Under-detection of endospore-forming Firmicutes in metagenomic data
Abstract
Microbial diversity studies based on metagenomic sequencing have greatly enhanced our knowledge of the microbial world. However, one caveat is the fact that not all microorganisms are equally well detected, questioning the universality of this approach. Firmicutes are known to be a dominant bacterial group. Several Firmicutes species are endospore formers and this property makes them hardy in potentially harsh conditions, and thus likely to be present in a wide variety of environments, even as residents and not functional players. While metagenomic libraries can be expected to contain endospore formers, endospores are known to be resilient to many traditional methods of DNA isolation and thus potentially undetectable. In this study we evaluated the representation of endospore-forming Firmicutes in 73 published metagenomic datasets using two molecular markers unique to this bacterial group (spo0A and gpr). Both markers were notably absent in well-known habitats of Firmicutes such as soil, with spo0A found only in three mammalian gut microbiomes. A tailored DNA extraction method resulted in the detection of a large diversity of endospore-formers in amplicon sequencing of the 16S rRNA and spo0A genes. However, shotgun classification was still poor with only a minor fraction of the community assigned to Firmicutes. Thus, removingmore »
- Authors:
-
- Univ. of Neuchatel (Switzerland). Inst. of Biology, Lab. of Microbiology
- Univ. of Neuchatel (Switzerland). Inst. of Biology, Lab. of Microbiology; Swiss Inst. of Bioformatics, Lausanne (Switzerland). Vital-IT Group
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1201745
- Grant/Contract Number:
- 31003A-132358/1; 31003A_152972
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Computational and Structural Biotechnology Journal
- Additional Journal Information:
- Journal Volume: 13; Journal Issue: C; Journal ID: ISSN 2001-0370
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; endospores; gpr; metagenomics; profile analysis; spo0A
Citation Formats
Filippidou, Sevasti, Junier, Thomas, Wunderlin, Tina, Lo, Chien -Chi, Li, Po -E, Chain, Patrick S., and Junier, Pilar. Under-detection of endospore-forming Firmicutes in metagenomic data. United States: N. p., 2015.
Web. doi:10.1016/j.csbj.2015.04.002.
Filippidou, Sevasti, Junier, Thomas, Wunderlin, Tina, Lo, Chien -Chi, Li, Po -E, Chain, Patrick S., & Junier, Pilar. Under-detection of endospore-forming Firmicutes in metagenomic data. United States. https://doi.org/10.1016/j.csbj.2015.04.002
Filippidou, Sevasti, Junier, Thomas, Wunderlin, Tina, Lo, Chien -Chi, Li, Po -E, Chain, Patrick S., and Junier, Pilar. Sat .
"Under-detection of endospore-forming Firmicutes in metagenomic data". United States. https://doi.org/10.1016/j.csbj.2015.04.002. https://www.osti.gov/servlets/purl/1201745.
@article{osti_1201745,
title = {Under-detection of endospore-forming Firmicutes in metagenomic data},
author = {Filippidou, Sevasti and Junier, Thomas and Wunderlin, Tina and Lo, Chien -Chi and Li, Po -E and Chain, Patrick S. and Junier, Pilar},
abstractNote = {Microbial diversity studies based on metagenomic sequencing have greatly enhanced our knowledge of the microbial world. However, one caveat is the fact that not all microorganisms are equally well detected, questioning the universality of this approach. Firmicutes are known to be a dominant bacterial group. Several Firmicutes species are endospore formers and this property makes them hardy in potentially harsh conditions, and thus likely to be present in a wide variety of environments, even as residents and not functional players. While metagenomic libraries can be expected to contain endospore formers, endospores are known to be resilient to many traditional methods of DNA isolation and thus potentially undetectable. In this study we evaluated the representation of endospore-forming Firmicutes in 73 published metagenomic datasets using two molecular markers unique to this bacterial group (spo0A and gpr). Both markers were notably absent in well-known habitats of Firmicutes such as soil, with spo0A found only in three mammalian gut microbiomes. A tailored DNA extraction method resulted in the detection of a large diversity of endospore-formers in amplicon sequencing of the 16S rRNA and spo0A genes. However, shotgun classification was still poor with only a minor fraction of the community assigned to Firmicutes. Thus, removing a specific bias in a molecular workflow improves detection in amplicon sequencing, but it was insufficient to overcome the limitations for detecting endospore-forming Firmicutes in whole-genome metagenomics. In conclusion, this study highlights the importance of understanding the specific methodological biases that can contribute to improve the universality of metagenomic approaches.},
doi = {10.1016/j.csbj.2015.04.002},
journal = {Computational and Structural Biotechnology Journal},
number = C,
volume = 13,
place = {United States},
year = {Sat Apr 25 00:00:00 EDT 2015},
month = {Sat Apr 25 00:00:00 EDT 2015}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 67 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities: Targeted metagenomics
journal, March 2011
- Suenaga, Hikaru
- Environmental Microbiology, Vol. 14, Issue 1
Building on basic metagenomics with complementary technologies
journal, January 2007
- Warnecke, Falk; Hugenholtz, Philip
- Genome Biology, Vol. 8, Issue 12
Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances: MICROBIAL ECOLOGICAL GENOMICS
journal, March 2006
- Xu, Jianping
- Molecular Ecology, Vol. 15, Issue 7
Unsuspected diversity among marine aerobic anoxygenic phototrophs
journal, February 2002
- Béjà, Oded; Suzuki, Marcelino T.; Heidelberg, John F.
