Human Thanatomicrobiome Succession and Time Since Death

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

Evaluation of the bacterial diversity of Pressure ulcers using bTEFAP pyrosequencing

<p>Abstract</p> <p>Background</p> <p>Decubitus ulcers, also known as bedsores or pressure ulcers, affect millions of hospitalized patients each year. The microflora of chronic wounds such as ulcers most commonly exist in the biofilm phenotype and have been known to significantly impair normal healing trajectories.</p> <p>Methods</p> <p>Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP), a universal bacterial identification method, was used to identify bacterial populations in 49 decubitus ulcers. Diversity estimators were utilized and wound community compositions analyzed in relation to metadata such as Age, race, gender, and comorbidities.</p> <p>Results</p> <p>Decubitus ulcers are shown to be polymicrobial in nature with no single bacterium exclusively colonizing the wounds. The microbial community among such ulcers is highly variable. While there are between 3 and 10 primary populations in each wound there can be hundreds of different species present many of which are in trace amounts. There is no clearly significant differences in the microbial ecology of decubitus ulcer in relation to metadata except when considering diabetes. The microbial populations and composition in the decubitus ulcers of diabetics may be significantly different from the communities in non-diabetics.</p> <p>Conclusions</p> <p>Based upon the continued elucidation of chronic wound bioburdens as polymicrobial infections, it is recommended that, in addition to traditional biofilm-based wound care strategies, an antimicrobial/antibiofilm treatment program can be tailored to each patient's respective wound microflora.</p

Vascular Dysfunction Induced in Offspring by Maternal Dietary Fat Involves Altered Arterial Polyunsaturated Fatty Acid Biosynthesis

Nutrition during development affects risk of future cardiovascular disease. Relatively little is known about whether the amount and type of fat in the maternal diet affect vascular function in the offspring. To investigate this, pregnant and lactating rats were fed either 7%(w/w) or 21%(w/w) fat enriched in either18:2n-6, trans fatty acids, saturated fatty acids, or fish oil. Their offspring were fed 4%(w/w) soybean oil from weaning until day 77. Type and amount of maternal dietary fat altered acetylcholine (ACh)-mediated vaso-relaxation in offspring aortae and mesenteric arteries, contingent on sex. Amount, but not type, of maternal dietary fat altered phenylephrine (Pe)-induced vasoconstriction in these arteries. Maternal 21% fat diet decreased 20:4n-6 concentration in offspring aortae. We investigated the role of Δ6 and Δ5 desaturases, showing that their inhibition in aortae and mesenteric arteries reduced vasoconstriction, but not vaso-relaxation, and the synthesis of specific pro-constriction eicosanoids. Removal of the aortic endothelium did not alter the effect of inhibition of Δ6 and Δ5 desaturases on Pe-mediated vasoconstriction. Thus arterial smooth muscle 20:4n-6 biosynthesis de novo appears to be important for Pe-mediated vasoconstriction. Next we studied genes encoding these desaturases, finding that maternal 21% fat reduced Fads2 mRNA expression and increased Fads1 in offspring aortae, indicating dysregulation of 20:4n-6 biosynthesis. Methylation at CpG −394 bp 5′ to the Fads2 transcription start site predicted its expression. This locus was hypermethylated in offspring of dams fed 21% fat. Pe treatment of aortae for 10 minutes increased Fads2, but not Fads1, mRNA expression (76%; P<0.05). This suggests that Fads2 may be an immediate early gene in the response of aortae to Pe. Thus both amount and type of maternal dietary fat induce altered regulation of vascular tone in offspring though differential effects on vaso-relaxation, and persistent changes in vasoconstriction via epigenetic processes controlling arterial polyunsaturated fatty acid biosynthesis

Molecular diversity within Melanomys caliginosus (Rodentia: Oryzomyini) : evidence for multiple species /

no.275 (2008

A new species of Tanyuromys Pine, Timm, and Weksler, 2012 (Rodentia: Cricetidae: Oryzomyini), with comments on relationships within the Oryzomyini

