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Santangelo BE, Apgar M, Colorado ASB, Martin CG, Sterrett J, Wall E, Joachimiak MP, Hunter LE, Lozupone CA. Integrating biological knowledge for mechanistic inference in the host-associated microbiome. Front Microbiol 2024; 15:1351678. [PMID: 38638909 PMCID: PMC11024261 DOI: 10.3389/fmicb.2024.1351678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/26/2024] [Indexed: 04/20/2024] Open
Abstract
Advances in high-throughput technologies have enhanced our ability to describe microbial communities as they relate to human health and disease. Alongside the growth in sequencing data has come an influx of resources that synthesize knowledge surrounding microbial traits, functions, and metabolic potential with knowledge of how they may impact host pathways to influence disease phenotypes. These knowledge bases can enable the development of mechanistic explanations that may underlie correlations detected between microbial communities and disease. In this review, we survey existing resources and methodologies for the computational integration of broad classes of microbial and host knowledge. We evaluate these knowledge bases in their access methods, content, and source characteristics. We discuss challenges of the creation and utilization of knowledge bases including inconsistency of nomenclature assignment of taxa and metabolites across sources, whether the biological entities represented are rooted in ontologies or taxonomies, and how the structure and accessibility limit the diversity of applications and user types. We make this information available in a code and data repository at: https://github.com/lozuponelab/knowledge-source-mappings. Addressing these challenges will allow for the development of more effective tools for drawing from abundant knowledge to find new insights into microbial mechanisms in disease by fostering a systematic and unbiased exploration of existing information.
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Affiliation(s)
- Brook E. Santangelo
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Madison Apgar
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | | | - Casey G. Martin
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | - John Sterrett
- Department of Integrative Physiology, University of Colorado, Boulder, CO, United States
| | - Elena Wall
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Marcin P. Joachimiak
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Biosystems Data Science Department, Berkeley, CA, United States
| | - Lawrence E. Hunter
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Catherine A. Lozupone
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
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Burkhart Colorado AS, Lazzaro A, Neff CP, Nusbacher N, Boyd K, Fiorillo S, Martin C, Siebert JC, Campbell TB, Borok M, Palmer BE, Lozupone C. Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe. MICROBIOME 2024; 12:18. [PMID: 38310301 PMCID: PMC10837999 DOI: 10.1186/s40168-023-01718-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 11/09/2023] [Indexed: 02/05/2024]
Abstract
BACKGROUND The widespread availability of antiretroviral therapy (ART) has dramatically reduced mortality and improved life expectancy for people living with HIV (PLWH). However, even with HIV-1 suppression, chronic immune activation and elevated inflammation persist and have been linked to a pro-inflammatory gut microbiome composition and compromised intestinal barrier integrity. PLWH in urban versus rural areas of sub-Saharan Africa experience differences in environmental factors that may impact the gut microbiome and immune system, in response to ART, yet this has not previously been investigated in these groups. To address this, we measured T cell activation/exhaustion/trafficking markers, plasma inflammatory markers, and fecal microbiome composition in PLWH and healthy participants recruited from an urban clinic in the city of Harare, Zimbabwe, and a district hospital that services surrounding rural villages. PLWH were either ART naïve at baseline and sampled again after 24 weeks of first-line ART and the antibiotic cotrimoxazole or were ART-experienced at both timepoints. RESULTS Although expected reductions in the inflammatory marker IL-6, T-cell activation, and exhaustion were observed with ART-induced viral suppression, these changes were much more pronounced in the urban versus the rural area. Gut microbiome composition was the most highly altered from healthy controls in ART experienced PLWH, and characterized by both reduced alpha diversity and altered composition. However, gut microbiome composition showed a pronounced relationship with T cell activation and exhaustion in ART-naïve PLWH, suggesting a particularly significant role for the gut microbiome in disease progression in uncontrolled infection. Elevated immune exhaustion after 24 weeks of ART did correlate with both living in the rural location and a more Prevotella-rich/Bacteroides-poor microbiome type, suggesting a potential role for rural-associated microbiome differences or their co-variates in the muted improvements in immune exhaustion in the rural area. CONCLUSION Successful ART was less effective at reducing gut microbiome-associated inflammation and T cell activation in PLWH in rural versus urban Zimbabwe, suggesting that individuals on ART in rural areas of Zimbabwe may be more vulnerable to co-morbidity related to sustained immune dysfunction in treated infection. Video Abstract.
