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Morrison ML, Xue KS, Rosenberg NA. Quantifying compositional variability in microbial communities with FAVA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601929. [PMID: 39005283 PMCID: PMC11244974 DOI: 10.1101/2024.07.03.601929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Microbial communities vary across space, time, and individual hosts, presenting new challenges for the development of statistics measuring the variability of community composition. To understand differences across microbiome samples from different host individuals, sampling times, spatial locations, or experimental replicates, we present FAVA, a new normalized measure for characterizing compositional variability across multiple microbiome samples. FAVA quantifies variability across many samples of taxonomic or functional relative abundances in a single index ranging between 0 and 1, equaling 0 when all samples are identical and equaling 1 when each sample is entirely comprised of a single taxon. Its definition relies on the population-genetic statisticF S T , with samples playing the role of "populations" and taxa playing the role of "alleles." Its convenient mathematical properties allow users to compare disparate data sets. For example, FAVA values are commensurable across different numbers of taxonomic categories and different numbers of samples considered. We introduce extensions that incorporate phylogenetic similarity among taxa and spatial or temporal distances between samples. We illustrate how FAVA can be used to describe across-individual taxonomic variability in ruminant microbiomes at different regions along the gastrointestinal tract. In a second example, a longitudinal analysis of gut microbiomes of healthy human adults taking an antibiotic, we use FAVA to quantify the increase in temporal variability of microbiomes following the antibiotic course and to measure the duration of the antibiotic's influence on microbial variability. We have implemented this tool in an R package, FAVA, which can fit easily into existing pipelines for the analysis of microbial relative abundances.
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Affiliation(s)
| | - Katherine S. Xue
- Department of Biology, Stanford University, Stanford, CA 94305 USA
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Sadler RA, Shoveller AK, Shandilya UK, Charchoglyan A, Wagter-Lesperance L, Bridle BW, Mallard BA, Karrow NA. Beyond the Coagulation Cascade: Vitamin K and Its Multifaceted Impact on Human and Domesticated Animal Health. Curr Issues Mol Biol 2024; 46:7001-7031. [PMID: 39057059 PMCID: PMC11276079 DOI: 10.3390/cimb46070418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/27/2024] [Accepted: 06/29/2024] [Indexed: 07/28/2024] Open
Abstract
Vitamin K (VK) is an essential micronutrient impacting many systems in the body. This lipid-soluble vitamin is found in various plant and animal products and is absorbed via the lymphatic system. This biomolecule's importance to human health includes but is not limited to its promotion of brain, cardiovascular, bone, and immune functions. These biological properties are also necessary for maintaining domesticated animal health. The synergistic impact of both VK and vitamin D (VD) maximizes these health benefits, specifically for the circulatory and skeletal systems. This manuscript reviews VK's properties, molecular structures, nutrikinetics, mechanisms of action, daily requirements, safety in supplemental form, biomarkers used for its detection, and impacts on various organs. The purpose of synthesizing this information is to evaluate the potential uses of VK for the treatment or prevention of diseases.
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Affiliation(s)
- Rebecka A. Sadler
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.A.S.); (A.K.S.); (U.K.S.)
| | - Anna K. Shoveller
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.A.S.); (A.K.S.); (U.K.S.)
| | - Umesh K. Shandilya
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.A.S.); (A.K.S.); (U.K.S.)
| | - Armen Charchoglyan
- ImmunoCeutica Inc., Cambridge, ON N1T 1N6, Canada; (A.C.); (L.W.-L.); (B.W.B.); (B.A.M.)
- Advanced Analysis Centre, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Lauraine Wagter-Lesperance
- ImmunoCeutica Inc., Cambridge, ON N1T 1N6, Canada; (A.C.); (L.W.-L.); (B.W.B.); (B.A.M.)
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Byram W. Bridle
- ImmunoCeutica Inc., Cambridge, ON N1T 1N6, Canada; (A.C.); (L.W.-L.); (B.W.B.); (B.A.M.)
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Bonnie A. Mallard
- ImmunoCeutica Inc., Cambridge, ON N1T 1N6, Canada; (A.C.); (L.W.-L.); (B.W.B.); (B.A.M.)
