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Fitzjerrells RL, Ollberding NJ, Mangalam AK. Looking at the full picture, using topic modeling to observe microbiome communities associated with disease. GUT MICROBES REPORTS 2024; 1:1-11. [PMID: 39183943 PMCID: PMC11340690 DOI: 10.1080/29933935.2024.2378067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/24/2024] [Accepted: 07/01/2024] [Indexed: 08/27/2024]
Abstract
The microbiome, a complex micro-ecosystem, helps the host with various vital physiological processes. Alterations of the microbiome (dysbiosis) have been linked with several diseases, and generally, differential abundance testing between the healthy and patient groups is performed to identify important bacteria. However, providing a singular species of bacteria to an individual as treatment has not been as successful as fecal microbiota transplant therapy, where the entire microbiome of a healthy individual is transferred. These observations suggest that a combination of bacteria might be crucial for the beneficial effects. Here we provide the framework to utilize topic modeling, an unsupervised machine learning approach, to identify a community of bacteria related to health or disease. Specifically, we used our previously published gut microbiome data of patients with multiple sclerosis (MS), a neurodegenerative disease linked to a dysbiotic gut microbiome. We identified communities of bacteria associated with MS, including genera previously discovered, but also others that would have been overlooked by differential abundance testing. This method can be a useful tool for analyzing the microbiome, and it should be considered along with the commonly utilized differential abundance tests to better understand the role of the gut microbiome in health and disease.
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Affiliation(s)
- Rachel L. Fitzjerrells
- Interdisciplinary Graduate Program in Informatics, University of Iowa, Iowa City, IA, 52242, USA
- College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Nicholas J. Ollberding
- Division of Biostatistics and Epidemiology; Cincinnati Children’s Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, USA
| | - Ashutosh K. Mangalam
- Interdisciplinary Graduate Program in Informatics, University of Iowa, Iowa City, IA, 52242, USA
- College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Iowa City VA Health Care System, 601 US-6 W, Iowa City, IA 52246, USA
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2
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Cao L, Kong Y, Fan Y, Ni M, Tourancheau A, Ksiezarek M, Mead EA, Koo T, Gitman M, Zhang XS, Fang G. mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome. Nat Methods 2024; 21:236-246. [PMID: 38177508 DOI: 10.1038/s41592-023-02125-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/08/2023] [Indexed: 01/06/2024]
Abstract
Metagenomics has enabled the comprehensive study of microbiomes. However, many applications would benefit from a method that sequences specific bacterial taxa of interest, but not most background taxa. We developed mEnrich-seq (in which 'm' stands for methylation and seq for sequencing) for enriching taxa of interest from metagenomic DNA before sequencing. The core idea is to exploit the self versus nonself differentiation by natural bacterial DNA methylation and rationally choose methylation-sensitive restriction enzymes, individually or in combination, to deplete host and background taxa while enriching targeted taxa. This idea is integrated with library preparation procedures and applied in several applications to enrich (up to 117-fold) pathogenic or beneficial bacteria from human urine and fecal samples, including species that are hard to culture or of low abundance. We assessed 4,601 bacterial strains with mapped methylomes so far and showed broad applicability of mEnrich-seq. mEnrich-seq provides microbiome researchers with a versatile and cost-effective approach for selective sequencing of diverse taxa of interest.
