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  1. Article ; Online: Stability of the Fecal and Oral Microbiome over 2 Years at -80°C for Multiple Collection Methods.

    Zouiouich, Semi / Byrd, Doratha A / Hua, Xing / Karwa, Smriti / Wan, Yunhu / Shi, Jianxin / Humphrey, Gregory C / Ackermann, Gail L / Knight, Rob / Abnet, Christian C / Vogtmann, Emily / Sinha, Rashmi

    Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

    2023  Volume 32, Issue 3, Page(s) 444–451

    Abstract: Background: In prospective cohorts, biological samples are generally stored over long periods before an adequate number of cases have accrued. We investigated the impact of sample storage at -80°C for 2 years on the stability of the V4 region of the 16S ...

    Abstract Background: In prospective cohorts, biological samples are generally stored over long periods before an adequate number of cases have accrued. We investigated the impact of sample storage at -80°C for 2 years on the stability of the V4 region of the 16S rRNA gene across seven different collection methods (i.e., no additive, 95% ethanol, RNAlater stabilization solution, fecal occult blood test cards, and fecal immunochemical test tubes for feces; OMNIgene ORAL tubes and Scope mouthwash for saliva) among 51 healthy volunteers.
    Methods: Intraclass correlation coefficients (ICC) were calculated for the relative abundance of the top three phyla, the 20 most abundant genera, three alpha-diversity metrics, and the first principal coordinates of three beta-diversity matrices.
    Results: The subject variability was much higher than the variability introduced by the sample collection type, and storage time. For fecal samples, microbial stability over 2 years was high across collection methods (range, ICCs = 0.70-0.99), except for the samples collected with no additive (range, ICCs = 0.23-0.83). For oral samples, most microbiome diversity measures were stable over time with ICCs above 0.74; however, ICCs for the samples collected with Scope mouthwash were lower for two alpha-diversity measures, Faith's phylogenetic diversity (0.23) and the observed number of operational taxonomic units (0.23).
    Conclusions: Fecal and oral samples in most used collection methods are stable for microbiome analyses after 2 years at -80°C, except for fecal samples with no additive.
    Impact: This study provides evidence that samples stored for an extended period from prospective studies are useful for microbiome analyses.
    MeSH term(s) Humans ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Microbiota ; Feces ; Specimen Handling/methods
    Chemical Substances RNA, Ribosomal, 16S
    Language English
    Publishing date 2023-01-16
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Intramural
    ZDB-ID 1153420-5
    ISSN 1538-7755 ; 1055-9965
    ISSN (online) 1538-7755
    ISSN 1055-9965
    DOI 10.1158/1055-9965.EPI-22-0883
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3693: Show issues Location:
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  2. Article ; Online: Gut microbiome and atrial fibrillation-results from a large population-based study.

    Palmu, Joonatan / Börschel, Christin S / Ortega-Alonso, Alfredo / Markó, Lajos / Inouye, Michael / Jousilahti, Pekka / Salido, Rodolfo A / Sanders, Karenina / Brennan, Caitriona / Humphrey, Gregory C / Sanders, Jon G / Gutmann, Friederike / Linz, Dominik / Salomaa, Veikko / Havulinna, Aki S / Forslund, Sofia K / Knight, Rob / Lahti, Leo / Niiranen, Teemu /
    Schnabel, Renate B

    EBioMedicine

    2023  Volume 91, Page(s) 104583

    Abstract: Background: Atrial fibrillation (AF) is an important heart rhythm disorder in aging populations. The gut microbiome composition has been previously related to cardiovascular disease risk factors. Whether the gut microbial profile is also associated with ...

