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Manus MB, Sardaro MLS, Dada O, Davis MI, Romoff MR, Torello SG, Ubadigbo E, Wu RC, Miller ES, Amato KR. Interactions with alloparents are associated with the diversity of infant skin and fecal bacterial communities in Chicago, United States. Am J Hum Biol 2023:e23972. [PMID: 37632331 DOI: 10.1002/ajhb.23972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/28/2023] Open
Abstract
INTRODUCTION Social interactions shape the infant microbiome by providing opportunities for caregivers to spread bacteria through physical contact. With most research focused on the impact of maternal-infant contact on the infant gut microbiome, it is unclear how alloparents (i.e., caregivers other than the parents) influence the bacterial communities of infant body sites that are frequently contacted during bouts of caregiving, including the skin. METHODS To begin to understand how allocare may influence the diversity of the infant microbiome, detailed questionnaire data on infant-alloparent relationships and specific allocare behaviors were coupled with skin and fecal microbiome samples (four body sites) from 48 infants living in Chicago, United States. RESULTS Data from 16S rRNA gene amplicon sequencing indicated that infant skin and fecal bacterial diversity showed strong associations (positive and negative) to having female adult alloparents. Alloparental feeding and co-sleeping displayed stronger associations to infant bacterial diversity compared to playing or holding. The associations with allocare behaviors differed in magnitude and direction across infant body sites. Bacterial relative abundances varied by infant-alloparent relationship and breastfeeding status. CONCLUSION This study provides some of the first evidence of an association between allocare and infant skin and fecal bacterial diversity. The results suggest that infants' exposure to bacteria from the social environment may vary based on infant-alloparent relationships and allocare behaviors. Since the microbiome influences immune system development, variation in allocare that impacts the diversity of infant bacterial communities may be an underexplored dimension of the social determinants of health in early life.
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Affiliation(s)
- Melissa B Manus
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Maria Luisa Savo Sardaro
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
- Department of Human Science and Promotion of the Quality of Life, University of San Raffaele, Rome, Italy
| | - Omolola Dada
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Maya I Davis
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Melissa R Romoff
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Stephanie G Torello
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Esther Ubadigbo
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Rebecca C Wu
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Emily S Miller
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
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2
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Singh A, Alexander SG, Martin S. Gut microbiome homeostasis and the future of probiotics in cancer immunotherapy. Front Immunol 2023; 14:1114499. [PMID: 37261348 PMCID: PMC10228691 DOI: 10.3389/fimmu.2023.1114499] [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: 12/06/2022] [Accepted: 04/17/2023] [Indexed: 06/02/2023] Open
Abstract
The gut microbiome has an impact on cancer immune surveillance and immunotherapy, with recent studies showing categorical differences between immunotherapy-sensitive and immunotherapy-resistant cancer patient cohorts. Although probiotics are traditionally being supplemented to promote treatments or sustain therapeutic benefits; the FDA has not approved any for use with immunotherapy. The first step in developing probiotics for immunotherapy is identifying helpful or harmful bacteria down to the strain level. The gut microbiome's heterogeneity before and during treatment is also being investigated to determine microbial strains that are important for immunotherapy. Moreover, Dietary fiber intake, prebiotic supplementation and fecal microbiota transplantation (FMT) were found to enhance intratumoral CD8+ T cell to T-reg ratio in the clinics. The possibility of probiotic immunotherapy as a "living adjuvant" to CAR treatment and checkpoint blockade resistance is actively being investigated.
