Publications by authors named "Jeremy E Wilkinson"

17 Publications

  • Page 1 of 1

The Sulfur Microbial Diet and Risk of Colorectal Cancer by Molecular Subtypes and Intratumoral Microbial Species in Adult Men.

Clin Transl Gastroenterol 2021 Aug 1;12(8):e00338. Epub 2021 Aug 1.

Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.

Introduction: We recently described the sulfur microbial diet, a pattern of intake associated with increased gut sulfur-metabolizing bacteria and incidence of distal colorectal cancer (CRC). We assessed whether this risk differed by CRC molecular subtypes or presence of intratumoral microbes involved in CRC pathogenesis (Fusobacterium nucleatum and Bifidobacterium spp.).

Methods: We performed Cox proportional hazards modeling to examine the association between the sulfur microbial diet and incidence of overall and distal CRC by molecular and microbial subtype in the Health Professionals Follow-Up Study (1986-2012).

Results: We documented 1,264 incident CRC cases among 48,246 men, approximately 40% of whom had available tissue data. After accounting for multiple hypothesis testing, the relationship between the sulfur microbial diet and CRC incidence did not differ by subtype. However, there was a suggestion of an association by prostaglandin synthase 2 (PTGS2) status with a multivariable adjusted hazard ratio for highest vs lowest tertile of sulfur microbial diet scores of 1.31 (95% confidence interval: 0.99-1.74, Ptrend = 0.07, Pheterogeneity = 0.04) for PTGS2-high CRC. The association of the sulfur microbial diet with distal CRC seemed to differ by the presence of intratumoral Bifidobacterium spp. with an adjusted hazard ratio for highest vs lowest tertile of sulfur microbial diet scores of 1.65 (95% confidence interval: 1.14-2.39, Ptrend = 0.01, Pheterogeneity = 0.03) for Bifidobacterium-negative distal CRC. We observed no apparent heterogeneity by other tested molecular markers.

Discussion: Greater long-term adherence to the sulfur microbial diet could be associated with PTGS2-high and Bifidobacterium-negative distal CRC in men. Additional studies are needed to further characterize the role of gut microbial sulfur metabolism and CRC.
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http://dx.doi.org/10.14309/ctg.0000000000000338DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8323793PMC
August 2021

New Approaches to Profile the Microbiome for Treatment of Neurodegenerative Disease.

J Alzheimers Dis 2021 ;82(4):1373-1401

Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.

Progressive neurodegenerative diseases represent some of the largest growing treatment challenges for public health in modern society. These diseases mainly progress due to aging and are driven by microglial surveillance and activation in response to changes occurring in the aging brain. The lack of efficacious treatment options for Alzheimer's disease (AD), as the focus of this review, and other neurodegenerative disorders has encouraged new approaches to address neuroinflammation for potential treatments. Here we will focus on the increasing evidence that dysbiosis of the gut microbiome is characterized by inflammation that may carry over to the central nervous system and into the brain. Neuroinflammation is the common thread associated with neurodegenerative diseases, but it is yet unknown at what point and how innate immune function turns pathogenic for an individual. This review will address extensive efforts to identify constituents of the gut microbiome and their neuroactive metabolites as a peripheral path to treatment. This approach is still in its infancy in substantive clinical trials and requires thorough human studies to elucidate the metabolic microbiome profile to design appropriate treatment strategies for early stages of neurodegenerative disease. We view that in order to address neurodegenerative mechanisms of the gut, microbiome and metabolite profiles must be determined to pre-screen AD subjects prior to the design of specific, chronic titrations of gut microbiota with low-dose antibiotics. This represents an exciting treatment strategy designed to balance inflammatory microglial involvement in disease progression with an individual's manifestation of AD as influenced by a coercive inflammatory gut.
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http://dx.doi.org/10.3233/JAD-210198DOI Listing
January 2021

Plant-Based Diet Index and Metabolic Risk in Men: Exploring the Role of the Gut Microbiome.

J Nutr 2021 Sep;151(9):2780-2789

Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.

Background: Healthy plant-based diet index (hPDI) is associated with a lower risk of cardiometabolic conditions, but its association as well as interactions with microbiome have not been elucidated.