We name and describe a new species of long-tailed sigmodontine rodent of the genus Tanyuromys, based on 3 specimens collected from 3 different localities in northern Ecuador, during the period 1953–2008. All 3 localities are at middle elevations on the Pacific Andean slopes and specimens were taken both in intact and disturbed forest areas. Tanyuromys previously has been treated as including a single species—T. aphrastus (Harris, 1932); however, using morphological and molecular characters (mitochondrial cytochrome b, Cytb; 1,143 bp), we herein recognize 2 species: T. aphrastus proper, which, so far as known, occurs only in Costa Rica and Panama, and a new species known only from Ecuador. The Ecuadoran species, like T. aphrastus, is characterized by a long tail (ca. 1.5 × length of head plus body); large, complexly constructed, pentalophodont molars; braincase with beaded supraorbital margins continuous with raised temporal ridges; short, anteriorly constricted incisive foramina; short, narrow palatines; and small auditory bullae. Although similar morphologically, which explains why the 2 species have hitherto been regarded as 1, the few specimens available of each differ in that the new species has, among other traits, a narrower interorbital breadth, narrower zygomatic plate, invariably (thus far) distinct supraorbital bead continuing posteriorly over parietal to lambdoidal crests as a prominent raised ridge, relatively large lateral wing of the parietal, skull with more angular rather than more rounded contours. Molecular and morphological characters confirm that specimens of T. aphrastus from Costa Rica and Panama are quite similar; they differ in Cytb sequences by 1.2%. The new species from Ecuador, in contrast, differs from the Central American T. aphrastus in Cytb sequences by 10.2%. The 2 species form a well-supported clade; we infer the genus’ phylogenetic associations within the Oryzomyini, based on the complete cytochrome b sequence. Nombramos y describimos una nueva especie de roedor sigmodontino en el género Tanyuromys Pine, Timm y Weksler, 2012, a partir de tres especímenes recolectados entre 1953 y 2008 en tres localidades diferentes en el norte de Ecuador. Las tres localidades se encuentran a altitudes medias en las laderas Andinas del lado Pacífico. Los especímenes fueron recolectados tanto en bosque intacto como perturbado. Hasta el momento, se ha considerado que Tanyuromys incluye una sola especie: T. aphrastus (Harris, 1932). Sin embargo, mediante datos tanto morfológicos como moleculares (del gen mitocondrial citocromo b, Cytb; de 1,143 pares de bases de longitud), reconocemos en el presente trabajo a dos especies: T. aphrastus propiamente dicho, el cual que se sepa solo habita Costa Rica y Panamá, así como una nueva especie que por el momento solo se conoce de Ecuador. La especie ecuatoriana se caracteriza—al igual que T. aphastus—por tener la cola extremadamente larga (aproximadamente 1.5 × el largo de la longitud cabeza-cuerpo; molares pentalofodontos grandes, de estructura compleja; caja cefálica con márgenes supraorbitarios rebordeados y continuos con una cresta temporal moderadamente elevada; los forámenes incisivos cortos, con constricción anterior; huesos palatinos cortos y estrechos; y bulla timpánica pequeña. Aunque las dos especies son similares (lo cual explica porque hasta ahora se han considerado una sola), los pocos especímenes de cada una difieren entre sí en que la nueva especie tiene, entre otras características, una anchura interorbitaria más estrecha; la placa cigomática más estrecha; el rebordeado supraorbitario prominentemente elevado, tal marcada cresta (en los especímenes que se conocen hasta el momento), continuando en dirección posterior sobre el hueso parietal hasta las crestas lambdoidales; las alas laterales de los parietales relativamente grandes; y los contornos del cráneo más angulares que redondeados. Los análisis moleculares y morfológicos coinciden en que los especímenes de Costa Rica y Panamá difieren poco entre sí: sus secuencias de ADN mitocondrial del citocromo b solo se distinguen en un 1.2%. En cambio, la nueva especie de Ecuador difiere de T. aphrastus centroamericano en 10.2%. Las dos especies forman un clado bien definido y apoyado. En este trabajo, inferimos las asociaciones filogenéticas del género Tanyuromys entre los Oryzomyini con base en secuencias completas del citocromo b

Molecular systematics of South American marsh rats of the genus Holochilus (Muroidea, Cricetidae, Sigmodontinae)