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Manus MB, Watson E, Kuthyar S, Carba D, Belarmino NM, McDade TW, Kuzawa CW, Amato KR. Prenatal household size and composition are associated with infant fecal bacterial diversity in Cebu, Philippines. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 181:45-58. [PMID: 36847111 DOI: 10.1002/ajpa.24720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 03/01/2023]
Abstract
OBJECTIVES The gut microbiome (GM) connects physical and social environments to infant health. Since the infant GM affects immune system development, there is interest in understanding how infants acquire microbes from mothers and other household members. MATERIALS AND METHODS As a part of the Cebu Longitudinal Health and Nutrition Survey (CLHNS), we paired fecal samples (proxy for the GM) collected from infants living in Metro Cebu, Philippines at 2 weeks (N = 39) and 6 months (N = 36) with maternal interviews about prenatal household composition. We hypothesized that relationships between prenatal household size and composition and infant GM bacterial diversity (as measured in fecal samples) would vary by infant age, as well as by household member age and sex. We also hypothesized that infant GM bacterial abundances would differ by prenatal household size and composition. RESULTS Data from 16 S rRNA bacterial gene sequencing show that prenatal household size was the most precise estimator of infant GM bacterial diversity, and that the direction of the association between this variable and infant GM bacterial diversity changed between the two time points. The abundances of bacterial families in the infant GM varied by prenatal household variables. CONCLUSIONS Results highlight the contributions of various household sources to the bacterial diversity of the infant GM, and suggest that prenatal household size is a useful measure for estimating infant GM bacterial diversity in this cohort. Future research should measure the effect of specific sources of household bacterial exposures, including social interactions with caregivers, on the infant GM.
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Affiliation(s)
- Melissa B Manus
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Elijah Watson
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Sahana Kuthyar
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA.,Department of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Delia Carba
- Office of Population Studies, University of San Carlos, Cebu City, Philippines
| | - Nikola M Belarmino
- Office of Population Studies, University of San Carlos, Cebu City, Philippines
| | - Thomas W McDade
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA.,Institute for Policy Research, Northwestern University, Evanston, Illinois, USA
| | - Christopher W Kuzawa
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA.,Institute for Policy Research, Northwestern University, Evanston, Illinois, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
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4
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Piperata BA, Scaggs SA, Dufour DL, Adams IK. Measuring food insecurity: An introduction to tools for human biologists and ecologists. Am J Hum Biol 2023; 35:e23821. [PMID: 36256611 DOI: 10.1002/ajhb.23821] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 08/20/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVE Food insecurity is a significant and growing concern undermining the wellbeing of 30% of the global population. Food in/security is a complex construct consisting of four dimensions: availability, access, utilization, and stability, making it challenging to measure. We provide a toolkit human biologists/ecologists can use to advance research on this topic. METHODS We review the strengths and limitations of common tools used to measure food access and utilization, the two dimensions most proximate to people's lived experience, and emphasize tools that provide data needed to best link food security with human biological outcomes. We also discuss methods that provide contextual data human biologists/ecologists will find useful for study design, ensuring instrument validity, and improving data quality. RESULTS Food access is principally measured using experience-based instruments that emphasize economic access. Social access, such as food sharing, is under-studied and we recommend using social network analysis to explore this dimension. In terms of utilization, emphasis has been on food choice measured as dietary diversity. Food preparation and intrahousehold distribution, also part of the utilization dimension, are less studied and standardized instruments for measuring both are lacking. The embodiment of food insecurity has focused on child growth, although a growing literature addresses adult mental wellbeing and chronic and infectious disease risk. CONCLUSIONS We see the potential to expand outcomes to include reproductive and immune function, physical activity, and the gut microbiome. Human biologists/ecologists are well-positioned to advance understanding of the human health impacts of food insecurity and provide data to support intervention efforts.
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Affiliation(s)
- Barbara A Piperata
- Department of Anthropology, The Ohio State University, Columbus, Ohio, USA
| | - Shane A Scaggs
- Department of Anthropology, The Ohio State University, Columbus, Ohio, USA
| | | | - Ingrid K Adams
- Department of Extension and School of Health and Rehabilitation Sciences, The Ohio State University, Columbus, Ohio, USA
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5
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Practical Opportunities for Microbiome Analyses and Bioinformatics in Poultry Processing. Poult Sci 2022; 101:101787. [PMID: 35346493 PMCID: PMC9079351 DOI: 10.1016/j.psj.2022.101787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/05/2022] [Indexed: 11/21/2022] Open
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Polyclonal Aptamers for Specific Fluorescence Labeling and Quantification of the Health Relevant Human Gut Bacterium Parabacteroides distasonis. Microorganisms 2021; 9:microorganisms9112284. [PMID: 34835410 PMCID: PMC8618460 DOI: 10.3390/microorganisms9112284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/27/2022] Open
Abstract
Single-stranded DNA aptamers as affinity molecules for the rapid, reliable detection of intestinal bacteria are of particular interest to equip health systems with novel robust and cheap diagnostic tools for monitoring the success of supplementation strategies with selected probiotic gut bacteria in the fight against major widespread threats, such as obesity and neurodegenerative diseases. The human gut bacterium Parabacteroides distasonis (P. distasonis) is positively associated with diseases such as obesity, non-alcoholic fatty liver disease and multiple sclerosis with reduced cell counts in these diseases and is thus a promising potential probiotic bacterium for future microbial supplementation. In this paper we report on the evolution of a specific polyclonal aptamer library by the fluorescence based FluCell-SELEX directed against whole cells of P. distasonis that specifically and efficiently binds and labels P. distasonis. The aptamer library showed high binding affinity and was suited to quantitatively discriminate P. distasonis from other prominent gut bacteria also in mixtures. We believe that this library against a promising probiotic bacterium as a prototype may open new routes towards the development of novel biosensors for the easy and efficient quantitative monitoring of microbial abundance in human microbiomes in general.