Objectives: We aimed to investigate the interrelations between hPDI, gut microbiome, and cardiometabolic risk markers.

Methods: hPDI was derived from dietary assessments by a validated FFQ and was examined in relation to metagenomic profiles of 911 fecal samples collected from 303 men aged 71 ± 4 y with an average BMI (in kg/m2) of 25.2 ± 3.6 in the Men's Lifestyle Validation Study. Principal coordinate (PCo) analysis based on Bray-Curtis dissimilarity was conducted, and interactions between hPDI and PCo were examined by using a metabolic risk score composed of blood lipids, BMI, and glycated hemoglobin.

Results: After multivariable adjustment, hPDI was significantly associated with the relative abundance of 7 species and 9 pathways. In particular, higher hPDI was significantly associated with a higher relative abundance of Bacteroides cellulosilyticus and Eubacterium eligens, amino acid biosynthesis pathways (l-isoleucine biosynthesis I and III and l-valine biosynthesis), and the pathway of pyruvate fermentation to isobutanol. A favorable association between hPDI and the metabolic risk score was more pronounced among men with a higher PCo characterized by higher abundance of Bacteroides uniformis and lower abundance of Prevotella copri. At the individual species level, a similar interaction was also observed between hPDI and P. copri, as well as with Clostridium clostridioforme or Blautia hydrogenotrophica (all P-interaction < 0.01).

Conclusion: A greater adherence to a healthy plant-based diet by older men was associated with a microbial profile characterized by a higher abundance of multiple species, including B. cellulosilyticus and E. eligens, as well as pathways in amino acid metabolism and pyruvate fermentation. In addition, inverse associations between healthy plant-based diet and human metabolic risk may partially depend on microbial compositions.
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http://dx.doi.org/10.1093/jn/nxab175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8417919PMC
September 2021

Interplay between diet and gut microbiome, and circulating concentrations of trimethylamine N-oxide: findings from a longitudinal cohort of US men.

Gut 2021 Apr 29. Epub 2021 Apr 29.

Nutrition, Harvard University T H Chan School of Public Health, Boston, Massachusetts, USA

Objectives: Gut-produced trimethylamine N-oxide (TMAO) is postulated as a possible link between red meat intake and poor cardiometabolic health. We investigated whether gut microbiome could modify associations of dietary precursors with TMAO concentrations and cardiometabolic risk markers among free-living individuals.

Design: We collected up to two pairs of faecal samples (n=925) and two blood samples (n=473), 6 months apart, from 307 healthy men in the Men's Lifestyle Validation Study. Diet was assessed repeatedly using food-frequency questionnaires and diet records. We profiled faecal metagenome and metatranscriptome using shotgun sequencing and identified microbial taxonomic and functional features.

Results: TMAO concentrations were associated with the overall microbial compositions (permutational analysis of variance (PERMANOVA) test p=0.001). Multivariable taxa-wide association analysis identified 10 bacterial species whose abundance was significantly associated with plasma TMAO concentrations (false discovery rate <0.05). Higher habitual intake of red meat and choline was significantly associated with higher TMAO concentrations among participants who were microbial TMAO-producers (p<0.05), as characterised based on four abundant TMAO-predicting species, but not among other participants (for red meat=0.003; for choline, =0.03). Among abundant TMAO-predicting species, significantly strengthened the positive association between red meat intake and HbA1c levels (=0.01). Secondary analyses revealed that some functional features, including choline trimethylamine-lyase activating enzymes, were associated with TMAO concentrations.

Conclusion: We identified microbial taxa that were associated with TMAO concentrations and modified the associations of red meat intake with TMAO concentrations and cardiometabolic risk markers. Our data underscore the interplay between diet and gut microbiome in producing potentially bioactive metabolites that may modulate cardiometabolic health.
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http://dx.doi.org/10.1136/gutjnl-2020-322473DOI Listing
April 2021

Overview of the Microbiome Among Nurses study (Micro-N) as an example of prospective characterization of the microbiome within cohort studies.

Nat Protoc 2021 06 21;16(6):2724-2731. Epub 2021 Apr 21.

Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.

A lack of prospective studies has been a major barrier for assessing the role of the microbiome in human health and disease on a population-wide scale. To address this significant knowledge gap, we have launched a large-scale collection targeting fecal and oral microbiome specimens from 20,000 women within the Nurses' Health Study II cohort (the Microbiome Among Nurses study, or Micro-N). Leveraging the rich epidemiologic data that have been repeatedly collected from this cohort since 1989; the established biorepository of archived blood, urine, buccal cell, and tumor tissue specimens; the available genetic and biomarker data; the cohort's ongoing follow-up; and the BIOM-Mass microbiome research platform, Micro-N furnishes unparalleled resources for future prospective studies to interrogate the interplay between host, environmental factors, and the microbiome in human health. These prospectively collected materials will provide much-needed evidence to infer causality in microbiome-associated outcomes, paving the way toward development of microbiota-targeted modulators, preventives, diagnostics and therapeutics. Here, we describe a generalizable, scalable and cost-effective platform used for stool and oral microbiome specimen and metadata collection in the Micro-N study as an example of how prospective studies of the microbiome may be carried out.
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http://dx.doi.org/10.1038/s41596-021-00519-zDOI Listing
June 2021

A framework for microbiome science in public health.

Nat Med 2021 05 5;27(5):766-774. Epub 2021 Apr 5.

Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.

Human microbiome science has advanced rapidly and reached a scale at which basic biology, clinical translation and population health are increasingly integrated. It is thus now possible for public health researchers, practitioners and policymakers to take specific action leveraging current and future microbiome-based opportunities and best practices. Here we provide an outline of considerations for research, education, interpretation and scientific communication concerning the human microbiome and public health. This includes guidelines for population-scale microbiome study design; necessary physical platforms and analysis methods; integration into public health areas such as epidemiology, nutrition, chronic disease, and global and environmental health; entrepreneurship and technology transfer; and educational curricula. Particularly in the near future, there are both opportunities for the incorporation of microbiome-based technologies into public health practice, and a growing need for policymaking and regulation around related areas such as prebiotic and probiotic supplements, novel live-cell therapies and fecal microbiota transplants.
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http://dx.doi.org/10.1038/s41591-021-01258-0DOI Listing
May 2021

A 28 Day Clinical Assessment of a Lactic Acid-containing Antimicrobial Intimate Gel Wash Formulation on Skin Tolerance and Impact on the Vulvar Microbiome.

Antibiotics (Basel) 2020 Feb 1;9(2). Epub 2020 Feb 1.

Alba Science Ltd., Edinburgh EH1 3RH, UK.

While intimate feminine hygiene products are widely used as part of daily cleansing routines, little is known about how these products impact the vulvovaginal area and its microbiome stability. This 4 week clinical study assessed tolerance of a novel gel wash containing lactic acid (pH 4.2) for external daily use when used on the external genital area and its effects on skin moisturization, vulvar skin pH, and the vulvar microbiome. After a 7 day pre-study conditioning period, 36 healthy females in three balanced age groups (18-29, 30-44, and 45-55 years) used the gel wash to cleanse their external genital area (mons pubis and vulva) and entire body at least once per day for 28 days. Skin tolerance of the gel wash was assessed by the gynecologist. Effects of the gel wash on vulvar skin microbiota were studied by performing bacterial 16S rRNA and fungal internal transcribed spacer (ITS) microbial richness and diversity analysis. Based on gynecologic assessment after 28 days of use, the gel wash showed acceptable tolerance, with no signs of increased dryness, redness, edema, itching, stinging, or burning. Use of the gel wash was associated with a significant increase in both short-term (single application) and longer-term (daily use for 28 days) skin moisturization. There was no significant change in vulvar skin pH over time with daily product use, and the gel wash did not significantly affect the natural vulvar microbiome species richness or diversity for bacteria or fungi. Results showed that this gel wash is a mild, moisturizing cleanser that maintains the natural pH and microbial diversity of vulvar skin. To our knowledge, this was the first study to assess the effect of an antimicrobial feminine gel wash on the natural pH and vulvar microbiome habitat of the skin using bacterial 16S rRNA and fungal ITS genetic sequencing techniques.
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http://dx.doi.org/10.3390/antibiotics9020055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7168340PMC
February 2020

The interleukin-33 receptor contributes to pulmonary responses to ozone in male mice: role of the microbiome.