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Affiliation(s)
- Lei Cao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yimeng Kong
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yu Fan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mi Ni
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alan Tourancheau
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Magdalena Ksiezarek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edward A Mead
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tonny Koo
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa Gitman
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xue-Song Zhang
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, NJ, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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3
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Gudra D, Silamikelis I, Pjalkovskis J, Danenberga I, Pupola D, Skenders G, Ustinova M, Megnis K, Leja M, Vangravs R, Fridmanis D. Abundance and prevalence of ESBL coding genes in patients undergoing first line eradication therapy for Helicobacter pylori. PLoS One 2023; 18:e0289879. [PMID: 37561723 PMCID: PMC10414638 DOI: 10.1371/journal.pone.0289879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 07/28/2023] [Indexed: 08/12/2023] Open
Abstract
The spread of extended-spectrum beta-lactamases (ESBLs) in nosocomial and community-acquired enterobacteria is an important challenge for clinicians due to the limited therapeutic options for infections that are caused by these organisms. Here, we developed a panel of ESBL coding genes, evaluated the abundance and prevalence of ESBL encoding genes in patients undergoing H. pylori eradication therapy, and summarized the effects of eradication therapy on functional profiles of the gut microbiome. To assess the repertoire of known beta lactamase (BL) genes, they were divided into clusters according to their evolutionary relation. Primers were designed for amplification of cluster marker regions, and the efficiency of this amplification panel was assessed in 120 fecal samples acquired from 60 patients undergoing H. pylori eradication therapy. In addition, fecal samples from an additional 30 patients were used to validate the detection efficiency of the developed ESBL panel. The presence for majority of targeted clusters was confirmed by NGS of amplification products. Metagenomic sequencing revealed that the abundance of ESBL genes within the pool of microorganisms was very low. The global relative abundances of the ESBL-coding gene clusters did not differ significantly among treatment states. However, at the level of each cluster, classical ESBL producers such as Klebsiella sp. for blaOXY (p = 0.0076), Acinetobacter sp. for blaADC (p = 0.02297) and others, differed significantly with a tendency to decrease compared to the pre- and post-eradication states. Only 13 clusters were common across all three datasets, suggesting a patient-specific distribution profile of ESBL-coding genes. The number of AMR genes detected in the post-eradication state was higher than that in the pre-eradication state, which could be attributed, at least in part, to the therapy. This study demonstrated that the ESBL screening panel was effective in targeting ESBL-coding gene clusters from bacterial DNA and that minor differences exist in the abundance and prevalence of ESBL-coding gene levels before and after eradication therapy.
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Affiliation(s)
- Dita Gudra
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | | | | | - Darta Pupola
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
| | - Girts Skenders
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
| | - Maija Ustinova
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Kaspars Megnis
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Marcis Leja
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Reinis Vangravs
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
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Krekosch P, Jonen V, Abdelaziz H. First periprosthetic hip infection caused by Eggerthella lenta. J Clin Orthop Trauma 2023; 43:102234. [PMID: 37601619 PMCID: PMC10432780 DOI: 10.1016/j.jcot.2023.102234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 07/17/2023] [Accepted: 08/03/2023] [Indexed: 08/22/2023] Open
Abstract
Periprosthetic joint infection (PJI) caused by anaerobic, Gram-positive bacilli is rare. We present here a case of an 83-year-old female patient who was admitted to our tertiary referral arthroplasty center to treat a complex PJI of her right hip joint after multiple failed surgeries. External and intraoperative cultures reveald growth of Eggerthella lenta (E. lenta). Microbiological identification was fast but in a very few samples. A successful management, comprising of radical debridement with one-stage exchange and an antibiotic treatment with multiple antibiotics, has been achieved at 24-month follow-up. To the best of our knowledge, we have provided the first case study of a hip PJI caused by E. lenta successfully treated with one-stage exchange and an adequate antibiotic treatment.
