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Zuñiga C, Zaramela L, Zengler K. Elucidation of complexity and prediction of interactions in microbial communities. Microb Biotechnol 2017; 10:1500-1522. [PMID: 28925555 PMCID: PMC5658597 DOI: 10.1111/1751-7915.12855] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 12/11/2022] Open
Abstract
Microorganisms engage in complex interactions with other members of the microbial community, higher organisms as well as their environment. However, determining the exact nature of these interactions can be challenging due to the large number of members in these communities and the manifold of interactions they can engage in. Various omic data, such as 16S rRNA gene sequencing, shotgun metagenomics, metatranscriptomics, metaproteomics and metabolomics, have been deployed to unravel the community structure, interactions and resulting community dynamics in situ. Interpretation of these multi-omic data often requires advanced computational methods. Modelling approaches are powerful tools to integrate, contextualize and interpret experimental data, thus shedding light on the underlying processes shaping the microbiome. Here, we review current methods and approaches, both experimental and computational, to elucidate interactions in microbial communities and to predict their responses to perturbations.
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Affiliation(s)
- Cristal Zuñiga
- Department of PediatricsUniversity of California, San Diego9500 Gilman DriveLa JollaCA92093‐0760USA
| | - Livia Zaramela
- Department of PediatricsUniversity of California, San Diego9500 Gilman DriveLa JollaCA92093‐0760USA
| | - Karsten Zengler
- Department of PediatricsUniversity of California, San Diego9500 Gilman DriveLa JollaCA92093‐0760USA
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52
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Javan GT, Finley SJ, Smith T, Miller J, Wilkinson JE. Cadaver Thanatomicrobiome Signatures: The Ubiquitous Nature of Clostridium Species in Human Decomposition. Front Microbiol 2017; 8:2096. [PMID: 29163394 PMCID: PMC5670113 DOI: 10.3389/fmicb.2017.02096] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/12/2017] [Indexed: 01/21/2023] Open
Abstract
Human thanatomicrobiome studies have established that an abundant number of putrefactive bacteria within internal organs of decaying bodies are obligate anaerobes, Clostridium spp. These microorganisms have been implicated as etiological agents in potentially life-threatening infections; notwithstanding, the scale and trajectory of these microbes after death have not been elucidated. We performed phylogenetic surveys of thanatomicrobiome signatures of cadavers' internal organs to compare the microbial diversity between the 16S rRNA gene V4 hypervariable region and V3-4 conjoined regions from livers and spleens of 45 cadavers undergoing forensic microbiological studies. Phylogenetic analyses of 16S rRNA gene sequences revealed that the V4 region had a significantly higher mean Chao1 richness within the total microbiome data. Permutational multivariate analysis of variance statistical tests, based on unweighted UniFrac distances, demonstrated that taxa compositions were significantly different between V4 and V3-4 hypervariable regions (p < 0.001). Of note, we present the first study, using the largest cohort of criminal cases to date, that two hypervariable regions show discriminatory power for human postmortem microbial diversity. In conclusion, here we propose the impact of hypervariable region selection for the 16S rRNA gene in differentiating thanatomicrobiomic profiles to provide empirical data to explain a unique concept, the Postmortem Clostridium Effect.
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Affiliation(s)
- Gulnaz T. Javan
- Forensic Science Program, Physical Sciences Department, Alabama State University, Montgomery, AL, United States
| | - Sheree J. Finley
- Physical Sciences Department, Alabama State University, Montgomery, AL, United States
| | - Tasia Smith
- Forensic Science Program, Physical Sciences Department, Alabama State University, Montgomery, AL, United States
| | - Joselyn Miller
- Forensic Science Program, Physical Sciences Department, Alabama State University, Montgomery, AL, United States
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53
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Arenas M, Pereira F, Oliveira M, Pinto N, Lopes AM, Gomes V, Carracedo A, Amorim A. Forensic genetics and genomics: Much more than just a human affair. PLoS Genet 2017; 13:e1006960. [PMID: 28934201 PMCID: PMC5608170 DOI: 10.1371/journal.pgen.1006960] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material-including other animal species, plants, or microorganisms-is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. Here, we explore how nonhuman forensic genetics is being revolutionized by the increasing variety of genetic markers, the establishment of faster, less error-burdened and cheaper sequencing technologies, and the emergence and improvement of models, methods, and bioinformatics facilities.
