Reference health
Archaea: Essential inhabitants of the human digestive microbiota
4 of 113 checkable references need attention · checked 2026-07-22
At the dated check, the references listed below either did not resolve in Crossref or DataCite, or carried a retraction notice. Each one is shown with the registry record that put it there.
3 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
References needing attention
marked retracted — notice via Crossref, record curated by Retraction Watch10.1038/ijo.2011.153
RETRACTED ARTICLE: Obesity-associated gut microbiota is enriched in Lactobacillus reuteri and depleted in Bifidobacterium animalis and Methanobrevibacter smithii
marked retracted — notice via Crossref, record curated by Retraction Watch10.1371/journal.pone.0084033
Development and Validation of a Microarray for the Investigation of the CAZymes Encoded by the Human Gut Microbiome
marked retracted — notice via Crossref, record curated by Retraction Watch10.1038/ijo.2013.20
RETRACTED ARTICLE: Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli
marked retracted — notice via Crossref, record curated by Retraction Watch10.1038/srep26051
RETRACTED ARTICLE: Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition
The 109 checked references that resolve
resolves10.1038/nrmicro2426
The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?
resolves10.1073/pnas.87.12.4576
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
resolves10.1111/j.1600-0463.2012.02899.x
Age‐related prevalence of <i><scp>M</scp>ethanomassiliicoccus luminyensis</i> in the human gut microbiome
resolves10.1128/JB.01867-12
Genome Sequence of “Candidatus Methanomethylophilus alvus” Mx1201, a Methanogenic Archaeon from the Human Gut Belonging to a Seventh Order of Methanogens
resolves10.1371/journal.pone.0007063
High Prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae Detected in the Human Gut Using an Improved DNA Detection Protocol
resolves10.1016/j.ijmm.2008.06.011
Methanogenic archaea in health and disease: A novel paradigm of microbial pathogenesis
resolves10.1128/AEM.02815-08
Assessment of the Microbial Ecology of Ruminal Methanogens in Cattle with Different Feed Efficiencies
resolves10.1128/AEM.00010-10
Characterization of Variation in Rumen Methanogenic Communities under Different Dietary and Host Feed Efficiency Conditions, as Determined by PCR-Denaturing Gradient Gel Electrophoresis Analysis
resolves10.1046/j.1365-2672.2001.01297.x
Crenarchaeota and Euryarchaeota in temperate estuarine sediments
resolves10.1371/journal.pone.0043346
Stratification of Archaea in the Deep Sediments of a Freshwater Meromictic Lake: Vertical Shift from Methanogenic to Uncultured Archaeal Lineages
resolves10.1128/AEM.02193-12
“Methanoplasmatales,” Thermoplasmatales-Related Archaea in Termite Guts and Other Environments, Are the Seventh Order of Methanogens
resolves10.1007/s00248-007-9351-x
Methanobrevibacter Phylotypes are the Dominant Methanogens in Sheep from Venezuela
resolves10.1099/ijs.0.033712-0
Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces
resolves10.1128/aem.48.2.449-450.1984
Methanogens and anaerobes in a colon segment isolated from the normal fecal stream
resolves10.3402/jom.v3i0.5940
Methanogenic <i>Archaea</i> and oral infections – ways to unravel the black box
resolves10.1128/JCM.44.4.1274-1282.2006
Identification and Quantification of Archaea Involved in Primary Endodontic Infections
resolves10.1093/jac/dkr251
The antimicrobial resistance pattern of cultured human methanogens reflects the unique phylogenetic position of archaea
resolves10.1111/j.1469-0691.2012.03913.x
Susceptibility of archaea to antimicrobial agents: applications to clinical microbiology
resolves10.1128/genomeA.00453-13
Genome Sequence of “
<i>Candidatus</i>
Methanomassiliicoccus intestinalis” Issoire-Mx1, a Third
<i>Thermoplasmatales</i>
-Related Methanogenic Archaeon from Human Feces
resolves10.1007/BF00423270
Methanosphaera stadtmaniae gen. nov., sp. nov.: a species that forms methane by reducing methanol with hydrogen
resolves10.1007/s10096-016-2627-7
Aerobic culture of methanogenic archaea without an external source of hydrogen
resolves10.1016/j.nmni.2016.05.007
Haloferax massiliensis sp. nov., the first human-associated halophilic archaea
resolves10.1093/ajcn/25.12.1324
Commentary on the Hungate technique for culture of anaerobic bacteria
resolves10.1128/aem.32.6.781-791.1976
New approach to the cultivation of methanogenic bacteria: 2-mercaptoethanesulfonic acid (HS-CoM)-dependent growth of Methanobacterium ruminantium in a pressureized atmosphere
resolves10.1016/S0580-9517(08)70503-8