- Nature, Vol. 415, Issue 6872
Bacterial Rhodopsin: Evidence for a New Type of Phototrophy in the Sea
journal, September 2000
- Beja, O.; Aravind, L.; Koonin, Eugene V.
- Science, Vol. 289, Issue 5486, p. 1902-1906
Community Proteomics of a Natural Microbial Biofilm
journal, June 2005
- Ram, R. J.
- Science, Vol. 308, Issue 5730
Environmental Genome Shotgun Sequencing of the Sargasso Sea
journal, April 2004
- Venter, J. C.
- Science, Vol. 304, Issue 5667
Soil-specific limitations for access and analysis of soil microbial communities by metagenomics: Limitations in soil metagenomics
journal, June 2011
- Lombard, Nathalie; Prestat, Emmanuel; van Elsas, Jan Dirk
- FEMS Microbiology Ecology, Vol. 78, Issue 1
Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing
journal, August 2006
- Pinard, Robert; de Winter, Alex; Sarkis, Gary J.
- BMC Genomics, Vol. 7, Issue 1
Stage 0 sporulation gene A as a molecular marker to study diversity of endospore-forming Firmicutes: Culture-independent study of endospore-forming Firmicutes
journal, September 2013
- Wunderlin, Tina; Junier, Thomas; Roussel-Delif, Ludovic
- Environmental Microbiology Reports, Vol. 5, Issue 6
Development and Bias Assessment of a Method for Targeted Metagenomic Sequencing of Marine Cyanobacteria
journal, December 2013
- Batmalle, Cécilia S.; Chiang, Hsin-I; Zhang, Kun
- Applied and Environmental Microbiology, Vol. 80, Issue 3
The genomic standards consortium: bringing standards to life for microbial ecology
journal, April 2011
- Yilmaz, Pelin; Gilbert, Jack A.; Knight, Rob
- The ISME Journal, Vol. 5, Issue 10
Microbial culturomics: paradigm shift in the human gut microbiome study
journal, December 2012
- Lagier, J. -C.; Armougom, F.; Million, M.
- Clinical Microbiology and Infection, Vol. 18, Issue 12
The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota
journal, January 2015
- Lagier, Jean-Christophe; Hugon, Perrine; Khelaifia, Saber
- Clinical Microbiology Reviews, Vol. 28, Issue 1
Resistance of Bacillus Endospores to Extreme Terrestrial and Extraterrestrial Environments
journal, September 2000
- Nicholson, W. L.; Munakata, N.; Horneck, G.
- Microbiology and Molecular Biology Reviews, Vol. 64, Issue 3
Roles of Bacillus endospores in the environment
journal, March 2002
- Nicholson, W. L.
- Cellular and Molecular Life Sciences (CMLS), Vol. 59, Issue 3
Overview: development in bacteria: spore formation in Bacillus subtilis
journal, March 2002
- Driks, A.