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Affiliation(s)
| | - Alessandro Lazzaro
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185, Rome, Italy
| | - Charles Preston Neff
- Department Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Nichole Nusbacher
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Kathryn Boyd
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, England
| | - Suzanne Fiorillo
- Department Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Casey Martin
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Janet C Siebert
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Thomas B Campbell
- Department Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Margaret Borok
- Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Brent E Palmer
- Department Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Catherine Lozupone
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
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Smith WP. Negative Lifestyle Factors Specific to Aging Persons Living with HIV and Multimorbidity. J Int Assoc Provid AIDS Care 2024; 23:23259582241245228. [PMID: 39051608 PMCID: PMC11273731 DOI: 10.1177/23259582241245228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 07/27/2024] Open
Abstract
The primary goal of medical care during the pre-antiretroviral therapy (ART) era was to keep persons living with human immunodeficiency virus (HIV) alive, whereas since the advent of ART, the treatment objective has shifted to decreasing viral loads and infectiousness while increasing CD4+ T-cell counts and longevity. The health crisis, however, is in preventing and managing multimorbidity (ie, type 2 diabetes), which develops at a more accelerated or accentuated pace among aging persons living with HIV. Relative to the general population and age-matched uninfected adults, it may be more difficult for aging HIV-positive persons who also suffer from multimorbidity to improve negative lifestyle factors to the extent that their behaviors could support the prevention and management of diseases. With recommendations and a viable solution, this article explores the impact of negative lifestyle factors (ie, poor mental health, suboptimal nutrition, physical inactivity, alcohol use) on the health of aging individuals living with HIV.
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Alif SM, Rahman MA. Do people living with HIV have accelerated lung function decline, despite adequate treatment? Thorax 2023; 78:529-530. [PMID: 36808082 DOI: 10.1136/thorax-2023-220011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 02/22/2023]
Affiliation(s)
- Sheikh M Alif
- School of Public Health and Preventive Medicine, Monash University, Clayton, Victoria, Australia .,School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Muhammad Aziz Rahman
- Institute of Health and Wellbeing, Federation University Australia, Berwick, Victoria, Australia
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Shaffer M, Thurimella K, Sterrett JD, Lozupone CA. SCNIC: Sparse correlation network investigation for compositional data. Mol Ecol Resour 2023; 23:312-325. [PMID: 36001047 PMCID: PMC9744196 DOI: 10.1111/1755-0998.13704] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 12/14/2022]
Abstract
Microbiome studies are often limited by a lack of statistical power due to small sample sizes and a large number of features. This problem is exacerbated in correlative studies of multi-omic datasets. Statistical power can be increased by finding and summarizing modules of correlated observations, which is one dimensionality reduction method. Additionally, modules provide biological insight as correlated groups of microbes can have relationships among themselves. To address these challenges, we developed SCNIC: Sparse Cooccurrence Network Investigation for compositional data. SCNIC is open-source software that can generate correlation networks and detect and summarize modules of highly correlated features. Modules can be formed using either the Louvain Modularity Maximization (LMM) algorithm or a Shared Minimum Distance algorithm (SMD) that we newly describe here and relate to LMM using simulated data. We applied SCNIC to two published datasets and we achieved increased statistical power and identified microbes that not only differed across groups, but also correlated strongly with each other, suggesting shared environmental drivers or cooperative relationships among them. SCNIC provides an easy way to generate correlation networks, identify modules of correlated features and summarize them for downstream statistical analysis. Although SCNIC was designed considering properties of microbiome data, such as compositionality and sparsity, it can be applied to a variety of data types including metabolomics data and used to integrate multiple data types. SCNIC allows for the identification of functional microbial relationships at scale while increasing statistical power through feature reduction.