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Affiliation(s)
- Philip Krekosch
- Department of Joint Replacement Surgery, Helios ENDO-Klinik Hamburg, Holstenstrasse 2, 22767, Hamburg, Germany
| | - Volker Jonen
- Department of Joint Replacement Surgery, Helios ENDO-Klinik Hamburg, Holstenstrasse 2, 22767, Hamburg, Germany
| | - Hussein Abdelaziz
- Department of Joint Replacement Surgery, Helios ENDO-Klinik Hamburg, Holstenstrasse 2, 22767, Hamburg, Germany
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Shrode RL, Ollberding NJ, Mangalam AK. Looking at the Full Picture: Utilizing Topic Modeling to Determine Disease-Associated Microbiome Communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.21.549984. [PMID: 37546903 PMCID: PMC10401927 DOI: 10.1101/2023.07.21.549984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The microbiome is a complex micro-ecosystem that provides the host with pathogen defense, food metabolism, and other vital processes. Alterations of the microbiome (dysbiosis) have been linked with a number of diseases such as cancers, multiple sclerosis (MS), Alzheimer's disease, etc. Generally, differential abundance testing between the healthy and patient groups is performed to identify important bacteria (enriched or depleted in one group). However, simply providing a singular species of bacteria to an individual lacking that species for health improvement has not been as successful as fecal matter transplant (FMT) therapy. Interestingly, FMT therapy transfers the entire gut microbiome of a healthy (or mixture of) individual to an individual with a disease. FMTs do, however, have limited success, possibly due to concerns that not all bacteria in the community may be responsible for the healthy phenotype. Therefore, it is important to identify the community of microorganisms linked to the health as well as the disease state of the host. Here we applied topic modeling, a natural language processing tool, to assess latent interactions occurring among microbes; thus, providing a representation of the community of bacteria relevant to healthy vs. disease state. Specifically, we utilized our previously published data that studied the gut microbiome of patients with relapsing-remitting MS (RRMS), a neurodegenerative autoimmune disease that has been linked to a variety of factors, including a dysbiotic gut microbiome. With topic modeling we identified communities of bacteria associated with RRMS, including genera previously discovered, but also other taxa that would have been overlooked simply with differential abundance testing. Our work shows that topic modeling can be a useful tool for analyzing the microbiome in dysbiosis and that it could be considered along with the commonly utilized differential abundance tests to better understand the role of the gut microbiome in health and disease.
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Affiliation(s)
- Rachel L. Shrode
- Department of Informatics, University of Iowa, Iowa City, IA, 52242, USA
- College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Nicholas J. Ollberding
- Division of Biostatistics and Epidemiology; Cincinnati Children’s Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, USA
| | - Ashutosh K. Mangalam
- Department of Informatics, University of Iowa, Iowa City, IA, 52242, USA
- College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- University of Iowa, 25 S Grand Ave, 1080-ML, Iowa City, IA, 52246, USA
- Clinician Scientist, Iowa City VA Health Care System, 601 US-6 W, Iowa City, IA 52246, USA
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Noecker C, Sanchez J, Bisanz JE, Escalante V, Alexander M, Trepka K, Heinken A, Liu Y, Dodd D, Thiele I, DeFelice BC, Turnbaugh PJ. Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta. PLoS Biol 2023; 21:e3002125. [PMID: 37205710 PMCID: PMC10234575 DOI: 10.1371/journal.pbio.3002125] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 06/01/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
Human gut bacteria perform diverse metabolic functions with consequences for host health. The prevalent and disease-linked Actinobacterium Eggerthella lenta performs several unusual chemical transformations, but it does not metabolize sugars and its core growth strategy remains unclear. To obtain a comprehensive view of the metabolic network of E. lenta, we generated several complementary resources: defined culture media, metabolomics profiles of strain isolates, and a curated genome-scale metabolic reconstruction. Stable isotope-resolved metabolomics revealed that E. lenta uses acetate as a key carbon source while catabolizing arginine to generate ATP, traits which could be recapitulated in silico by our updated metabolic model. We compared these in vitro findings with metabolite shifts observed in E. lenta-colonized gnotobiotic mice, identifying shared signatures across environments and highlighting catabolism of the host signaling metabolite agmatine as an alternative energy pathway. Together, our results elucidate a distinctive metabolic niche filled by E. lenta in the gut ecosystem. Our culture media formulations, atlas of metabolomics data, and genome-scale metabolic reconstructions form a freely available collection of resources to support further study of the biology of this prevalent gut bacterium.