    Abstract Background: Atrial fibrillation (AF) is an important heart rhythm disorder in aging populations. The gut microbiome composition has been previously related to cardiovascular disease risk factors. Whether the gut microbial profile is also associated with the risk of AF remains unknown.
    Methods: We examined the associations of prevalent and incident AF with gut microbiota in the FINRISK 2002 study, a random population sample of 6763 individuals. We replicated our findings in an independent case-control cohort of 138 individuals in Hamburg, Germany.
    Findings: Multivariable-adjusted regression models revealed that prevalent AF (N = 116) was associated with nine microbial genera. Incident AF (N = 539) over a median follow-up of 15 years was associated with eight microbial genera with false discovery rate (FDR)-corrected P < 0.05. Both prevalent and incident AF were associated with the genera Enorma and Bifidobacterium (FDR-corrected P < 0.001). AF was not significantly associated with bacterial diversity measures. Seventy-five percent of top genera (Enorma, Paraprevotella, Odoribacter, Collinsella, Barnesiella, Alistipes) in Cox regression analyses showed a consistent direction of shifted abundance in an independent AF case-control cohort that was used for replication.
    Interpretation: Our findings establish the basis for the use of microbiome profiles in AF risk prediction. However, extensive research is still warranted before microbiome sequencing can be used for prevention and targeted treatment of AF.
    Funding: This study was funded by European Research Council, German Ministry of Research and Education, Academy of Finland, Finnish Medical Foundation, and the Finnish Foundation for Cardiovascular Research, the Emil Aaltonen Foundation, and the Paavo Nurmi Foundation.
    MeSH term(s) Humans ; Atrial Fibrillation/etiology ; Atrial Fibrillation/complications ; Gastrointestinal Microbiome ; Heart ; Bacteria/genetics ; Aging ; Incidence
    Language English
    Publishing date 2023-04-27
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2851331-9
    ISSN 2352-3964
    ISSN (online) 2352-3964
    DOI 10.1016/j.ebiom.2023.104583
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  3. Article ; Online: Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection.

    Mu, Andre / McDonald, Daniel / Jarmusch, Alan K / Martino, Cameron / Brennan, Caitriona / Bryant, Mackenzie / Humphrey, Gregory C / Toronczak, Julia / Schwartz, Tara / Nguyen, Dominic / Ackermann, Gail / D'Onofrio, Anthony / Strathdee, Steffanie A / Schooley, Robert T / Dorrestein, Pieter C / Knight, Rob / Aslam, Saima

    Microbiome

    2021  Volume 9, Issue 1, Page(s) 92

    Abstract: Background: Infectious bacterial diseases exhibiting increasing resistance to antibiotics are a serious global health issue. Bacteriophage therapy is an anti-microbial alternative to treat patients with serious bacterial infections. However, the impacts ...

    Abstract Background: Infectious bacterial diseases exhibiting increasing resistance to antibiotics are a serious global health issue. Bacteriophage therapy is an anti-microbial alternative to treat patients with serious bacterial infections. However, the impacts to the host microbiome in response to clinical use of phage therapy are not well understood.
    Results: Our paper demonstrates a largely unchanged microbiota profile during 4 weeks of phage therapy when added to systemic antibiotics in a single patient with Staphylococcus aureus device infection. Metabolomic analyses suggest potential indirect cascading ecological impacts to the host (skin) microbiome. We did not detect genomes of the three phages used to treat the patient in metagenomic samples taken from saliva, stool, and skin; however, phages were detected using endpoint-PCR in patient serum.
    Conclusion: Results from our proof-of-principal study supports the use of bacteriophages as a microbiome-sparing approach to treat bacterial infections. Video abstract.
    MeSH term(s) Anti-Bacterial Agents/therapeutic use ; Bacteriophages/genetics ; Humans ; Microbiota ; Phage Therapy ; Staphylococcal Infections/drug therapy
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2021-04-14
    Publishing country England
    Document type Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Video-Audio Media
    ZDB-ID 2697425-3
    ISSN 2049-2618 ; 2049-2618
    ISSN (online) 2049-2618
    ISSN 2049-2618
    DOI 10.1186/s40168-021-01026-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Association Between the Gut Microbiota and Blood Pressure in a Population Cohort of 6953 Individuals.

    Palmu, Joonatan / Salosensaari, Aaro / Havulinna, Aki S / Cheng, Susan / Inouye, Michael / Jain, Mohit / Salido, Rodolfo A / Sanders, Karenina / Brennan, Caitriona / Humphrey, Gregory C / Sanders, Jon G / Vartiainen, Erkki / Laatikainen, Tiina / Jousilahti, Pekka / Salomaa, Veikko / Knight, Rob / Lahti, Leo / Niiranen, Teemu J

    Journal of the American Heart Association

    2020  Volume 9, Issue 15, Page(s) e016641

    Abstract: Background Several small-scale animal studies have suggested that gut microbiota and blood pressure (BP) are linked. However, results from human studies remain scarce and conflicting. We wanted to elucidate the multivariable-adjusted association between ... ...