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Goolam Mahomed T, Peters RPH, Allam M, Ismail A, Mtshali S, Goolam Mahomed A, Ueckermann V, Kock MM, Ehlers MM. Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa. Sci Rep 2021; 11:19758. [PMID: 34611216 PMCID: PMC8492659 DOI: 10.1038/s41598-021-99127-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.
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Affiliation(s)
- T. Goolam Mahomed
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - R. P. H. Peters
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.442327.40000 0004 7860 2538Foundation for Professional Development, Research Unit, East London, South Africa
| | - M. Allam
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - A. Ismail
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - S. Mtshali
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | | | - V. Ueckermann
- grid.49697.350000 0001 2107 2298Department of Internal Medicine, University of Pretoria, Pretoria, South Africa
| | - M. M. Kock
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.416657.70000 0004 0630 4574Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Johannesburg, South Africa
| | - M. M. Ehlers
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.416657.70000 0004 0630 4574Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Johannesburg, South Africa
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FluCell-SELEX Aptamers as Specific Binding Molecules for Diagnostics of the Health Relevant Gut Bacterium Akkermansia muciniphila. Int J Mol Sci 2021; 22:ijms221910425. [PMID: 34638764 PMCID: PMC8509069 DOI: 10.3390/ijms221910425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 12/14/2022] Open
Abstract
Based on their unique properties, oligonucleotide aptamers have been named a gift of biological chemistry to life science. We report the development of DNA aptamers as the first high-affinity binding molecules available for fast and rapid labeling of the human gut bacterium Akkermansia muciniphila with a certain impact on Alzheimer´s disease. Fast and reliable analyses of the composition of microbiomes is an emerging field in microbiology. We describe the molecular evolution and biochemical characterization of a specific aptamer library by a FluCell-SELEX and the characterization of specific molecules from the library by bioinformatics. The aptamer AKK13.1 exerted universal applicability in different analysis techniques in modern microbiology, including fluorimetry, confocal laser scanning microscopy and flow cytometry. It was also functional as a specific binding entity hybridized to anchor primers chemically coupled via acrydite-modification to the surface of a polyacrylamide-hydrogel, which can be prototypically used for the construction of affinity surfaces in sensor chips. Together, the performance and methodological flexibility of the aptamers presented here may open new routes not only to develop novel Akkermansia-specific assays for clinical microbiology and the analyses of human stool samples but may also be an excellent starting point for the construction of novel electronic biosensors.
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Jiang R, Li WV, Li JJ. mbImpute: an accurate and robust imputation method for microbiome data. Genome Biol 2021; 22:192. [PMID: 34183041 PMCID: PMC8240317 DOI: 10.1186/s13059-021-02400-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/04/2021] [Indexed: 12/22/2022] Open
Abstract
A critical challenge in microbiome data analysis is the existence of many non-biological zeros, which distort taxon abundance distributions, complicate data analysis, and jeopardize the reliability of scientific discoveries. To address this issue, we propose the first imputation method for microbiome data-mbImpute-to identify and recover likely non-biological zeros by borrowing information jointly from similar samples, similar taxa, and optional metadata including sample covariates and taxon phylogeny. We demonstrate that mbImpute improves the power of identifying disease-related taxa from microbiome data of type 2 diabetes and colorectal cancer, and mbImpute preserves non-zero distributions of taxa abundances.