- Cellular and Molecular Life Sciences (CMLS), Vol. 59, Issue 3
Sporulation genes in members of the low G+C Gram-type-positive phylogenetic branch (Firmicutes)
journal, August 2004
- Onyenwoke, RobU.; Brill, JuliaA.; Farahi, Kamyar
- Archives of Microbiology, Vol. 182, Issue 2-3
Differential gene expression in genetically identical sister cells: the initiation of sporulation in Bacillus subtilis †: Differential gene expression in sporulation
journal, March 2005
- Yudkin, Michael D.; Clarkson, Joanna
- Molecular Microbiology, Vol. 56, Issue 3
Microbial biogeography: putting microorganisms on the map
journal, February 2006
- Martiny, Jennifer B. Hughes; Bohannan, Brendan J. M.; Brown, James H.
- Nature Reviews Microbiology, Vol. 4, Issue 2
Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments
journal, February 2007
- von Mering, C.; Hugenholtz, P.; Raes, J.
- Science, Vol. 315, Issue 5815
Endospore-enriched sequencing approach reveals unprecedented diversity of Firmicutes in sediments: Endospore-forming enrichment
journal, June 2014
- Wunderlin, Tina; Junier, Thomas; Roussel-Delif, Ludovic
- Environmental Microbiology Reports, Vol. 6, Issue 6
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997
- Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
- Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
OrthoDB: the hierarchical catalog of eukaryotic orthologs
journal, December 2007
- Kriventseva, E. V.; Rahman, N.; Espinosa, O.
- Nucleic Acids Research, Vol. 36, Issue Database
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
journal, July 2002
- Katoh, K.
- Nucleic Acids Research, Vol. 30, Issue 14
Comparisons of different hypervariable regions of rrs genes for fingerprinting of microbial communities in paddy soils
journal, May 2009
- Li, Hui; Zhang, Ying; Li, Dong-sheng
- Soil Biology and Biochemistry, Vol. 41, Issue 5
QIIME allows analysis of high-throughput community sequencing data
journal, April 2010
- Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
- Nature Methods, Vol. 7, Issue 5
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
journal, March 1998
- Ewing, Brent; Green, Phil
- Genome Research, Vol. 8, Issue 3
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
journal, October 2003
- Guindon, Stéphane; Gascuel, Olivier
- Systematic Biology, Vol. 52, Issue 5
Accurate read-based metagenome characterization using a hierarchical suite of unique signatures
journal, March 2015
- Freitas, Tracey Allen K.; Li, Po-E; Scholz, Matthew B.
- Nucleic Acids Research, Vol. 43, Issue 10
Fast and accurate short read alignment with Burrows-Wheeler transform
journal, May 2009
- Li, H.; Durbin, R.
- Bioinformatics, Vol. 25, Issue 14
Metagenomic microbial community profiling using unique clade-specific marker genes
journal, June 2012
- Segata, Nicola; Waldron, Levi; Ballarini, Annalisa
- Nature Methods, Vol. 9, Issue 8
Fast gapped-read alignment with Bowtie 2
journal, March 2012
- Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 9, Issue 4
RefSeq: an update on mammalian reference sequences
journal, November 2013
- Pruitt, Kim D.; Brown, Garth R.; Hiatt, Susan M.
- Nucleic Acids Research, Vol. 42, Issue D1
Metagenomic species profiling using universal phylogenetic marker genes
journal, October 2013
- Sunagawa, Shinichi; Mende, Daniel R.; Zeller, Georg
- Nature Methods, Vol. 10, Issue 12
Scalable metagenomic taxonomy classification using a reference genome database
journal, July 2013
- Ames, Sasha K.; Hysom, David A.; Gardner, Shea N.
- Bioinformatics, Vol. 29, Issue 18
MOLECULAR GENETICS OF SPORULATION IN BACILLUS SUBTILIS
journal, December 1996
- Stragier, Patrick; Losick, Richard
- Annual Review of Genetics, Vol. 30, Issue 1
Gene Conservation among Endospore-Forming Bacteria Reveals Additional Sporulation Genes in Bacillus subtilis
journal, November 2012
- Traag, Bjorn A.; Pugliese, Antonia; Eisen, Jonathan A.
- Journal of Bacteriology, Vol. 195, Issue 2
Genomic determinants of sporulation in Bacilli and Clostridia : towards the minimal set of sporulation-specific genes : Distribution of sporulation genes in
journal, August 2012
- Galperin, Michael Y.; Mekhedov, Sergei L.; Puigbo, Pere
- Environmental Microbiology, Vol. 14, Issue 11
Profile analysis: detection of distantly related proteins.
journal, July 1987
- Gribskov, M.; McLachlan, A. D.; Eisenberg, D.