    Abstract Background Several small-scale animal studies have suggested that gut microbiota and blood pressure (BP) are linked. However, results from human studies remain scarce and conflicting. We wanted to elucidate the multivariable-adjusted association between gut metagenome and BP in a large, representative, well-phenotyped population sample. We performed a focused analysis to examine the previously reported inverse associations between sodium intake and
    MeSH term(s) Adult ; Aged ; Blood Pressure ; Cohort Studies ; Female ; Gastrointestinal Microbiome ; Humans ; Hypertension/microbiology ; Lactobacillus ; Male ; Metagenome ; Middle Aged ; Sodium, Dietary/urine
    Chemical Substances Sodium, Dietary
    Language English
    Publishing date 2020-07-21
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2653953-6
    ISSN 2047-9980 ; 2047-9980
    ISSN (online) 2047-9980
    ISSN 2047-9980
    DOI 10.1161/JAHA.120.016641
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Taxonomic signatures of cause-specific mortality risk in human gut microbiome.

    Salosensaari, Aaro / Laitinen, Ville / Havulinna, Aki S / Meric, Guillaume / Cheng, Susan / Perola, Markus / Valsta, Liisa / Alfthan, Georg / Inouye, Michael / Watrous, Jeramie D / Long, Tao / Salido, Rodolfo A / Sanders, Karenina / Brennan, Caitriona / Humphrey, Gregory C / Sanders, Jon G / Jain, Mohit / Jousilahti, Pekka / Salomaa, Veikko /
    Knight, Rob / Lahti, Leo / Niiranen, Teemu

    Nature communications

    2021  Volume 12, Issue 1, Page(s) 2671

    Abstract: The collection of fecal material and developments in sequencing technologies have enabled standardised and non-invasive gut microbiome profiling. Microbiome composition from several large cohorts have been cross-sectionally linked to various lifestyle ... ...

    Abstract The collection of fecal material and developments in sequencing technologies have enabled standardised and non-invasive gut microbiome profiling. Microbiome composition from several large cohorts have been cross-sectionally linked to various lifestyle factors and diseases. In spite of these advances, prospective associations between microbiome composition and health have remained uncharacterised due to the lack of sufficiently large and representative population cohorts with comprehensive follow-up data. Here, we analyse the long-term association between gut microbiome variation and mortality in a well-phenotyped and representative population cohort from Finland (n = 7211). We report robust taxonomic and functional microbiome signatures related to the Enterobacteriaceae family that are associated with mortality risk during a 15-year follow-up. Our results extend previous cross-sectional studies, and help to establish the basis for examining long-term associations between human gut microbiome composition, incident outcomes, and general health status.
    MeSH term(s) Adolescent ; Adult ; Aged ; Cause of Death/trends ; Cohort Studies ; Cross-Sectional Studies ; Enterobacteriaceae/classification ; Enterobacteriaceae/genetics ; Feces/microbiology ; Female ; Finland ; Gastrointestinal Microbiome/genetics ; Humans ; Male ; Middle Aged ; Population Surveillance/methods ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Young Adult
    Chemical Substances RNA, Ribosomal, 16S
    Language English
    Publishing date 2021-05-11
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-021-22962-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Associations of healthy food choices with gut microbiota profiles.

    Koponen, Kari K / Salosensaari, Aaro / Ruuskanen, Matti O / Havulinna, Aki S / Männistö, Satu / Jousilahti, Pekka / Palmu, Joonatan / Salido, Rodolfo / Sanders, Karenina / Brennan, Caitriona / Humphrey, Gregory C / Sanders, Jon G / Meric, Guillaume / Cheng, Susan / Inouye, Michael / Jain, Mohit / Niiranen, Teemu J / Valsta, Liisa M / Knight, Rob /
    Salomaa, Veikko V

    The American journal of clinical nutrition

    2021  Volume 114, Issue 2, Page(s) 605–616

    Abstract: Background: Diet has a major influence on the human gut microbiota, which has been linked to health and disease. However, epidemiological studies on associations of a healthy diet with the microbiota utilizing a whole-diet approach are still scant.: ... ...