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Affiliation(s)
- Cecilia Noecker
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Juan Sanchez
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Jordan E. Bisanz
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Veronica Escalante
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Margaret Alexander
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Kai Trepka
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Almut Heinken
- School of Medicine, National University of Ireland, Galway, Ireland
| | - Yuanyuan Liu
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Dylan Dodd
- Department of Pathology, Stanford University, Stanford, California, United States of America
- Department of Microbiology & Immunology, Stanford University, Stanford, California, United States of America
| | - Ines Thiele
- School of Medicine, National University of Ireland, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Brian C. DeFelice
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Peter J. Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
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7
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Buttimer C, Khokhlova EV, Stein L, Hueston CM, Govi B, Draper LA, Ross RP, Shkoporov AN, Hill C. Temperate bacteriophages infecting the mucin-degrading bacterium Ruminococcus gnavus from the human gut. Gut Microbes 2023; 15:2194794. [PMID: 36994608 PMCID: PMC10072058 DOI: 10.1080/19490976.2023.2194794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
Ruminococcus gnavus is a prevalent gut microbe reported to occur in higher abundance among individuals with inflammatory bowel disease (IBD). This study reports the isolation and characterization of six bacteriophages (phages) isolated from human fecal material and environmental samples that infect this species. Isolated phages have a siphovirus morphology, with genomes ranging between 36.5 and 37.8 kbp. Genome analysis indicates that the phages have a temperate lifestyle, which was confirmed by their ability to form lysogens on their host bacterial species. In contrast to the finding that phages lyse their host in liquid medium, results from a mouse trial indicate these phages can co-exist with the host bacterium in the gut without causing a significant reduction of R. gnavus. The bacterial counts in the feces of phage-treated mice did not significantly differ in the presence of phage. Furthermore, analysis of publicly available gut virome sequence data indicates a high abundance of these phages among individuals suffering from IBD. This work provides the first insight into how phages interact with R. gnavus in the human gut microbiome.
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Affiliation(s)
- Colin Buttimer
- APC Microbiome Ireland and School of Microbiology, University College, Cork, Ireland
| | | | - Lisa Stein
- APC Microbiome Ireland and School of Microbiology, University College, Cork, Ireland
| | - Cara M. Hueston
- APC Microbiome Ireland and School of Microbiology, University College, Cork, Ireland
| | - Bianca Govi
- APC Microbiome Ireland and School of Microbiology, University College, Cork, Ireland
| | - Lorraine A. Draper
- APC Microbiome Ireland and School of Microbiology, University College, Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Ireland and School of Microbiology, University College, Cork, Ireland
| | | | - Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College, Cork, Ireland
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Li X, Xu E, Shi C, Qiao G, Chen S, Xu Y, Liu Y, Bao X. Identification and Antibiotic Susceptibility of Eggerthella lenta in Bloodstream Infections. Pol J Microbiol 2022; 71:257-261. [PMID: 35716165 PMCID: PMC9252136 DOI: 10.33073/pjm-2022-024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 05/14/2022] [Indexed: 12/03/2022] Open
Abstract
The identification and antibiotic susceptibility of two clinical isolates of Eggerthella lenta from bloodstream infections were determined. This microorganism is rarely pathogenic, and the findings are presented here to promote the detection and awareness of this infection. The bacteria were obtained from one patient with pressure sores and another with a malignant gastric tumor. Smears were prepared, stained, and examined by microscopy. Single colonies were analyzed by Gram staining, MALDI-TOF MS, and the 16S rRNA gene sequencing. Antibiotic sensitivity was assessed by the agar dilution method. The bacilli were found to be Gram-positive, and the MS results showed 99.8% homology with E. lenta. It was confirmed by gene sequencing. Antibiotic susceptibility tests demonstrated that E. lenta was sensitive to piperacillin-tazobactam, ampicillin-sulbactam, imipenem, meropenem, metronidazole, clindamycin, and vancomycin. This study could increase awareness of this rare infection. ![]()
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Affiliation(s)
- Xiangyun Li
- Department of Laboratory Medicine, the First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Enjun Xu
- Department of Laboratory Medicine, the First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Cuixiao Shi
- Department of Laboratory Medicine, the First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Guanhua Qiao
- Department of Laboratory Medicine, Anhui Medical University, Hefei, People's Republic of China
| | - Shuyi Chen
- Department of Laboratory Medicine, Anhui Medical University, Hefei, People's Republic of China
| | - Yuanhong Xu
- Department of Laboratory Medicine, the First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Yajing Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, Anhui Medical University, Hefei, People's Republic of China
| | - Xundi Bao
- Department of Laboratory Medicine, Anhui Chest Hospital, Hefei, People's Republic of China
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