Respir Res 2019 Aug 27;20(1):197. Epub 2019 Aug 27.

Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, 665 Huntington Av Bld1 room 319, Boston, MA, 02115, USA.

Background: Interleukin-33 is released in the airways following acute ozone exposure and has the ability to cause airway hyperresponsiveness, a defining feature of asthma. Ozone causes greater airway hyperresponsiveness in male than female mice. Moreover, sex differences in the gut microbiome account for sex differences in this response to ozone. The purpose of this study was to determine whether there were sex differences in the role of interleukin-33 in ozone-induced airway hyperresponsiveness and to examine the role of the microbiome in these events.

Methods: Wildtype mice and mice genetically deficient in ST2, the interleukin-33 receptor, were housed from weaning with either other mice of the same genotype and sex, or with mice of the same sex but opposite genotype. At 15 weeks of age, fecal pellets were harvested for 16S rRNA sequencing and the mice were then exposed to air or ozone. Airway responsiveness was measured and a bronchoalveolar lavage was performed 24 h after exposure.

Results: In same-housed mice, ozone-induced airway hyperresponsiveness was greater in male than female wildtype mice. ST2 deficiency reduced ozone-induced airway hyperresponsiveness in male but not female mice and abolished sex differences in the response to ozone. However, sex differences in the role of interleukin-33 were unrelated to type 2 cytokine release: ozone-induced increases in bronchoalveolar lavage interleukin-5 were greater in females than males and ST2 deficiency virtually abolished interleukin-5 in both sexes. Since gut microbiota contribute to sex differences in ozone-induced airway hyperresponsiveness, we examined the role of the microbiome in these ST2-dependent sex differences. To do so, we cohoused wildtype and ST2 deficient mice, a situation that allows for transfer of microbiota among cage-mates. Cohousing altered the gut microbial community structure, as indicated by 16S rRNA gene sequencing of fecal DNA and reversed the effect of ST2 deficiency on pulmonary responses to ozone in male mice.

Conclusions: The data indicate that the interleukin-33 /ST2 pathway contributes to ozone-induced airway hyperresponsiveness in male mice and suggest that the role of interleukin-33 is mediated at the level of the gut microbiome.
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http://dx.doi.org/10.1186/s12931-019-1168-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6712741PMC
August 2019

Obligate anaerobes are abundant in human necrotizing soft tissue infection samples - a metagenomics analysis.

APMIS 2019 Aug 19;127(8):577-587. Epub 2019 Jun 19.

Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, USA.

Necrotizing soft tissue infections (NSTIs) are associated with high morbidity and mortality and are increasing in incidence. Proper identification of the microbial causes of NSTIs is a crucial step in diagnosis and treatment, but the majority of data collected are culture based, which is biased against fastidious organisms, including obligate anaerobes. The goal of this study was to address this gap in knowledge by characterizing NSTI microbial communities through molecular diagnostics. We performed 16S rRNA sequencing on human NSTI samples and identified five genera most commonly found in NSTIs (Prevotella, Bacteroides, Peptoniphilus, Porphyromonas, and Enterococcus). We found that a >70% contribution of obligate anaerobes to the bacterial population distribution was associated with NSTI mortality, and that NSTI samples, from both survivors and non-survivors, had an increased relative abundance of gram negative bacteria compared to those of abscess patients. Based on our data, we conclude that obligate anaerobes are abundant in NSTIs and a high relative abundance of anaerobes is associated with a worse outcome. We recommend increasing anaerobe antibiotic coverage during the treatment of NSTIs even when anaerobes are not found by traditional clinical microbiology methods, and especially when there is a clinical suspicion for anaerobe involvement.
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http://dx.doi.org/10.1111/apm.12969DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6852132PMC
August 2019

Traditional culture methods fail to detect principle pathogens in necrotising soft tissue infection: a case report.