- Proceedings of the National Academy of Sciences, Vol. 84, Issue 13
Metagenomic Analysis of the Human Distal Gut Microbiome
journal, June 2006
- Gill, S. R.; Pop, M.; DeBoy, R. T.
- Science, Vol. 312, Issue 5778
Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes
journal, January 2007
- Kurokawa, Ken; Itoh, Takehiko; Kuwahara, Tomomi
- DNA Research, Vol. 14, Issue 4
A microbial world within us.
journal, March 2006
- Zoetendal, Erwin G.; Vaughan, Elaine E.; de Vos, Willem M.
- Molecular Microbiology, Vol. 59, Issue 6
Geographical variation of human gut microbial composition
journal, February 2014
- Suzuki, Taichi A.; Worobey, Michael
- Biology Letters, Vol. 10, Issue 2
Isolation and Biodiversity of Hitherto Undescribed Soil Bacteria Related to Bacillus niacini
journal, March 2004
- Felske, A. D. M.; Tzeneva, V.; Heyrman, J.
- Microbial Ecology, Vol. 48, Issue 1
Recognition of greater diversity of Bacillus species and related bacteria in human faeces
journal, January 2012
- Hoyles, Lesley; Honda, Harue; Logan, Niall A.
- Research in Microbiology, Vol. 163, Issue 1
Metagenomics - a guide from sampling to data analysis
journal, February 2012
- Thomas, Torsten; Gilbert, Jack; Meyer, Folker
- Microbial Informatics and Experimentation, Vol. 2, Issue 1
Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores
journal, July 2010
- Pope, P. B.; Denman, S. E.; Jones, M.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 33
Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community
journal, January 2010
- Allgaier, Martin; Reddy, Amitha; Park, Joshua I.
- PLoS ONE, Vol. 5, Issue 1
Classification of Bacteria and Archaea: Past, present and future
journal, December 2009
- Schleifer, Karl Heinz
- Systematic and Applied Microbiology, Vol. 32, Issue 8
rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea
journal, January 2009
- Lee, Z. M. -P.; Bussema, C.; Schmidt, T. M.
- Nucleic Acids Research, Vol. 37, Issue Database
Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis
journal, February 2012
- Scholz, Matthew B.; Lo, Chien-Chi; Chain, Patrick SG
- Current Opinion in Biotechnology, Vol. 23, Issue 1
Measurement of in Situ Activities of Nonphotosynthetic Microorganisms in Aquatic and Terrestrial Habitats
journal, October 1985
- Staley, J. T.; Konopka, A.
- Annual Review of Microbiology, Vol. 39, Issue 1
Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
journal, January 1995
- Amann, R. I.; Ludwig, W.; Schleifer, K. H.
- Microbiological reviews, Vol. 59, Issue 1
The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell
journal, May 2010
- Junier, T.; Zdobnov, E. M.
- Bioinformatics, Vol. 26, Issue 13
Overview: development in bacteria: spore formation in Bacillus subtilis
journal, March 2002
- Driks, A.
- Cellular and Molecular Life Sciences (CMLS), Vol. 59, Issue 3
Roles of Bacillus endospores in the environment
journal, March 2002
- Nicholson, W. L.
- Cellular and Molecular Life Sciences (CMLS), Vol. 59, Issue 3
Sporulation genes in members of the low G+C Gram-type-positive phylogenetic branch (Firmicutes)
journal, August 2004
- Onyenwoke, RobU.; Brill, JuliaA.; Farahi, Kamyar
- Archives of Microbiology, Vol. 182, Issue 2-3
Isolation and Biodiversity of Hitherto Undescribed Soil Bacteria Related to Bacillus niacini
journal, March 2004
- Felske, A. D. M.; Tzeneva, V.; Heyrman, J.
- Microbial Ecology, Vol. 48, Issue 1
Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis
journal, February 2012
- Scholz, Matthew B.; Lo, Chien-Chi; Chain, Patrick SG
- Current Opinion in Biotechnology, Vol. 23, Issue 1
Recognition of greater diversity of Bacillus species and related bacteria in human faeces
journal, January 2012
- Hoyles, Lesley; Honda, Harue; Logan, Niall A.