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Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Filipe Pereira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Porto, Portugal
| | - Manuela Oliveira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Nadia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Centre of Mathematics of the University of Porto, Porto, Portugal
| | - Alexandra M. Lopes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Veronica Gomes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Angel Carracedo
- Institute of Forensic Sciences Luis Concheiro, University of Santiago de Compostela, Santiago de Compostela, Spain
- Genomics Medicine Group, CIBERER, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
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54
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Affiliation(s)
- Valentina Bugelli
- Dept. of Medicine and Health Sciences (DiMeS) University of Molise via De Sanctis, - 86100, Campobasso, Italy.
| | - Carlo Pietro Campobasso
- Dept. of Experimental Medicine, University "L. Vanvitelli" of Campania, via Santa Maria di Costantinopoli, 80138, Naples, Italy
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55
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Pascual J, von Hoermann C, Rottler-Hoermann AM, Nevo O, Geppert A, Sikorski J, Huber KJ, Steiger S, Ayasse M, Overmann J. Function of bacterial community dynamics in the formation of cadaveric semiochemicals during in situ carcass decomposition. Environ Microbiol 2017. [PMID: 28631411 DOI: 10.1111/1462-2920.13828] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The decomposition of dead mammalian tissue involves a complex temporal succession of epinecrotic bacteria. Microbial activity may release different cadaveric volatile organic compounds which in turn attract other key players of carcass decomposition such as scavenger insects. To elucidate the dynamics and potential functions of epinecrotic bacteria on carcasses, we monitored bacterial communities developing on still-born piglets incubated in different forest ecosystems by combining high-throughput Illumina 16S rRNA sequencing with gas chromatography-mass spectrometry of volatiles. Our results show that the community structure of epinecrotic bacteria and the types of cadaveric volatile compounds released over the time course of decomposition are driven by deterministic rather than stochastic processes. Individual cadaveric volatile organic compounds were correlated with specific taxa during the first stages of decomposition which are dominated by bacteria. Through best-fitting multiple linear regression models, the synthesis of acetic acid, indole and phenol could be linked to the activity of Enterobacteriaceae, Tissierellaceae and Xanthomonadaceae, respectively. These conclusions are also commensurate with the metabolism described for the dominant taxa identified for these families. The predictable nature of in situ synthesis of cadaveric volatile organic compounds by epinecrotic bacteria provides a new basis for future chemical ecology and forensic studies.
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Affiliation(s)
- Javier Pascual
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Christian von Hoermann
- Department of Biology, Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Ann-Marie Rottler-Hoermann
- Department of Biology, Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Omer Nevo
- Department of Biology, Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Alicia Geppert
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Johannes Sikorski
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Katharina J Huber
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Sandra Steiger
- Department of Biology, Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Manfred Ayasse
- Department of Biology, Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.,Technische Universität Braunschweig, Braunschweig, Germany
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56
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Zhao Y, Jaber V, Lukiw WJ. Secretory Products of the Human GI Tract Microbiome and Their Potential Impact on Alzheimer's Disease (AD): Detection of Lipopolysaccharide (LPS) in AD Hippocampus. Front Cell Infect Microbiol 2017; 7:318. [PMID: 28744452 PMCID: PMC5504724 DOI: 10.3389/fcimb.2017.00318] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/27/2017] [Indexed: 12/12/2022] Open
Abstract
Although the potential contribution of the human gastrointestinal (GI) tract microbiome to human health, aging, and disease is becoming increasingly acknowledged, the molecular mechanics and signaling pathways of just how this is accomplished is not well-understood. Major bacterial species of the GI tract, such as the abundant Gram-negative bacilli Bacteroides fragilis (B. fragilis) and Escherichia coli (E. coli), secrete a remarkably complex array of pro-inflammatory neurotoxins which, when released from the confines of the healthy GI tract, are pathogenic and highly detrimental to the homeostatic function of neurons in the central nervous system (CNS). For the first time here we report the presence of bacterial lipopolysaccharide (LPS) in brain lysates from the hippocampus and superior temporal lobe neocortex of Alzheimer's disease (AD) brains. Mean LPS levels varied from two-fold increases in the neocortex to three-fold increases in the hippocampus, AD over age-matched controls, however some samples from advanced AD hippocampal cases exhibited up to a 26-fold increase in LPS over age-matched controls. This “Perspectives” paper will further highlight some very recent research on GI tract microbiome signaling to the human CNS, and will update current findings that implicate GI tract microbiome-derived LPS as an important internal contributor to inflammatory degeneration in the CNS.