J Wound Care 2018 Apr;27(Sup4):S24-S28

Department of Surgery, Texas Tech University Health Sciences Center, TTUHSC Burn Center of Research Excellence, Texas Tech University Health Sciences Center.

Objective: Necrotising soft tissue infections (NSTIs) progress rapidly and mortality remains high, ranging from 10% to 30%, representing a significant challenge for health professionals. Early accurate diagnosis is crucial because timely and aggressive surgical intervention remains the number one indicator for a better clinical outcome. Understanding the microbial background of NSTIs would aid early diagnosis.

Presentation: We present a case of NSTI, in a seemingly healthy adult male, originating from a tooth abscess. The NSTI progressed rapidly, and eventually covered the patient's chest and abdominal skin and underlying soft tissue.

Results: Traditional blood and tissue culture only found Group C Streptococcus where 16S sequencing detected abundant Prevotella spp., a more likely causal organisms of the NSTI. The use of antibiotics with the approriate anaerobe coverage, in combination with timely surgical intervention, contributed to the ultimate successful clinical outcome. Complete wound healing and successful graft was achieved within one month of diagnosis of the microbes present.

Conclusion: While surgical intervention remains the most important consideration in treatment of NSTI, correct identifcation of the microbial flora could also contribute to successful treatment.
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http://dx.doi.org/10.12968/jowc.2018.27.Sup4.S24DOI Listing
April 2018

Efficacy of hyperbaric oxygen therapy in bacterial biofilm eradication.

J Wound Care 2018 Jan;27(Sup1):S20-S28

Medical Director; Certified Hyperbaric Technician; Southwest Regional Wound Care Center, Lubbock, Texas.

Objective: Chronic wounds typically require several concurrent therapies, such as debridement, pressure offloading, and systemic and/or topical antibiotics. The aim of this study was to examine the efficacy of hyperbaric oxygen therapy (HBOT) towards reducing or eliminating bacterial biofilms in vitro and in vivo.

Method: Efficacy was determined using in vitro grown biofilms subjected directly to HBOT for 30, 60 and 90 minutes, followed by cell viability determination using propidium monoazide-polymerase chain reaction (PMA-PCR). The efficacy of HBOT in vivo was studied by searching our chronic patient wound database and comparing time-to-healing between patients who did and did not receive HBOT as part of their treatment.

Results: In vitro data showed small but significant decreases in cell viability at the 30- and 90-minute time points in the HBOT group. The in vivo data showed reductions in bacterial load for patients who underwent HBOT, and ~1 week shorter treatment durations. Additionally, in patients' chronic wounds there was a considerable emergence of anaerobic bacteria and fungi between intermittent HBOT treatments.

Conclusion: The data demonstrate that HBOT does possess a certain degree of biofilm killing capability. Moreover, as an adjuvant to standard treatment, more favourable patient outcomes are achieved through a quicker time-to-healing which reduces the chance of complications. Furthermore, the data provided insights into biofilm adaptations to challenges presented by this treatment strategy which should be kept in mind when treating chronic wounds. Further studies will be necessary to evaluate the benefits and mechanisms of HBOT, not only for patients with chronic wounds but other chronic infections caused by bacterial biofilms.
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http://dx.doi.org/10.12968/jowc.2018.27.Sup1.S20DOI Listing
January 2018

Cadaver Thanatomicrobiome Signatures: The Ubiquitous Nature of Species in Human Decomposition.

Front Microbiol 2017 30;8:2096. Epub 2017 Oct 30.

Research and Testing Laboratory, RTL Genomics, Lubbock, TX, United States.

Human thanatomicrobiome studies have established that an abundant number of putrefactive bacteria within internal organs of decaying bodies are obligate anaerobes, 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 ( < 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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http://dx.doi.org/10.3389/fmicb.2017.02096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5670113PMC
October 2017

Microbiome Structural and Functional Interactions across Host Dietary Niche Space.

Integr Comp Biol 2017 10;57(4):743-755

Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.