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Affiliation(s)
- Ruochen Jiang
- Department of Statistics, University of California, Los Angeles, 90095-1554, CA, USA
| | - Wei Vivian Li
- Department of Statistics, University of California, Los Angeles, 90095-1554, CA, USA
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, 08854, NJ, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, 90095-1554, CA, USA.
- Department of Human Genetics, University of California, Los Angeles, 90095-7088, CA, USA.
- Department of Computational Medicine, University of California, Los Angeles, 90095-1766, CA, USA.
- Department of Biostatistics, University of California, Los Angeles, 90095-1772, CA, USA.
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10
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Manus MB, Kuthyar S, Perroni-Marañón AG, de la Mora AN, Amato KR. Comparing different sample collection and storage methods for field-based skin microbiome research. Am J Hum Biol 2021; 34:e23584. [PMID: 33644952 DOI: 10.1002/ajhb.23584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES The skin, as well as its microbial communities, serves as the primary interface between the human body and the surrounding environment. In order to implement the skin microbiome into human biology research, there is a need to explore the effects of different sample collection and storage methodologies, including the feasibility of conducting skin microbiome studies in field settings. METHODS We collected 99 skin microbiome samples from nine infants living in Veracruz, Mexico using a dual-tipped "dry" swab on the right armpit, palm, and forehead and a "wet" swab (0.15 M NaCl and 0.1% Tween 20) on the same body parts on the left side of the body. One swab from each collection method was stored in 95% ethanol while the other was frozen at -20°C. 16S rRNA amplicon sequencing generated data on bacterial diversity and community composition, which were analyzed using PERMANOVA, linear mixed effects models, and an algorithm-based classifier. RESULTS Treatment (wet_ethanol, wet_freezer, dry_ethanol, and dry_freezer) had an effect (~10% explanatory power) on the bacterial community diversity and composition of skin samples, although body site exhibited a stronger effect (~20% explanatory power). Within treatments, the collection method (wet vs. dry) affected measures of bacterial diversity to a greater degree than did the storage method (ethanol vs. freezer). CONCLUSIONS Our study provides novel information on skin microbiome sample collection and storage methods, suggesting that ethanol storage is suitable for research in resource-limited settings. Our results highlight the need for future study design to account for interbody site microbial variation.
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Affiliation(s)
- Melissa B Manus
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Sahana Kuthyar
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA.,Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | | | | | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
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11
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Challenges in Human Skin Microbial Profiling for Forensic Science: A Review. Genes (Basel) 2020; 11:genes11091015. [PMID: 32872386 PMCID: PMC7564248 DOI: 10.3390/genes11091015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022] Open
Abstract
The human microbiome is comprised of the microbes that live on and within an individual, as well as immediately surrounding them. Microbial profiling may have forensic utility in the identification or association of individuals with criminal activities, using microbial signatures derived from a personal microbiome. This review highlights some important aspects of recent studies, many of which have revealed issues involving the effect of contamination of microbial samples from both technical and environmental sources and their impacts on microbiome research and the potential forensic applications of microbial profiling. It is imperative that these challenges be discussed and evaluated within a forensic context to better understand the future directions and potential applications of microbial profiling for human identification. It is necessary that the limitations identified be resolved prior to the adoption of microbial profiling, or, at a minimum, acknowledged by those applying this new approach.
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12
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Hoke MK, Schell LM. Doing biocultural anthropology: Continuity and change. Am J Hum Biol 2020; 32:e23471. [PMID: 32681558 DOI: 10.1002/ajhb.23471] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/27/2022] Open
Abstract
Biocultural anthropology has long represented an important approach in the study of human biology. However, despite demonstrated utility, its somewhat amorphous identity leaves some scholars questioning just what it means to be biocultural. In this article, rather than providing proscriptive doctrine, we contribute to these conversations about the nature of biocultural anthropology by considering what biocultural research does. We begin with a consideration of some of the foundational themes of biocultural work including recognition of the dialectical nature of sociocultural and biological forces, interest in inequality, and incorporation of both evolutionary and political economic perspectives. To emphasize the consistency of biocultural work over time, we also trace these themes from originating work to their appearance in current research. We then identify some of the key actions of the biocultural approach, noting that biocultural work can execute any number though rarely all of these actions simultaneously. We then offer brief introductions to the articles that make up this special issue, highlighting the ways in which each piece undertakes key biocultural actions. Following these introductions, we provide a discussion of some of the types of biocultural work that are not present in this special issue, recognizing the breadth of biocultural research across multiple subfields of anthropology. Finally, we point to some potentially fruitful directions for future biocultural research. In the end, we conclude that while biocultural anthropology may not have a cohesive or set agenda, it does have a clear and recognizable form of content and methodology illuminated by its actions.