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Niel A. Karrow
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.A.S.); (A.K.S.); (U.K.S.)
- ImmunoCeutica Inc., Cambridge, ON N1T 1N6, Canada; (A.C.); (L.W.-L.); (B.W.B.); (B.A.M.)
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Zhou X, Ganz AB, Rayner A, Cheng TY, Oba H, Rolnik B, Lancaster S, Lu X, Li Y, Johnson JS, Hoyd R, Spakowicz DJ, Slavich GM, Snyder MP. Dynamic Human Gut Microbiome and Immune Shifts During an Immersive Psychosocial Therapeutic Program. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600881. [PMID: 38979211 PMCID: PMC11230355 DOI: 10.1101/2024.06.26.600881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Background Depression is a leading cause of disability worldwide yet its underlying factors, particularly microbial associations, are poorly understood. Methods We examined the longitudinal interplay between the microbiome and immune system in the context of depression during an immersive psychosocial intervention. 142 multi-omics samples were collected from 52 well-characterized participants before, during, and three months after a nine-day inquiry-based stress reduction program. Results We found that depression was associated with both an increased presence of putatively pathogenic bacteria and reduced microbial beta-diversity. Following the intervention, we observed reductions in neuroinflammatory cytokines and improvements in several mental health indicators. Interestingly, participants with a Prevotella-dominant microbiome showed milder symptoms when depressed, along with a more resilient microbiome and more favorable inflammatory cytokine profile, including reduced levels of CXCL-1. Conclusions Our findings reveal a protective link between the Prevotella-dominant microbiome and depression, associated with a less inflammatory environment and moderated symptoms. These insights, coupled with observed improvements in neuroinflammatory markers and mental health from the intervention, highlight potential avenues for microbiome-targeted therapies in depression management.
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Affiliation(s)
- Xin Zhou
- Department of Genetics, Stanford University School of Medicine, CA, USA
- Stanford Center for Genomics and Personalized Medicine, Stanford university School of Medicine, CA, USA
- These authors contributed equally to the work
| | - Ariel B. Ganz
- Department of Genetics, Stanford University School of Medicine, CA, USA
- Stanford Healthcare Innovation Lab, Stanford University, CA, USA
- These authors contributed equally to the work
| | - Andre Rayner
- Department of Genetics, Stanford University School of Medicine, CA, USA
| | - Tess Yan Cheng
- Department of Genetics, Stanford University School of Medicine, CA, USA
- Department of Microbiology, College of Arts and Sciences, University of Washington, WA, USA
| | - Haley Oba
- Department of Genetics, Stanford University School of Medicine, CA, USA
| | - Benjamin Rolnik
- Department of Genetics, Stanford University School of Medicine, CA, USA
- Stanford Healthcare Innovation Lab, Stanford University, CA, USA
| | - Samuel Lancaster
- Department of Genetics, Stanford University School of Medicine, CA, USA
| | - Xinrui Lu
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Sichuan, China
| | - Yizhou Li
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Sichuan, China
| | - Jethro S. Johnson
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Rebecca Hoyd
- The Ohio State University Comprehensive Cancer Center, OH, USA
| | | | - George M. Slavich
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Michael P. Snyder
- Department of Genetics, Stanford University School of Medicine, CA, USA
- Stanford Center for Genomics and Personalized Medicine, Stanford university School of Medicine, CA, USA
- Stanford Healthcare Innovation Lab, Stanford University, CA, USA
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Maqsood R, Holland LA, Wu LI, Begnel ER, Adhiambo J, Owiti P, Chohan BH, Gantt S, Kinuthia J, Wamalwa D, Ojee E, Richardson BA, Slyker J, Lehman DA, Lim ES. Gut virome and microbiome dynamics before and after SARS-CoV-2 infection in women living with HIV and their infants. RESEARCH SQUARE 2024:rs.3.rs-4257515. [PMID: 38699305 PMCID: PMC11065063 DOI: 10.21203/rs.3.rs-4257515/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Microbiome perturbations can have long-term effects on health. The dynamics of the gut microbiome and virome in women living with HIV (WLHIV) and their newborn infants is poorly understood. Here, we performed metagenomic sequencing analyses on longitudinal stool samples including 23 mothers (13 WLHIV, 10 HIV-negative) and 12 infants that experienced SARS-CoV-2 infection with mild disease, as well as 40 mothers (18 WLHIV, 22 HIV-negative) and 60 infants that remained SARS-CoV-2 seronegative throughout the study follow-up. Regardless of HIV or SARS-CoV-2 status, maternal bacterial and viral profiles were distinct from infants. Using linear mixed effects models, we showed that while the microbiome alpha diversity trajectory was not significantly different between SARS-CoV-2 seropositive and seronegative women. However, seropositive women's positive trajectory while uninfected was abruptly reversed after SARS-CoV-2 infection (p = 0.015). However, gut virome signatures of women were not associated with SARS-CoV-2. Alterations in infant microbiome and virome diversities were generally not impacted by SARS-CoV-2 but were rather driven by development. We did not find statistically significant interactions between HIV and SARS-CoV-2 on the gut microbiome and virome. Overall, our study provides insights into the complex interplay between maternal and infant bacterial microbiome, virome, and the influence of SARS-CoV-2 and HIV status.