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Affiliation(s)
- Michael Shaffer
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kumar Thurimella
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA,Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - John D. Sterrett
- Department of Integrative Physiology, University of Colorado, Boulder, Colorado, USA
| | - Catherine A. Lozupone
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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Littlefield KM, Schneider JM, Neff CP, Soesanto V, Siebert JC, Nusbacher NM, Moreno-Huizar N, Cartwright IM, Armstrong AJS, Colgen SP, Lozupone CA, Palmer BE. Elevated inflammatory fecal immune factors in men who have sex with men with HIV associate with microbiome composition and gut barrier function. Front Immunol 2022; 13:1072720. [PMID: 36605218 PMCID: PMC9808389 DOI: 10.3389/fimmu.2022.1072720] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction People living with HIV infection (PLWH) exhibit elevated levels of gastrointestinal inflammation. Potential causes of this inflammation include HIV infection and associated immune dysfunction, sexual behaviors among men who have sex with men (MSM) and gut microbiome composition. Methods To better understand the etiology of gastrointestinal inflammation we examined levels of 28 fecal soluble immune factors (sIFs) and the fecal microbiome in well-defined cohorts of HIV seronegative MSM (MSM-SN), MSM with untreated HIV infection (MSM-HIV) and MSM with HIV on anti-retroviral treatment (MSMART). Additionally, fecal solutes from these participants were used to stimulate T-84 colonic epithelial cells to assess barrier function. Results Both MSM cohorts with HIV had elevated levels of fecal calprotectin, a clinically relevant marker of GI inflammation, and nine inflammatory fecal sIFs (GM-CSF, ICAM-1, IL-1β, IL-12/23, IL-15, IL-16, TNF-β, VCAM-1, and VEGF). Interestingly, four sIFs (GM-CSF, ICAM-1, IL-7 and IL-12/23) were significantly elevated in MSM-SN compared to seronegative male non-MSM. Conversely, IL-22 and IL-13, cytokines beneficial to gut health, were decreased in all MSM with HIV and MSM-SN respectively. Importantly, all of these sIFs significantly correlated with calprotectin, suggesting they play a role in GI inflammation. Principal coordinate analysis revealed clustering of fecal sIFs by MSM status and significant associations with microbiome composition. Additionally, fecal solutes from participants in the MSM-HIV cohort significantly decreased colonic transcellular fluid transport in vitro, compared to non-MSM-SN, and this decrease associated with overall sIF composition and increased concentrations of eight inflammatory sIFs in participants with HIV. Lastly, elevated levels of plasma, sCD14 and sCD163, directly correlated with decreased transcellular transport and microbiome composition respectively, indicating that sIFs and the gut microbiome are associated with, and potentially contribute to, bacterial translocation. Conclusion Taken together, these data demonstrate that inflammatory sIFs are elevated in MSM, regardless of HIV infection status, and are associated with the gut microbiome and intestinal barrier function.