- Research in Microbiology, Vol. 163, Issue 1
Classification of Bacteria and Archaea: Past, present and future
journal, December 2009
- Schleifer, Karl Heinz
- Systematic and Applied Microbiology, Vol. 32, Issue 8
Unsuspected diversity among marine aerobic anoxygenic phototrophs
journal, February 2002
- Béjà, Oded; Suzuki, Marcelino T.; Heidelberg, John F.
- Nature, Vol. 415, Issue 6872
The genomic standards consortium: bringing standards to life for microbial ecology
journal, April 2011
- Yilmaz, Pelin; Gilbert, Jack A.; Knight, Rob
- The ISME Journal, Vol. 5, Issue 10
Fast gapped-read alignment with Bowtie 2
journal, March 2012
- Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 9, Issue 4
Metagenomic microbial community profiling using unique clade-specific marker genes
journal, June 2012
- Segata, Nicola; Waldron, Levi; Ballarini, Annalisa
- Nature Methods, Vol. 9, Issue 8
Metagenomic species profiling using universal phylogenetic marker genes
journal, October 2013
- Sunagawa, Shinichi; Mende, Daniel R.; Zeller, Georg
- Nature Methods, Vol. 10, Issue 12
QIIME allows analysis of high-throughput community sequencing data
journal, April 2010
- Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
- Nature Methods, Vol. 7, Issue 5
Microbial biogeography: putting microorganisms on the map
journal, February 2006
- Martiny, Jennifer B. Hughes; Bohannan, Brendan J. M.; Brown, James H.
- Nature Reviews Microbiology, Vol. 4, Issue 2
Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores
journal, July 2010
- Pope, P. B.; Denman, S. E.; Jones, M.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 33
Profile analysis: detection of distantly related proteins.
journal, July 1987
- Gribskov, M.; McLachlan, A. D.; Eisenberg, D.
- Proceedings of the National Academy of Sciences, Vol. 84, Issue 13
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
journal, October 2003
- Guindon, Stéphane; Gascuel, Olivier
- Systematic Biology, Vol. 52, Issue 5
Fast and accurate short read alignment with Burrows-Wheeler transform
journal, May 2009
- Li, H.; Durbin, R.
- Bioinformatics, Vol. 25, Issue 14
The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell
journal, May 2010
- Junier, T.; Zdobnov, E. M.
- Bioinformatics, Vol. 26, Issue 13
Scalable metagenomic taxonomy classification using a reference genome database
journal, July 2013
- Ames, Sasha K.; Hysom, David A.; Gardner, Shea N.
- Bioinformatics, Vol. 29, Issue 18
Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes
journal, January 2007
- Kurokawa, Ken; Itoh, Takehiko; Kuwahara, Tomomi
- DNA Research, Vol. 14, Issue 4
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
journal, July 2002
- Katoh, K.
- Nucleic Acids Research, Vol. 30, Issue 14
RefSeq: an update on mammalian reference sequences
journal, November 2013
- Pruitt, Kim D.; Brown, Garth R.; Hiatt, Susan M.
- Nucleic Acids Research, Vol. 42, Issue D1
Geographical variation of human gut microbial composition
journal, February 2014
- Suzuki, Taichi A.; Worobey, Michael
- Biology Letters, Vol. 10, Issue 2
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
journal, March 1998
- Ewing, Brent; Green, Phil
- Genome Research, Vol. 8, Issue 3
Microbial culturomics: paradigm shift in the human gut microbiome study
journal, December 2012
- Lagier, J. -C.; Armougom, F.; Million, M.
- Clinical Microbiology and Infection, Vol. 18, Issue 12
Endospore-enriched sequencing approach reveals unprecedented diversity of Firmicutes in sediments: Endospore-forming enrichment
journal, June 2014
- Wunderlin, Tina; Junier, Thomas; Roussel-Delif, Ludovic
- Environmental Microbiology Reports, Vol. 6, Issue 6
Differential gene expression in genetically identical sister cells: the initiation of sporulation in Bacillus subtilis †: Differential gene expression in sporulation
journal, March 2005
- Yudkin, Michael D.; Clarkson, Joanna
- Molecular Microbiology, Vol. 56, Issue 3
Genomic determinants of sporulation in Bacilli and Clostridia : towards the minimal set of sporulation-specific genes : Distribution of sporulation genes in
journal, August 2012
- Galperin, Michael Y.; Mekhedov, Sergei L.; Puigbo, Pere
- Environmental Microbiology, Vol. 14, Issue 11
Bacterial Rhodopsin: Evidence for a New Type of Phototrophy in the Sea
journal, September 2000
- Beja, O.; Aravind, L.; Koonin, Eugene V.
