Analysis of Microbial Communities: An Emerging Tool in Forensic Sciences

The objective of forensic sciences is to find clues in a crime scene in order to reconstruct the scenario. Classical samples include DNA or fingerprints, but both have inherent limitations and can be uninformative. Another type of sample has emerged recently in the form of the microbiome. Supported by the Human Microbiome Project, the characteristics of the microbial communities provide real potential in forensics. They are highly specific and can be used to differentiate and classify the originating body site of a human biological trace. Skin microbiota is also highly specific and different between individuals, leading to its possibility as an identification tool. By extension, the possibilities of the microbial communities to be deposited on everyday objects has also been explored. Other uses include the determination of the post-mortem interval or the analysis of soil communities. One challenge is that the microbiome changes over time and can be influenced by many environmental and lifestyle factors. This review offers an overview of the main methods and applications to demonstrate the benefit of the microbiome to provide forensically relevant information.

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ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework

F1000Research ◽

10.12688/f1000research.28608.1 ◽

2021 ◽

Vol 10 ◽

pp. 103 ◽

Cited By ~ 1

Author(s):

Subina Mehta ◽

Marie Crane ◽

Emma Leith ◽

Bérénice Batut ◽

Saskia Hiltemann ◽

...

Keyword(s):

Microbial Communities ◽

Human Health ◽

Genetic Material ◽

Human Microbiome ◽

Human Microbiome Project ◽

Taxonomic Composition ◽

Sequencing Technologies ◽

The Galaxy ◽

Next Generation Sequencing Ngs ◽

Ngs Data

The Human Microbiome Project (HMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the ‘microbiome’) in human health and disease. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). Conversely, metatranscriptomics, the study of a microbial community’s RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome. In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking. In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.

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Identification of Complex Multidimensional Patterns in Microbial Communities

10.1101/540815 ◽

2019 ◽

Author(s):

Golovko George ◽

Khanipov Kamil ◽

Albayrak Levent ◽

Fofanov Yuriy

Keyword(s):

Microbial Communities ◽

Statistical Significance ◽

Source Code ◽

Three Dimensional ◽

Human Microbiome ◽

Human Microbiome Project ◽

Site Specific ◽

Information Coefficient ◽

Complex Relationships ◽

Project Data

AbstractMotivationIdentification of complex relationships within members of microbial communities is key to understand and guide microbial transplantation and provide personalized anti-microbial and probiotic treatments. Since members of a given microbial community can be simultaneously involved in multiple relations that altogether will determine their abundance, not all significant relations between organisms are expected to be manifested as visually uninterrupted patterns and be detected using traditional correlation nor mutual information coefficient based approaches.ResultsThis manuscript proposes a pattern specific way to quantify the strength and estimate the statistical significance of two-dimensional co-presence, co-exclusion, and one-way relations patterns between abundance profiles of two organisms which can be extended to three or more dimensional patterns. Presented approach can also be extended by including a variety of physical (pH, temperature, oxygen concentration) and biochemical (antimicrobial susceptibility, nutrient and metabolite concentration) variables into the search for multidimensional patterns. The presented approach has been tested using 2,380 microbiome samples from the Human Microbiome Project resulting in body-site specific networks of statistically significant 2D patterns. We also were able to demonstrate the presence of several 3D patterns in the Human Microbiome Project data.AvailabilityC++ source code for two and three-dimensional patterns, as well as executable files for the Pickle pipeline, are in the attached supplementary [email protected]

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Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota

Microbiome ◽

10.1186/s40168-020-00983-x ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Ryan A. Blaustein ◽

Lisa-Marie Michelitsch ◽

Adam J. Glawe ◽

Hansung Lee ◽

Stefanie Huttelmaier ◽

...