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Affiliation(s)
- Morgan K Hoke
- Department of Anthropology & Population Studies Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lawrence M Schell
- Department of Anthropology, Department of Epidemiology and Statistics, & the Center for the Elimination of Minority Health Disparities, University at Albany, Albany, New York, USA
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13
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Feye KM, Thompson DR, Rothrock MJ, Kogut MH, Ricke SC. Poultry processing and the application of microbiome mapping. Poult Sci 2020; 99:678-688. [PMID: 32029154 PMCID: PMC7587767 DOI: 10.1016/j.psj.2019.12.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Indexed: 01/28/2023] Open
Abstract
Chicken is globally one of the most popular food animals. However, it is also one of the major reservoirs for foodborne pathogens, annually resulting in continued morbidity and mortality incidences worldwide. In an effort to reduce the threat of foodborne disease, the poultry industry has implemented a multifaceted antimicrobial program that incorporates not only chemical compounds, but also extensive amounts of water application and pathogen monitoring. Unfortunately, the pathogen detection methods currently used by the poultry industry lack speed, relying on microbiological plate methods and molecular detection systems that take time and lack precision. In many cases, the time to data acquisition can take 12 to 24 h. This is problematic if shorter-term answers are required which is becoming more likely as the public demand for chicken meat is only increasing, leading to new pressures to increase line speed. Therefore, new innovations in detection methods must occur to mitigate the risk of foodborne pathogens that could result from faster slaughter and processing speeds. Future technology will have 2 tracks: rapid methods that are meant to detect pathogens and indicator organisms within a few hours, and long-term methods that use microbiome mapping to evaluate sanitation and antimicrobial efficacy. Together, these methods will provide rapid, comprehensive data capable of being applied in both risk-assessment algorithms and used by management to safeguard the public.
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Affiliation(s)
- K M Feye
- Southern Plains Agricultural Research Center, USDA-ARS, Athens, TX 30605
| | - D R Thompson
- Department of Computer Science and Engineering, University of Arkansas, Fayetteville, AR 72704
| | - M J Rothrock
- US National Poultry Research Center, Egg Safety and Quality Research, USDA-ARS, Athens, GA 30605
| | - M H Kogut
- Southern Plains Agricultural Research Center, USDA-ARS, Athens, TX 30605
| | - S C Ricke
- Center for Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR 72704.
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Karoly HC, Mueller RL, Bidwell LC, Hutchison KE. Cannabinoids and the Microbiota-Gut-Brain Axis: Emerging Effects of Cannabidiol and Potential Applications to Alcohol Use Disorders. Alcohol Clin Exp Res 2019; 44:340-353. [PMID: 31803950 DOI: 10.1111/acer.14256] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/25/2019] [Indexed: 02/06/2023]
Abstract
The endocannabinoid system (ECS) has emerged in recent years as a potential treatment target for alcohol use disorders (AUD). In particular, the nonpsychoactive cannabinoid cannabidiol (CBD) has shown preclinical promise in ameliorating numerous clinical symptoms of AUD. There are several proposed mechanism(s) through which cannabinoids (and CBD in particular) may confer beneficial effects in the context of AUD. First, CBD may directly impact specific brain mechanisms underlying AUD to influence alcohol consumption and the clinical features of AUD. Second, CBD may influence AUD symptoms through its actions across the digestive, immune, and central nervous systems, collectively known as the microbiota-gut-brain axis (MGBA). Notably, emerging work suggests that alcohol and cannabinoids exert opposing effects on the MGBA. Alcohol is linked to immune dysfunction (e.g., chronic systemic inflammation in the brain and periphery) as well as disturbances in gut microbial species (microbiota) and increased intestinal permeability. These MGBA disruptions have been associated with AUD symptoms such as craving and impaired cognitive control. Conversely, existing preclinical data suggest that cannabinoids may confer beneficial effects on the gastrointestinal and immune system, such as reducing intestinal permeability, regulating gut bacteria, and reducing inflammation. Thus, cannabinoids may exert AUD harm-reduction effects, at least in part, through their beneficial actions across the MGBA. This review will provide a brief introduction to the ECS and the MGBA, discuss the effects of cannabinoids (particularly CBD) and alcohol in the brain, gut, and immune system (i.e., across the MGBA), and put forth a theoretical framework to inform future research questions.