Chapter IV A Roll Tube Method for Cultivation of Strict Anaerobes
resolves10.1016/S0014-5793(99)01026-1
Novel reactions involved in energy conservation by methanogenic archaea
resolves10.1038/nrmicro1888
Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques
resolves10.1128/AEM.72.3.2110-2117.2006
Phylogenetic Analysis and In Situ Identification of
<i>Bacteria</i>
Community Composition in an Acidic
<i>Sphagnum</i>
Peat Bog
resolves10.1046/j.1462-2920.1999.00065.x
Fluorescence
<i>in situ</i>
hybridization analysis of the prokaryotic community inhabiting crystallizer ponds
resolves10.1038/srep25775
Restricted diversity of dental calculus methanogens over five centuries, France
resolves10.1016/j.resmic.2008.06.007
A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene
resolves10.1111/j.1758-2229.2009.00116.x
Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age‐associated increase of the diversity
resolves10.1186/1471-2180-8-79
Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis
resolves10.1007/s12275-008-0199-7
Bacterial, archaeal, and eukaryal diversity in the intestines of Korean people
resolves10.1038/ismej.2011.90
Abundance and diversity of mucosa-associated hydrogenotrophic microbes in the healthy human colon
resolves10.1111/j.1399-302X.2009.00539.x
T‐RFLP‐based <i>mcrA</i> gene analysis of methanogenic archaea in association with oral infections and evidence of a novel <i>Methanobrevibacter</i> phylotype
resolves10.1073/pnas.1000071108
Pan-genome of the dominant human gut-associated archaeon,
<i>Methanobrevibacter smithii</i>
, studied in twins
resolves10.1371/journal.pone.0066019
Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents
resolves10.1111/1574-6968.12592
Dual investigation of methanogenic processes by quantitative PCR and quantitative microscopic fingerprinting
resolves10.1128/JCM.02863-12
Real-Time PCR Quantification of Methanobrevibacter oralis in Periodontitis
resolves10.1128/JB.01861-07
Quantitative Analysis of Three Hydrogenotrophic Microbial Groups, Methanogenic Archaea, Sulfate-Reducing Bacteria, and Acetogenic Bacteria, within Plaque Biofilms Associated with Human Periodontal Disease
resolves10.1016/j.archoralbio.2014.05.011
Prevalence and quantification of the uncommon Archaea phylotype Thermoplasmata in chronic periodontitis
resolves10.1128/genomeA.00073-14
Draft Genome Sequencing of Methanobrevibacter oralis Strain JMR01, Isolated from the Human Intestinal Microbiota
resolves10.1099/ijs.0.63984-0
Methanobrevibacter millerae sp. nov. and Methanobrevibacter olleyae sp. nov., methanogens from the ovine and bovine rumen that can utilize formate for growth
resolves10.1016/j.anaerobe.2012.04.006
McrA and 16S rRNA gene analysis suggests a novel lineage of Archaea phylogenetically affiliated with Thermoplasmatales in human subgingival plaque
resolves10.1111/j.1600-0765.2011.01347.x
Prevalence and microbiological diversity of Archaea in peri-implantitis subjects by 16S ribosomal RNA clonal analysis
resolves10.1111/j.1600-051X.2011.01734.x
Diversity and quantitative analysis of Archaea in aggressive periodontitis and periodontally healthy subjects
resolves10.1007/s00284-005-0036-8
Recovery of Partial 16S rDNA Sequences Suggests the Presence of Crenarchaeota in the Human Digestive Ecosystem
resolves10.1111/1574-6976.12075
The first 1000 cultured species of the human gastrointestinal microbiota
resolves10.1099/ijs.0.013722-0
Halarchaeum acidiphilum gen. nov., sp. nov., a moderately acidophilic haloarchaeon isolated from commercial solar salt
resolves10.1099/ijs.0.65644-0
Natrinema gari sp. nov., a halophilic archaeon isolated from fish sauce in Thailand
resolves10.1099/ijs.0.021790-0
Haloarcula salaria sp. nov. and Haloarcula tradensis sp. nov., isolated from salt in Thai fish sauce
resolves10.1099/ijs.0.65121-0
Halalkalicoccus jeotgali sp. nov., a halophilic archaeon from shrimp jeotgal, a traditional Korean fermented seafood
resolves10.1099/00222615-15-2-189
The Microbial Ecology of the Large Bowel of Breastfed and Formula-fed Infants During the First Year of Life
resolves10.1128/aem.55.10.2468-2473.1989
Increase in colonic methanogens and total anaerobes in aging rats
resolves10.1073/pnas.1000081107
Succession of microbial consortia in the developing infant gut microbiome
resolves10.1016/j.clp.2011.03.008
Cesarean Versus Vaginal Delivery: Long-term Infant Outcomes and the Hygiene Hypothesis
resolves10.1111/j.1572-0241.2000.02319.x
Shared and Unique Environmental Factors Determine The Ecology of Methanogens in Humans and Rats
resolves10.1016/j.syapm.2008.02.001
Volatilisation of metals and metalloids: An inherent feature of methanoarchaea?
