exposed to drought or alkaline condition, the bacterium depends on its host to survive. Data are consistent with the view of the plant phenotype as the primary factor enabling symbiotic nitrogen fixing bacteria to survive in otherwise limiting environments.
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Affiliation(s)
- Gaurav Sablok
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
| | - Riccardo Rosselli
- Division de Microbiología, Universidad Miguel HernandezSan Juan de Alicante, Spain
| | - Torsten Seeman
- Victorian Bioinformatics Consortium, Monash UniversityMelbourne, VIC, Australia
| | - Robin van Velzen
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen UniversityWageningen, Netherlands
| | - Elisa Polone
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen UniversityWageningen, Netherlands
| | - Alessio Giacomini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of PadovaLegnaro, Italy
| | - Nicola La Porta
- Department of Sustainable Agrobiosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy.,MOUNTFOR Project Centre, European Forest InstituteSan Michele all'Adige, Italy
| | - Rene Geurts
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen UniversityWageningen, Netherlands
| | - Rosella Muresu
- Institute of Animal Production Systems in Mediterranean Environments-National Research CouncilSassari, Italy
| | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of PadovaLegnaro, Italy
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