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Affiliation(s)
| | | | - Charles P. Neff
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Victoria Soesanto
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Janet C. Siebert
- Department of Medicine, University of Colorado, Aurora, CO, United States
- CytoAnalytics, Denver, CO, United States
| | - Nichole M. Nusbacher
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Nancy Moreno-Huizar
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Ian M. Cartwright
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Abigail J. S. Armstrong
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Sean P. Colgen
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Catherine A. Lozupone
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Brent E. Palmer
- Department of Medicine, University of Colorado, Aurora, CO, United States
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Chen Y, Lin H, Cole M, Morris A, Martinson J, Mckay H, Mimiaga M, Margolick J, Fitch A, Methe B, Srinivas VR, Peddada S, Rinaldo CR. Signature changes in gut microbiome are associated with increased susceptibility to HIV-1 infection in MSM. MICROBIOME 2021; 9:237. [PMID: 34879869 PMCID: PMC8656045 DOI: 10.1186/s40168-021-01168-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/14/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Men who have sex with men (MSM) have been disproportionately affected by HIV-1 since the beginning of the AIDS pandemic, particularly in the USA and Europe. Compared to men who have sex with women (MSW), MSM have a distinct fecal microbiome regardless of HIV-1 infection. However, it is unclear whether the MSM-associated gut microbiome affects the susceptibility and progression of HIV-1 infection. We studied fecal microbiome profiles, short-chain fatty acids, and blood plasma inflammatory cytokines of 109 HIV-1 seroconverters (SC) from the early, 1984-1985 phase of the HIV-1 pandemic in the Multicenter AIDS Cohort Study (MACS) before and after HIV-1 infection compared to 156 HIV-1-negative MACS MSM (negative controls [NC]). RESULTS We found that family Succinivibrionaceae, S24-7, Mogibacteriaceae, Coriobacteriaceae, and Erysipelotrichaceae were significantly higher (p<0.05), whereas Odoribacteraceae, Verucomicrobiaceae, Bacteroidaceae, Barnesiellaceae, and Rikenellaceae were significantly lower (p<0.05), in SC before HIV-1 infection compared to NC. At the species level, Prevotella stercorea, Eubacterium biforme, and Collinsella aerofaciens were significantly higher (p<0.05), and Eubacterium dolichum, Desulfovibrio D168, Alistipes onderdonkii, Ruminococcus torques, Bacteroides fragilis, Bacteroides caccae, Alistipes putredinis, Akkermansia muciniphila, Bacteroides uniformis, and Bacteroides ovatus were significantly lower (p<0.05) in SC before HIV-1 infection compared to NC. After HIV-1 infection, family Prevotellaceae and Victivallaceae and species Bacteroides fragilis and Eubacterium cylindroides were significantly higher (p<0.05) in SC who developed AIDS within 5 years compared to the SC who were AIDS free for more than 10 years without antiretroviral therapy (ART). In addition, family Victivallaceae and species Prevotella stercorea, Coprococcus eutactus, and Butyrivibrio crossotus were significantly higher (p<0.05) and Gemmiger formicilis and Blautia obeum were significantly lower (p<0.05) after HIV-1 infection in SC who developed AIDS within 5-10 years compared to the SC who were AIDS-free for more than 10 years without ART. Furthermore, plasma inflammatory cytokine levels of sCD14, sCD163, interleukin 6, and lipopolysaccharide binding protein were significantly higher in SC with p<0.05 before HIV-1 infection compared to NC. CONCLUSIONS Our results suggest that pathogenic changes in the gut microbiome were present in MSM several months prior to infection with HIV-1 in the early phase of the AIDS pandemic in the USA. This was associated with increased inflammatory biomarkers in the blood and risk for development of AIDS. Video abstract.
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Affiliation(s)
- Yue Chen
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA USA
| | - Huang Lin
- Current address: Biostatistics and Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD USA
- Department of Biostatistics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA USA
| | - Mariah Cole
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA USA
- Present address: Wilmot Cancer Center, University of Rochester Medical Center, Rochester, NY USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Jeremy Martinson
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA USA
| | - Heather Mckay
- Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Matthew Mimiaga
- Department of Epidemiology, Fielding School of Public Health, University of California at Los Angeles, Los Angeles, CA USA
| | - Joseph Margolick
- Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Adam Fitch
- Present address: Wilmot Cancer Center, University of Rochester Medical Center, Rochester, NY USA
| | - Barbara Methe
- Present address: Wilmot Cancer Center, University of Rochester Medical Center, Rochester, NY USA
| | - Vatsala Rangachar Srinivas
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA USA
| | - Shyamal Peddada
- Current address: Biostatistics and Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD USA
- Department of Biostatistics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA USA
| | - Charles R. Rinaldo
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA USA
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