Host-associated microbiomes are integral components of host health, but microbiome community structure varies among and within hosts. Reconciling community variability with the apparent dependence of hosts on community function, and characterizing how functional divergence proceeds across niches, remains challenging. Here, through the study of gut microbiomes and diets of three insectivorous bat species we characterize how community structure is shaped by predicted functional properties of community members. We found that while host diet and microbiome community composition do not significantly relate to each other, host diet and metagenome function do, suggesting that diet directly selects metagenomic functions rather than communities. We use a novel inference framework to show how the discordance between community structure and functional variation derives from functional equivalence and is influenced by the continuum of shared and derived gene sets across microbial lineages. Our findings help clarify how metagenome community structure-function relationships contribute to deterministic processes in community assembly, and describe the basis for metagenomic differences across ecologically similar hosts.
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http://dx.doi.org/10.1093/icb/icx011DOI Listing
October 2017

Postmortem microbial communities in burial soil layers of skeletonized humans.

J Forensic Leg Med 2017 Jul 3;49:43-49. Epub 2017 May 3.

Forensic Science Program, Physical Sciences Department, Alabama State University, Montgomery, AL 36104, United States. Electronic address:

Microorganisms are major ecological participants in the successional decomposition of vertebrates. The relative abundance, or the scarcity, of certain microbial taxa in gravesoil has the potential to determine the ecological status of skeletons. However, there are substantial knowledge gaps that warrant consideration in the context of the surrounding terrestrial ecosystem. In the current study, we hypothesized that i.) soil microbial diversity is disparate in the latter stage of decomposition (skeletonization) compared to the earlier stages (fresh, bloat, active and advanced decay), and ii.) the three layers of gravesoil (top, middle, and bottom) encompass similar microbial taxa and are analogous with control soil. To test these hypotheses, microbial communities in layers of burial soil of skeletonized bodies (treated) and from control soil, obtained from burial plots with no bodies (untreated), were compared using sequencing data of the 16S rRNA gene. The results demonstrated that Acidobacteria was confirmed as the most abundant microbial genus in all treated and untreated soil layers. Furthermore, Proteobacteria demonstrated a relatively low abundance in skeletonized gravesoil which is dissimilar from previous findings that assessed soil from earlier stages of human decomposition. Also, these results determined that soil microbial signatures were analogous in all three soil layers under the effects of similar abiotic and biotic factors, and they were similar to the communities in untreated soil. Therefore, the current study produced empirical data that give conclusive evidence of soil microbial successional changes, particularly for Proteobacteria, for potential use in forensic microbiology research.
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http://dx.doi.org/10.1016/j.jflm.2017.05.009DOI Listing
July 2017

Fate and impact of zero-valent copper nanoparticles on geographically-distinct soils.

Sci Total Environ 2016 Dec 30;573:661-670. Epub 2016 Aug 30.

Department of Natural Sciences, Southern University at New Orleans, New Orleans, LA 70126, USA.

The fate of engineered zero-valent copper nanoparticles (Cu NPs) in soils collected from geographically-distinct regions of the continental United States and incubated under controlled conditions was investigated with respect to NP affinity for soil surfaces and changes in speciation, as well as their impact on bacterial communities. Soil geochemical properties had a great influence on Cu NP migration and transformation. Translocation of Cu NPs was low in soils enriched in organic matter and high in clay and sandy soils. X-ray absorption spectroscopic analysis showed that the highest rates for transformation to Cu ions and adsorption complexes was in acidic soils. Although there was some change in overall bacterial community richness at the level of order in experimental soil, the level of perturbation was evident in side-by-side comparisons of orders using a 50% microbial community change value (MCC). This assessment revealed that generally, Sphingomonas, known for its importance for remediation, and Rhizobiales, symbiotic partners with certain plants appeared susceptible to Cu NPs and their transformation products. The ecological importance of organisms from these orders and its greater vulnerability to Cu NPs suggests need for future targeted studies.
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http://dx.doi.org/10.1016/j.scitotenv.2016.08.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7384298PMC
December 2016

Human Thanatomicrobiome Succession and Time Since Death.

Sci Rep 2016 07 14;6:29598. Epub 2016 Jul 14.

Department of Entomology, Texas A&M University, College Station, TX, 77843 USA.

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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http://dx.doi.org/10.1038/srep29598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4944132PMC
July 2016
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