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Álvarez-Santacruz C, Tyrkalska SD, Candel S. The Microbiota in Long COVID. Int J Mol Sci 2024; 25:1330. [PMID: 38279329 PMCID: PMC10816132 DOI: 10.3390/ijms25021330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/19/2024] [Accepted: 01/20/2024] [Indexed: 01/28/2024] Open
Abstract
Interest in the coronavirus disease 2019 (COVID-19) has progressively decreased lately, mainly due to the great effectivity of vaccines. Furthermore, no new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants able to circumvent the protection of these vaccines, while presenting high transmissibility and/or lethality, have appeared. However, long COVID has emerged as a huge threat to human health and economy globally. The human microbiota plays an important role in health and disease, participating in the modulation of innate and adaptive immune responses. Thus, multiple studies have found that the nasopharyngeal microbiota is altered in COVID-19 patients, with these changes associated with the onset and/or severity of the disease. Nevertheless, although dysbiosis has also been reported in long COVID patients, mainly in the gut, little is known about the possible involvement of the microbiota in the development of this disease. Therefore, in this work, we aim to fill this gap in the knowledge by discussing and comparing the most relevant studies that have been published in this field up to this point. Hence, we discuss that the relevance of long COVID has probably been underestimated, and that the available data suggest that the microbiota could be playing a pivotal role on the pathogenesis of the disease. Further research to elucidate the involvement of the microbiota in long COVID will be essential to explore new therapeutic strategies based on manipulation of the microbiota.
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Affiliation(s)
| | - Sylwia D. Tyrkalska
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain;
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Pascual Parrilla, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Sergio Candel
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain;
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Pascual Parrilla, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Ge P, Luo Y, Liu J, Liu J, Wen H, Zhang G, Chen H. Eliminating COVID-19 as the immediate culprit for igniting pancreatitis. J Med Virol 2023; 95:e29272. [PMID: 38054501 DOI: 10.1002/jmv.29272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/24/2023] [Accepted: 11/16/2023] [Indexed: 12/07/2023]
Abstract
The impact of severe acute respiratory syndrome coronavirus 2 infection on the potential development of pancreatitis is a subject of ongoing debate within academic discourse. Establishing a causal link between COVID-19 and pancreatitis may not be fully supported by relying only on retrospective studies or case reports. This study examined the relationship between COVID-19 phenotypes and pancreatitis by Mendelian randomization (MR) method. The identification of instrumental variables (single nucleotide polymorphisms) that exhibit a robust association with the COVID-19 phenotypes was accomplished through a meticulous process of rigorous screening procedures. We included acute pancreatitis and chronic pancreatitis (CP) as the outcomes in the MR analysis, even though no definitive studies exist between COVID-19 and CP. A direct causal relationship between genetically predicted COVID-19 phenotypes and pancreatitis risk cannot be established. There is an ongoing debate over the designation of COVID-19 as a definitive cause of pancreatitis.
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Affiliation(s)
- Peng Ge
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yalan Luo
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jie Liu
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jin Liu
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Haiyun Wen
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Guixin Zhang
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Hailong Chen
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
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