Keyword(s):

Built Environment ◽

Microbial Communities ◽

Human Microbiome ◽

Human Microbiome Project ◽

Well Being ◽

Taxonomic Diversity ◽

Influential Factors ◽

Multidrug Efflux ◽

Antimicrobial Resistance Gene ◽

Health And Well Being

Abstract Background While indoor microbiomes impact our health and well-being, much remains unknown about taxonomic and functional transitions that occur in human-derived microbial communities once they are transferred away from human hosts. Toothbrushes are a model to investigate the potential response of oral-derived microbiota to conditions of the built environment. Here, we characterize metagenomes of toothbrushes from 34 subjects to define the toothbrush microbiome and resistome and possible influential factors. Results Toothbrush microbiomes often comprised a dominant subset of human oral taxa and less abundant or site-specific environmental strains. Although toothbrushes contained lower taxonomic diversity than oral-associated counterparts (determined by comparison with the Human Microbiome Project), they had relatively broader antimicrobial resistance gene (ARG) profiles. Toothbrush resistomes were enriched with a variety of ARGs, notably those conferring multidrug efflux and putative resistance to triclosan, which were primarily attributable to versatile environmental taxa. Toothbrush microbial communities and resistomes correlated with a variety of factors linked to personal health, dental hygiene, and bathroom features. Conclusions Selective pressures in the built environment may shape the dynamic mixture of human (primarily oral-associated) and environmental microbiota that encounter each other on toothbrushes. Harboring a microbial diversity and resistome distinct from human-associated counterparts suggests toothbrushes could potentially serve as a reservoir that may enable the transfer of ARGs.

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Identification of multidimensional Boolean patterns in microbial communities

Microbiome ◽

10.1186/s40168-020-00853-6 ◽

2020 ◽

Vol 8 (1) ◽

Author(s):

George Golovko ◽

Khanipov Kamil ◽

Levent Albayrak ◽

Anna M. Nia ◽

Renato Salomon Arroyo Duarte ◽

...

Keyword(s):

Microbial Communities ◽

Network Inference ◽

Statistical Significance ◽

Human Microbiome ◽

Human Microbiome Project ◽

Specific Method ◽

Interaction Patterns ◽

Two Dimensional ◽

Community Members ◽

Project Data

Abstract Background Identification of complex multidimensional interaction patterns within microbial communities is the key to understand, modulate, and design beneficial microbiomes. Every community has members that fulfill an essential function affecting multiple other community members through secondary metabolism. Since microbial community members are often simultaneously involved in multiple relations, not all interaction patterns for such microorganisms are expected to exhibit a visually uninterrupted pattern. As a result, such relations cannot be detected using traditional correlation, mutual information, principal coordinate analysis, or covariation-based network inference approaches. Results We present a novel pattern-specific method to quantify the strength and estimate the statistical significance of two-dimensional co-presence, co-exclusion, and one-way relation patterns between abundance profiles of two organisms as well as extend this approach to allow search and visualize three-, four-, and higher dimensional patterns. The proposed approach has been tested using 2380 microbiome samples from the Human Microbiome Project resulting in body site-specific networks of statistically significant 2D patterns as well as revealed the presence of 3D patterns in the Human Microbiome Project data. Conclusions The presented study suggested that search for Boolean patterns in the microbial abundance data needs to be pattern specific. The reported presence of multidimensional patterns (which cannot be reduced to a combination of two-dimensional patterns) suggests that multidimensional (multi-organism) relations may play important roles in the organization of microbial communities, and their detection (and appropriate visualization) may lead to a deeper understanding of the organization and dynamics of microbial communities.

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Detection of Multidimensional Co-Exclusion Patterns in Microbial Communities

10.1101/315473 ◽

2018 ◽

Author(s):

Levent Albayrak ◽

Kamil Khanipov ◽

George Golovko ◽

Yuriy Fofanov

Keyword(s):