resolves10.1111/1574-6976.12031
Microbial source tracking markers for detection of fecal contamination in environmental waters: relationships between pathogens and human health outcomes
resolves10.1111/j.1365-2672.2010.04824.x
A real-time qPCR assay for the detection of the nifH gene of Methanobrevibacter smithii, a potential indicator of sewage pollution
resolves10.1128/AEM.01430-12
Performance of Two Quantitative PCR Methods for Microbial Source Tracking of Human Sewage and Implications for Microbial Risk Assessment in Recreational Waters
resolves10.1111/j.1365-2672.2006.02989.x
Detection of the nifH gene of Methanobrevibacter smithii: a potential tool to identify sewage pollution in recreational waters
resolves10.1016/j.watres.2009.06.029
Validation and field testing of library-independent microbial source tracking methods in the Gulf of Mexico
resolves10.1128/AEM.00024-12
Association of Fecal Indicator Bacteria with Human Viruses and Microbial Source Tracking Markers at Coastal Beaches Impacted by Nonpoint Source Pollution
resolves10.1021/es203372u
Evaluation of the <i>nifH</i> Gene Marker of <i>Methanobrevibacter smithii</i> for the Detection of Sewage Pollution in Environmental Waters in Southeast Queensland, Australia
resolves10.1371/journal.pone.0099411
The Intestinal Archaea Methanosphaera stadtmanae and Methanobrevibacter smithii Activate Human Dendritic Cells
resolves10.1152/ajpgi.00574.2004
Methane, a gas produced by enteric bacteria, slows intestinal transit and augments small intestinal contractile activity
resolves10.1038/ajg.2009.655
Methanogenic Flora Is Associated With Altered Colonic Transit but Not Stool Characteristics in Constipation Without IBS
resolves10.1111/j.1572-0241.2007.01072.x
The Degree of Breath Methane Production in IBS Correlates With the Severity of Constipation
resolves10.1016/j.cmi.2016.09.007
Methanobrevibacter smithii and Bacteroides thetaiotaomicron cultivated from a chronic paravertebral muscle abscess
resolves10.1023/B:DDAS.0000011607.24171.c0
IBS Subjects with Methane on Lactulose Breath Test Have Lower Postprandial Serotonin Levels Than Subjects with Hydrogen
resolves10.1023/A:1021738515885
Methane Production During Lactulose Breath Test Is Associated with Gastrointestinal Disease Presentation
resolves10.5056/jnm.2011.17.2.185
Slow Transit Constipation Associated With Excess Methane Production and Its Improvement Following Rifaximin Therapy: A Case Report
resolves10.1073/pnas.0602187103
A humanized gnotobiotic mouse model of host–archaeal–bacterial mutualism
resolves10.1371/journal.pone.0007125
Monitoring Bacterial Community of Human Gut Microbiota Reveals an Increase in Lactobacillus in Obese Patients and Methanogens in Anorexic Patients
The 3 references without a DOI — listed, not checked
no DOI — not checkedCharacterization of Methanobrevibacter arboriphilicus SA Isolated from a Paddy Field Soil and DNA-DNA Hybridization among M. arboriphilicus strains
no DOI — not checked10.1016/j.humic.2016.11.005_b0395
no DOI — not checkedLife with no sugars?
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