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Affiliation(s)
- Yuhai Zhao
- LSU Neuroscience Center, Louisiana State University Health Science CenterNew Orleans, LA, United States.,Department of Anatomy and Cell Biology, Louisiana State University Health Science CenterNew Orleans, LA, United States
| | - Vivian Jaber
- LSU Neuroscience Center, Louisiana State University Health Science CenterNew Orleans, LA, United States
| | - Walter J Lukiw
- LSU Neuroscience Center, Louisiana State University Health Science CenterNew Orleans, LA, United States.,Department of Ophthalmology, Louisiana State University Health Science CenterNew Orleans, LA, United States.,Department of Neurology, Louisiana State University Health Science CenterNew Orleans, LA, United States
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57
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From Evolutionary Advantage to Disease Agents: Forensic Reevaluation of Host-Microbe Interactions and Pathogenicity. Microbiol Spectr 2017; 5. [PMID: 28155809 DOI: 10.1128/microbiolspec.emf-0009-2016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
As the "human microbiome era" continues, there is an increasing awareness of our resident microbiota and its indispensable role in our fitness as holobionts. However, the host-microbe relationship is not so clearly defined for some human symbionts. Here we discuss examples of "accidental pathogens," meaning previously nonpathogenic and/or environmental microbes thought to have inadvertently experienced an evolutionary shift toward pathogenicity. For instance, symbionts such as Helicobacter pylori and JC polyomavirus have been shown to have accompanied humans since prehistoric times and are still abundant in extant populations as part of the microbiome. And yet, the relationship between a subgroup of these microbes and their human hosts seems to have changed with time, and they have recently gained notoriety as gastrointestinal and neuropathogens, respectively. On the other hand, environmental microbes such as Legionella spp. have recently experienced a shift in host range and are now a major problem in industrialized countries as a result of artificial ecosystems. Other variables involved in this accidental phenomenon could be the apparent change or reduction in the diversity of human-associated microbiota because of modern medicine and lifestyles. All of this could result in an increased prevalence of accidental pathogens in the form of emerging pathogens.
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Na JY, Park JH, Kim SH, Park JT. Bacteria as Normal Flora in Postmortem Body Fluid Samples. ACTA ACUST UNITED AC 2017. [DOI: 10.7580/kjlm.2017.41.4.87] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Joo-Young Na
- Biomedical Research Institute, Chonnam National University Hospital, Gwangju, Korea
| | - Ji Hye Park
- Forensic Medicine Division, National Forensic Service Gwangju Institute, Jangseong, Korea
| | - Soo-Hyun Kim
- Department of Laboratory Medicine, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Jong-Tae Park
- Department of Forensic Medicine, Chonnam National University Medical School, Gwangju, Korea
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59
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Lukiw WJ. The microbiome, microbial-generated proinflammatory neurotoxins, and Alzheimer's disease. JOURNAL OF SPORT AND HEALTH SCIENCE 2016; 5:393-396. [PMID: 28446989 PMCID: PMC5403149 DOI: 10.1016/j.jshs.2016.08.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 06/07/2023]
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60
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Human Thanatomicrobiome Succession and Time Since Death. Sci Rep 2016; 6:29598. [PMID: 27412051 PMCID: PMC4944132 DOI: 10.1038/srep29598] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/22/2016] [Indexed: 12/16/2022] Open
Abstract
The thanatomicrobiome (thanatos, Greek for death) is a relatively new term and is the study of the microbes colonizing the internal organs and orifices after death. Recent scientific breakthroughs in an initial study of the thanatomicrobiome have revealed that a majority of the microbes within the human body are the obligate anaerobes, Clostridium spp., in the internal postmortem microbial communities. We hypothesized that time-dependent changes in the thanatomicrobiome within internal organs can estimate the time of death as a human body decays. Here we report a cross-sectional study of the sampling of 27 human corpses from criminal cases with postmortem intervals between 3.5–240 hours. The impetus for examining microbial communities in different internal organs is to address the paucity of empirical data on thanatomicrobiomic succession caused by the limited access to these organs prior to death and a dearth of knowledge regarding the movement of microbes within remains. Our sequencing results of 16S rRNA gene amplicons of 27 postmortem samples from cadavers demonstrated statistically significant time-, organ-, and sex-dependent changes. These results suggest that comprehensive knowledge of the number and abundance of each organ’s signature microorganisms could be useful to forensic microbiologists as a new source of data for estimating postmortem interval.
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