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Affiliation(s)
- Hollis C Karoly
- Institute of Cognitive Science, University of Colorado Boulder, Boulder, Colorado
| | - Raeghan L Mueller
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, Colorado
| | - L Cinnamon Bidwell
- Institute of Cognitive Science, University of Colorado Boulder, Boulder, Colorado.,Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, Colorado
| | - Kent E Hutchison
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, Colorado
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Attaye I, Pinto-Sietsma SJ, Herrema H, Nieuwdorp M. A Crucial Role for Diet in the Relationship Between Gut Microbiota and Cardiometabolic Disease. Annu Rev Med 2019; 71:149-161. [PMID: 31479620 DOI: 10.1146/annurev-med-062218-023720] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cardiometabolic disease (CMD), such as type 2 diabetes mellitus and cardiovascular disease, contributes significantly to morbidity and mortality on a global scale. The gut microbiota has emerged as a potential target to beneficially modulate CMD risk, possibly via dietary interventions. Dietary interventions have been shown to considerably alter gut microbiota composition and function. Moreover, several diet-derived microbial metabolites are able to modulate human metabolism and thereby alter CMD risk. Dietary interventions that affect gut microbiota composition and function are therefore a promising, novel, and cost-efficient method to reduce CMD risk. Studies suggest that fermentable carbohydrates can beneficially alter gut microbiota composition and function, whereas high animal protein and high fat intake negatively impact gut microbiota function and composition. This review focuses on the role of macronutrients (i.e., carbohydrate, protein, and fat) and dietary patterns (e.g., vegetarian/vegan and Mediterranean diet) in gut microbiota composition and function in the context of CMD.
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Affiliation(s)
- Ilias Attaye
- Department of Vascular Medicine, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, 1081 HV Amsterdam, The Netherlands; .,Department of Experimental Vascular Medicine, Amsterdam Cardiovascular Sciences, University Medical Centers, 1081 HV Amsterdam, The Netherlands
| | - Sara-Joan Pinto-Sietsma
- Department of Vascular Medicine, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, 1081 HV Amsterdam, The Netherlands; .,Department of Clinical Epidemiology and Biostatistics, University Medical Centers, 1081 HV Amsterdam, The Netherlands
| | - Hilde Herrema
- Department of Experimental Vascular Medicine, Amsterdam Cardiovascular Sciences, University Medical Centers, 1081 HV Amsterdam, The Netherlands
| | - Max Nieuwdorp
- Department of Vascular Medicine, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, 1081 HV Amsterdam, The Netherlands; .,Department of Experimental Vascular Medicine, Amsterdam Cardiovascular Sciences, University Medical Centers, 1081 HV Amsterdam, The Netherlands.,Department of Internal Medicine, Amsterdam Diabetes Center, Amsterdam University Medical Centers, 1081 HV Amsterdam, The Netherlands.,Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
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16
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Hagerty SL, Ellingson JM, Helmuth TB, Bidwell LC, Hutchison KE, Bryan AD. An Overview and Proposed Research Framework for Studying Co-Occurring Mental- and Physical-Health Dysfunction. PERSPECTIVES ON PSYCHOLOGICAL SCIENCE 2019; 14:633-645. [PMID: 31173535 PMCID: PMC6778441 DOI: 10.1177/1745691619827010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mental- and physical-health conditions co-occur at a rate much higher than chance. Of patients who have a mental-health condition, more than half also have a physical disease, and these cases are associated with increased human suffering and societal cost. Comorbidity research to date has focused on co-occurring mental- and physical-health disorders separately, and relatively little research has examined the co-occurrence of mental- and physical-health dysfunction. In addition, even less is known about why mental- and physical-health dysfunction co-occurs or how to treat these cases. Thus, the aims of this article are to highlight the need for research at the intersection of physical- and mental-health dysfunction and to provide guidance on how to research cases of comorbidity. Toward these ends, we begin by presenting a selective overview of the possible role of biological processes in the co-occurrence of physical- and mental-health dysfunction using specific illustrative examples. Specifically, we outline how biological processes within the immune system and gastrointestinal system could underlie depression, irritable bowel syndrome, and their co-occurrence. We then advance and discuss a proposed research framework, including methodological and analytic guidance, that researchers could use when studying the phenomenon of co-occurring physical- and mental-health dysfunction.