- Science, Vol. 289, Issue 5486, p. 1902-1906
Quantification of Endospore-Forming Firmicutes by Quantitative PCR with the Functional Gene spo0A
journal, June 2013
- Bueche, Matthieu; Wunderlin, Tina; Roussel-Delif, Ludovic
- Applied and Environmental Microbiology, Vol. 79, Issue 17
Accessing the Soil Metagenome for Studies of Microbial Diversity
journal, December 2010
- Delmont, Tom O.; Robe, Patrick; Cecillon, Sébastien
- Applied and Environmental Microbiology, Vol. 77, Issue 4
Prospecting for Novel Biocatalysts in a Soil Metagenome
journal, October 2003
- Voget, S.; Leggewie, C.; Uesbeck, A.
- Applied and Environmental Microbiology, Vol. 69, Issue 10
A Genomic Signature and the Identification of New Sporulation Genes
journal, February 2013
- Abecasis, A. B.; Serrano, M.; Alves, R.
- Journal of Bacteriology, Vol. 195, Issue 9
Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
journal, January 1995
- Amann, R. I.; Ludwig, W.; Schleifer, K. H.
- Microbiological reviews, Vol. 59, Issue 1
MOLECULAR GENETICS OF SPORULATION IN BACILLUS SUBTILIS
journal, December 1996
- Stragier, Patrick; Losick, Richard
- Annual Review of Genetics, Vol. 30, Issue 1
Measurement of in Situ Activities of Nonphotosynthetic Microorganisms in Aquatic and Terrestrial Habitats
journal, October 1985
- Staley, J. T.; Konopka, A.
- Annual Review of Microbiology, Vol. 39, Issue 1
Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing
journal, August 2006
- Pinard, Robert; de Winter, Alex; Sarkis, Gary J.
- BMC Genomics, Vol. 7, Issue 1
Metagenomics - a guide from sampling to data analysis
journal, February 2012
- Thomas, Torsten; Gilbert, Jack; Meyer, Folker
- Microbial Informatics and Experimentation, Vol. 2, Issue 1
Building on basic metagenomics with complementary technologies
journal, January 2007
- Warnecke, Falk; Hugenholtz, Philip
- Genome Biology, Vol. 8, Issue 12
Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community
journal, January 2010
- Allgaier, Martin; Reddy, Amitha; Park, Joshua I.
- PLoS ONE, Vol. 5, Issue 1
Works referencing / citing this record:
Differential fecal microbiota are retained in broiler chicken lines divergently selected for fatness traits
journal, November 2016
- Hou, Qiangchuan; Kwok, Lai-Yu; Zheng, Yi
- Scientific Reports, Vol. 6, Issue 1
Microbial genomes retrieved from High Arctic lake sediments encode for adaptation to cold and oligotrophic environments
journal, January 2020
- Ruuskanen, Matti O.; Colby, Graham; St. Pierre, Kyra A.
- Limnology and Oceanography, Vol. 65, Issue S1
Microbial communities associated with barley growing in an oil sands reclamation area in Alberta, Canada
journal, December 2018
- Kovalski Mitter, Eduardo; de Freitas, Renato; Germida, James J.
- Canadian Journal of Microbiology, Vol. 64, Issue 12
Metagenomic Sequencing of Diamondback Moth Gut Microbiome Unveils Key Holobiont Adaptations for Herbivory
journal, April 2017
- Xia, Xiaofeng; Gurr, Geoff M.; Vasseur, Liette
- Frontiers in Microbiology, Vol. 8
Systematic processing of ribosomal RNA gene amplicon sequencing data
journal, December 2019
- Tremblay, Julien; Yergeau, Etienne
- GigaScience, Vol. 8, Issue 12
Responses of soil bacterial communities, enzyme activities, and nutrients to agricultural-to-natural ecosystem conversion in the Loess Plateau, China
journal, August 2018
- Cui, Yongxing; Fang, Linchuan; Guo, Xiaobin
- Journal of Soils and Sediments, Vol. 19, Issue 3
Effect of fermentation system on the physicochemical and microbial community dynamics during enset ( Ensete ventricosum ) fermentation
journal, January 2019
- Andeta, A. F.; Vandeweyer, D.; Teffera, E. F.