    Abstract Background: Diet has a major influence on the human gut microbiota, which has been linked to health and disease. However, epidemiological studies on associations of a healthy diet with the microbiota utilizing a whole-diet approach are still scant.
    Objectives: To assess associations between healthy food choices and human gut microbiota composition, and to determine the strength of association with functional potential.
    Methods: This population-based study sample consisted of 4930 participants (ages 25-74; 53% women) in the FINRISK 2002 study. Intakes of recommended foods were assessed using a food propensity questionnaire, and responses were transformed into healthy food choices (HFC) scores. Microbial diversity (alpha diversity) and compositional differences (beta diversity) and their associations with the HFC score and its components were assessed using linear regression. Multiple permutational multivariate ANOVAs were run from whole-metagenome shallow shotgun-sequenced samples. Associations between specific taxa and HFC were analyzed using linear regression. Functional associations were derived from Kyoto Encyclopedia of Genes and Genomes orthologies with linear regression models.
    Results: Both microbial alpha diversity (β/SD, 0.044; SE, 6.18 × 10-5; P = 2.21 × 10-3) and beta diversity (R2, 0.12; P ≤ 1.00 × 10-3) were associated with the HFC score. For alpha diversity, the strongest associations were observed for fiber-rich breads, poultry, fruits, and low-fat cheeses (all positive). For beta diversity, the most prominent associations were observed for vegetables, followed by berries and fruits. Genera with fiber-degrading and SCFA-producing capacities were positively associated with the HFC score. The HFC score was associated positively with functions such as SCFA metabolism and synthesis, and inversely with functions such as fatty acid biosynthesis and the sulfur relay system.
    Conclusions: Our results from a large, population-based survey confirm and extend findings of other, smaller-scale studies that plant- and fiber-rich dietary choices are associated with a more diverse and compositionally distinct microbiota, and with a greater potential to produce SCFAs.
    MeSH term(s) Adult ; Aged ; Bacteria/classification ; Choice Behavior ; Diet Surveys ; Diet, Healthy ; Female ; Food ; Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged
    Language English
    Publishing date 2021-05-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 280048-2
    ISSN 1938-3207 ; 0002-9165
    ISSN (online) 1938-3207
    ISSN 0002-9165
    DOI 10.1093/ajcn/nqab077
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system.

    Metcalf, Jessica L / Wegener Parfrey, Laura / Gonzalez, Antonio / Lauber, Christian L / Knights, Dan / Ackermann, Gail / Humphrey, Gregory C / Gebert, Matthew J / Van Treuren, Will / Berg-Lyons, Donna / Keepers, Kyle / Guo, Yan / Bullard, James / Fierer, Noah / Carter, David O / Knight, Rob

    eLife

    2013  Volume 2, Page(s) e01104

    Abstract: Establishing the time since death is critical in every death investigation, yet existing techniques are susceptible to a range of errors and biases. For example, forensic entomology is widely used to assess the postmortem interval (PMI), but errors can ... ...

    Abstract Establishing the time since death is critical in every death investigation, yet existing techniques are susceptible to a range of errors and biases. For example, forensic entomology is widely used to assess the postmortem interval (PMI), but errors can range from days to months. Microbes may provide a novel method for estimating PMI that avoids many of these limitations. Here we show that postmortem microbial community changes are dramatic, measurable, and repeatable in a mouse model system, allowing PMI to be estimated within approximately 3 days over 48 days. Our results provide a detailed understanding of bacterial and microbial eukaryotic ecology within a decomposing corpse system and suggest that microbial community data can be developed into a forensic tool for estimating PMI. DOI:http://dx.doi.org/10.7554/eLife.01104.001.
    MeSH term(s) Animals ; Forensic Sciences ; Mice ; Microbiota ; Models, Animal ; Postmortem Changes
    Language English
    Publishing date 2013-10-15
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2687154-3
    ISSN 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.01104
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