Microbial Communities ◽

Statistical Significance ◽

Source Code ◽

Human Microbiome ◽

Correlation Coefficients ◽

Human Microbiome Project ◽

Supplementary Information ◽

P Value ◽

Complex Relationships ◽

And Control

AbstractMotivationIdentification of complex relationships among members of microbial communities is key to understand and control the microbiota. Co-exclusion is arguably one of the most important patterns reflecting microorganisms’ intolerance to each other’s presence. Knowing these relations opens an opportunity to manipulate microbiotas, personalize anti-microbial and probiotic treatments as well as guide microbiota transplantation. The co-exclusion pattern however, cannot be appropriately described by a linear function nor its strength be estimated using covariance or (negative) Pearson and Spearman correlation coefficients. This manuscript proposes a way to quantify the strength and evaluate the statistical significance of co-exclusion patterns between two, three or more variables describing a microbiota and allows one to extend analysis beyond microorganism abundance by including other microbiome associated measurements such as, pH, temperature etc., as well as estimate the expected numbers of false positive co-exclusion patterns in a co-exclusion network.ResultsThe implemented computational pipeline (CoEx) tested against 2,380 microbial profiles (samples) from The Human Microbiome Project resulted in body-site specific pairwise co-exclusion patterns.AvailabilityC++ source code for calculation of the score and p-value for 2, 3, and 4 dimensional co-exclusion patterns as well as source code and executable files for the CoEx pipeline are available at https://scsb.utmb.edu/labgroups/fofanov/co-exclusion_in_microbial_communities.aspContactlealbayr@utmb.eduSupplementary informationSupplementary data are available at biorxiv online.

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NIH Human Microbiome Project

Microbe Magazine ◽

10.1128/microbe.4.393.1 ◽

2009 ◽

Vol 4 (9) ◽

pp. 393-393

Keyword(s):

Human Microbiome ◽

Human Microbiome Project

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Sequence Comparison of Vaginolysin from Different Gardnerella Species

Pathogens ◽

10.3390/pathogens10020086 ◽

2021 ◽

Vol 10 (2) ◽

pp. 86

Author(s):

Erin M. Garcia ◽

Myrna G. Serrano ◽

Laahirie Edupuganti ◽

David J. Edwards ◽

Gregory A. Buck ◽

...

Keyword(s):

Amino Acid ◽

Human Microbiome ◽

Human Microbiome Project ◽

Distinct Species ◽

Vaginal Swab ◽

Metagenomic Data ◽

Gardnerella Vaginalis ◽

Vaginal Epithelial Cells ◽

Species Specific

Gardnerella vaginalis has recently been split into 13 distinct species. In this study, we tested the hypotheses that species-specific variations in the vaginolysin (VLY) amino acid sequence could influence the interaction between the toxin and vaginal epithelial cells and that VLY variation may be one factor that distinguishes less virulent or commensal strains from more virulent strains. This was assessed by bioinformatic analyses of publicly available Gardnerella spp. sequences and quantification of cytotoxicity and cytokine production from purified, recombinantly produced versions of VLY. After identifying conserved differences that could distinguish distinct VLY types, we analyzed metagenomic data from a cohort of female subjects from the Vaginal Human Microbiome Project to investigate whether these different VLY types exhibited any significant associations with symptoms or Gardnerella spp.-relative abundance in vaginal swab samples. While Type 1 VLY was most prevalent among the subjects and may be associated with increased reports of symptoms, subjects with Type 2 VLY dominant profiles exhibited increased relative Gardnerella spp. abundance. Our findings suggest that amino acid differences alter the interaction of VLY with vaginal keratinocytes, which may potentiate differences in bacterial vaginosis (BV) immunopathology in vivo.

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Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework

Microbiome ◽

10.1186/s40168-021-01023-y ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Alberto Pascual-García

Keyword(s):

Microbial Communities ◽

Microbial Ecology ◽

Environmental Conditions ◽

The Novel ◽

Methodological Framework ◽

Operational Taxonomic Units ◽

Traditional Classification ◽

Taxonomical Classification ◽

Novel Concept

AbstractIn this comment, we analyse the conceptual framework proposed by Aguirre de Cárcer (Microbiome 7:142, 2019), introducing the novel concept of Phylogenetic Core Groups (PCGs). This notion aims to complement the traditional classification in operational taxonomic units (OTUs), widely used in microbial ecology, to provide a more intrinsic taxonomical classification which avoids the use of pre-determined thresholds. However, to introduce this concept, the author frames his proposal in a wider theoretical framework based on a conceptualization of selection that we argue is a tautology. This blurs the subsequent formulation of an assembly principle for microbial communities, favouring that some contradictory examples introduced to support the framework appear aligned in their conclusions. And more importantly, under this framework and its derived methodology, it is not possible to infer PCGs from data in a consistent way. We reanalyse the proposal to identify its logical and methodological flaws and, through the analysis of synthetic scenarios, we propose a number of methodological refinements to contribute towards the determination of PCGs in a consistent way. We hope our analysis will promote the exploration of PCGs as a potentially valuable tool, helping to bridge the gap between environmental conditions and community composition in microbial ecology.