- Journal of Applied Microbiology, Vol. 126, Issue 3
Metagenomic sequencing reveals the relationship between microbiota composition and quality of Chinese Rice Wine
journal, May 2016
- Hong, Xutao; Chen, Jing; Liu, Lin
- Scientific Reports, Vol. 6, Issue 1
Generating amplicon reads for microbial community assessment with next‐generation sequencing
journal, August 2019
- Gołębiewski, M.; Tretyn, A.
- Journal of Applied Microbiology, Vol. 128, Issue 2
Bacterial community diversity of the deep-sea octocoral Paramuricea placomus
journal, January 2016
- Kellogg, Christina A.; Ross, Steve W.; Brooke, Sandra D.
- PeerJ, Vol. 4
Microbial dormancy in the marine subsurface: Global endospore abundance and response to burial
journal, February 2019
- Wörmer, Lars; Hoshino, Tatsuhiko; Bowles, Marshall W.
- Science Advances, Vol. 5, Issue 2
Shifts in microbial community composition in tannery-contaminated soil in response to increased gamma radiation
journal, December 2019
- Al-Najjar, Mohammad A. A.; Albokari, Majed M.
- Annals of Microbiology, Vol. 69, Issue 13
Introducing the sporobiota and sporobiome
journal, June 2017
- Tetz, George; Tetz, Victor
- Gut Pathogens, Vol. 9, Issue 1
A Combination of Extreme Environmental Conditions Favor the Prevalence of Endospore-Forming Firmicutes
journal, November 2016
- Filippidou, Sevasti; Wunderlin, Tina; Junier, Thomas
- Frontiers in Microbiology, Vol. 7
Phylogenetic diversity of aerobic spore-forming Bacillalles isolated from Brazilian soils
journal, May 2019
- Orem, J. C.; Silva, W. M. C.; Raiol, T.
- International Microbiology, Vol. 22, Issue 4
Contrasting community composition of endospores and vegetative Firmicutes in a marine sediment suggests both endogenous and exogenous sources of endospore accumulation
journal, September 2018
- Cupit, Carina; Lomstein, Bente Aagaard; Kjeldsen, Kasper Urup
- Environmental Microbiology Reports, Vol. 11, Issue 3
Detection and Enumeration of Spore-Forming Bacteria in Powdered Dairy Products
journal, January 2017
- McHugh, Aoife J.; Feehily, Conor; Hill, Colin
- Frontiers in Microbiology, Vol. 8
Nutrient germination improves DNA recovery from industrial Bacillus subtilis endospores during qPCR enumeration assays
journal, December 2019
- Gorsuch, John P.; Woodruff, Peyton
- Heliyon, Vol. 5, Issue 12
Differential fecal microbiota are retained in broiler chicken lines divergently selected for fatness traits
journal, November 2016
- Hou, Qiangchuan; Kwok, Lai-Yu; Zheng, Yi
- Scientific Reports, Vol. 6, Issue 1
Introducing the sporobiota and sporobiome
journal, June 2017
- Tetz, George; Tetz, Victor
- Gut Pathogens, Vol. 9, Issue 1
A Combination of Extreme Environmental Conditions Favor the Prevalence of Endospore-Forming Firmicutes
journal, November 2016
- Filippidou, Sevasti; Wunderlin, Tina; Junier, Thomas
- Frontiers in Microbiology, Vol. 7
Metagenomic Sequencing of Diamondback Moth Gut Microbiome Unveils Key Holobiont Adaptations for Herbivory
journal, April 2017
- Xia, Xiaofeng; Gurr, Geoff M.; Vasseur, Liette
- Frontiers in Microbiology, Vol. 8
High-Alpine Permafrost and Active-Layer Soil Microbiomes Differ in Their Response to Elevated Temperatures
journal, April 2019
- Luláková, Petra; Perez-Mon, Carla; Šantrůčková, Hana
- Frontiers in Microbiology, Vol. 10