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Affiliation(s)
- Sarah L. Hagerty
- Department of Psychology and Neuroscience, University of Colorado Boulder
| | | | - Timothy B. Helmuth
- Department of Psychology and Neuroscience, University of Colorado Boulder
| | | | - Kent E. Hutchison
- Department of Psychology and Neuroscience, University of Colorado Boulder
| | - Angela D. Bryan
- Department of Psychology and Neuroscience, University of Colorado Boulder
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17
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Abdel-Aziz MI, Vijverberg SJH, Neerincx AH, Kraneveld AD, Maitland-van der Zee AH. The crosstalk between microbiome and asthma: Exploring associations and challenges. Clin Exp Allergy 2019; 49:1067-1086. [PMID: 31148278 PMCID: PMC6852296 DOI: 10.1111/cea.13444] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/17/2022]
Abstract
With the advancement of high‐throughput DNA/RNA sequencing and computational analysis techniques, commensal bacteria are now considered almost as important as pathological ones. Understanding the interaction between these bacterial microbiota, host and asthma is crucial to reveal their role in asthma pathophysiology. Several airway and/or gut microbiome studies have shown associations between certain bacterial taxa and asthma. However, challenges remain before gained knowledge from these studies can be implemented into clinical practice, such as inconsistency between studies in choosing sampling compartments and/or sequencing approaches, variability of results in asthma studies, and not taking into account medication intake and diet composition especially when investigating gut microbiome. Overcoming those challenges will help to better understand the complex asthma disease process. The therapeutic potential of using pro‐ and prebiotics to prevent or reduce risk of asthma exacerbations requires further investigation. This review will focus on methodological issues regarding setting up a microbiome study, recent developments in asthma bacterial microbiome studies, challenges and future therapeutic potential.
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Affiliation(s)
- Mahmoud I Abdel-Aziz
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Clinical Pharmacy, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Susanne J H Vijverberg
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Anne H Neerincx
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Aletta D Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.,Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Anke H Maitland-van der Zee
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Pediatric Respiratory Medicine, Amsterdam UMC, Emma Children's Hospital, Amsterdam, The Netherlands
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18
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Abstract
Understanding the role of the microbiome in human health and how it can be modulated is becoming increasingly relevant for preventive medicine and for the medical management of chronic diseases. The development of high-throughput sequencing technologies has boosted microbiome research through the study of microbial genomes and allowing a more precise quantification of microbiome abundances and function. Microbiome data analysis is challenging because it involves high-dimensional structured multivariate sparse data and because of its compositional nature. In this review we outline some of the procedures that are most commonly used for microbiome analysis and that are implemented in R packages. We place particular emphasis on the compositional structure of microbiome data. We describe the principles of compositional data analysis and distinguish between standard methods and those that fit into compositional data analysis.
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Affiliation(s)
- M Luz Calle
- Biosciences Department, Faculty of Science and Technology, University of Vic - Central University of Catalonia, Vic 08500, Spain
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19
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Hagerty SL, Ellingson JM, Hutchison KE. Biological Systems Are a Common Link Between Alcohol Use Disorder and Co-Occurring Psychiatric and Medical Conditions. Alcohol Clin Exp Res 2018; 42:248-251. [PMID: 29197116 DOI: 10.1111/acer.13570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 11/27/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Sarah L Hagerty
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, Colorado
| | - Jarrod M Ellingson
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, Colorado
| | - Kent E Hutchison
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, Colorado
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