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Impact of the Human Microbiome in Forensic Sciences: a Systematic Review

Applied and Environmental Microbiology ◽

10.1128/aem.01451-20 ◽

2020 ◽

Vol 86 (22) ◽

Author(s):

Manuel G. García ◽

María D. Pérez-Cárceles ◽

Eduardo Osuna ◽

Isabel Legaz

Keyword(s):

Systematic Review ◽

Forensic Science ◽

Human Microbiome ◽

Geographical Location ◽

Postmortem Interval ◽

Forensic Sciences ◽

Content Type ◽

Microbiome Analysis ◽

Location Of Death ◽

Microbiome Research

ABSTRACT Numerous studies relate differences in microbial communities to human health and disease; however, little is known about microbial changes that occur postmortem or the possible applications of microbiome analysis in the field of forensic science. The aim of this review was to study the microbiome and its applications in forensic sciences and to determine the main lines of investigation that are emerging, as well as its possible contributions to the forensic field. A systematic review of the human microbiome in relation to forensic science was carried out by following PRISMA guidelines. This study sheds light on the role of microbiome research in the postmortem interval during the process of decomposition, identifying death caused by drowning or sudden death, locating the geographical location of death, establishing a connection between the human microbiome and personal items, sexual contact, and the identification of individuals. Actinomycetaceae, Bacteroidaceae, Alcaligenaceae, and Bacilli play an important role in determining the postmortem interval. Aeromonas can be used to determine the cause of death, and Corynebacterium or Helicobacter pylori can be used to ascertain personal identity or geographical location. Several studies point to a promising future for microbiome analysis in the different fields of forensic science, opening up an important new area of research.

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Dispersive evaluation and surface chemistry of advanced, multifunctional silica/lignin hybrid biomaterials

Open Chemistry ◽

10.2478/s11532-013-0322-4 ◽

2013 ◽

Vol 11 (11) ◽

pp. 1860-1873 ◽

Cited By ~ 6

Author(s):

Magdalena Nowacka ◽

Łukasz Klapiszewski ◽

Małgorzata Norman ◽

Teofil Jesionowski

Keyword(s):

Zeta Potential ◽

Surface Charge ◽

Electrochemical Sensors ◽

Relevant Information ◽

Structural Features ◽

Kraft Lignin ◽

Morphological Properties ◽

Wide Range ◽

Hybrid Biomaterials

AbstractAdvanced silica/lignin hybrid biomaterials were obtained using hydrated or fumed silicas (Aerosil®200) and Kraft lignin as precursors, which is a cheap and biodegradable natural polymer. To extend the possible range of applications, the silicas were first modified with N-2-(aminoethyl)-3-aminopropyltrimethoxsysilane, and then with Kraft lignin, which had been oxidized with sodium periodate. The SiO2/lignin hybrids and precursors were characterised by means of determination of their physicochemical and dispersive-morphological properties. The effectiveness of silica binding to lignin was verified by FT-IR spectroscopy. The zeta potential value provides relevant information regarding interactions between colloid particles. Measurement of the zeta potential values enabled an indirect assessment of stability for the studied hybrid systems. Determination of zeta potential and density of surface charge also permitted the quantitative analysis of changes in surface charge, and indirectly confirmed the effectiveness of the proposed method for synthesis of SiO2/lignin hybrid materials. A particularly attractive feature for practical use is their stability, especially electrokinetic stability. It is expected that silica/lignin hybrids will find a wide range of applications (polymer fillers, biosorbents, electrochemical sensors), as they combine the unique properties of silica with the specific structural features of lignin. This makes these hybrids biomaterials advanced and multifunctional.

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