We present a comprehensive systematic study of Holochilus, a sigmodontine genus of large, herbivorous, and semiaquatic rodents widely distributed in South America. Remarkably, given its complex taxonomic history and large economic as well as epidemiological importance, the alpha taxonomy of Holochilus has not benefited from a molecular-based approach. The study is based on sequences of 1 mitochondrial and 3 nuclear loci that were analyzed by maximum likelihood and Bayesian inference. Analyses include sequences of specimens from localities from Argentina, Bolivia, Brazil, Colombia, Paraguay, Peru, Suriname, and Uruguay, representing all but 2 of the species currently recognized in the genus. Of the 4 data matrices, the mitochondrial data set contains the largest geographic coverage and recovered 6 species-level lineages that form 2 well-supported species groups: the brasiliensis species group formed by H. brasiliensis and H. vulpinus and the sciureus species group composed by H. chacarius, H. sciureus, and 2 currently unnamed forms. Surprisingly, in the cytochrome b gene analyses, the 2 species groups are not sister to each other; i.e., Holochilus is not monophyletic, although these topologies lack significant support. However, the monophyly of Holochilus was supported by the 3 nuclear loci as well as by the combined analysis of all 4 loci. These genealogical results are the basis of taxonomic and biogeographic considerations.Presentamos un estudio sistemático comprensivo sobre Holochilus, un género sigmodontino de grandes roedores herbívoros y semi-acuáticos ampliamente distribuido en América del Sur. Llamativamente, dada su compleja historia taxonómica y el gran impacto económico y epidemiológico, la taxonomía alfa de Holochilus no se ha beneficiado de un abordaje basado en evidencia molecular. El estudio se basa en secuencias de 1 gen mitocondrial y de 3 nucleares que fueron analizadas con máxima verosimilitud e inferencia Bayesiana. Los análisis incluyen secuencias de especímenes colectados en localidades de Argentina, Bolivia, Brasil, Colombia, Paraguay, Perú, Surinam y Uruguay, representando todas, con excepción de 2, las especies actualmente reconocidas en el género. La genealogía mitocondrial, que es la que tiene la mayor cobertura geográfica de Holochilus, recobra 6 linajes de nivel de especie que forman 2 grupos de especies bien apoyados: el grupo de especies brasiliensis integrado por H. brasiliensis y H. vulpinus y el grupo de especies sciureus que está compuesto por H. chacarius, H. sciureus y 2 formas aparentemente sin nominar. Llamativamente, en los análisis basados en el gen mitocondrial los 2 grupos de especies no son hermanos; i.e., Holochilus no es monofilético, aunque esta topología no tiene apoyo significativo. Sin embargo la monofilia de Holochilus es apoyada por los análisis de los 3 genes nucleares y por el análisis combinado de los 4 genes. Estos resultados genealógicos son la base de consideraciones taxonómicas y biogeográficas.Fil: D'elía, Guillermo. Universidad Austral de Chile; ChileFil: Hanson, J. Delton. RTL Genomics; Estados UnidosFil: Mauldin, Matthew R.. Centers for Disease Control and Prevention; Estados UnidosFil: Teta, Pablo Vicente. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales ; ArgentinaFil: Pardiñas, Ulises Francisco J.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; Argentin

Data from: Multilocus characterization of a woodrat (genus Neotoma) hybrid zone

In order to investigate hybridization between 2 species of woodrats, Neotoma floridana and Neotoma micropus, 103 specimens were collected, in March of 1988, from a known area of sympatry, and compared with reference collections from areas of allopatry. Ten genetic markers, consisting of 7 microsatellite loci, 1 mitochondrial gene (cytochrome-b [Cytb]), and 2 nuclear introns (intron 2 of the vertebrate alcohol dehydrogenase gene [Adh1-I2] and intron 7 of the beta-fibrinogen gene [Fgb-I7]) were used to develop a composite genotype for each individual and for detection of hybridization. Six individuals were identified as pure parental N. micropus, 96 as hybrids, and 1 as pure parental N. floridana. Hybrids were formed primarily through matings between complex genotypes, resulting in a high prevalence of individuals classified as backcrosses. The ratio of hybrid classes, population substructure, and presence of significant linkage disequilibrium within the zone of contact could not reject either the hybrid superiority or hybrid equilibrium model as responsible for maintenance of this hybrid zone. The collection date of this dataset (1988) provided not only a point in time assessment of the hybrid zone but also provided opportunities for future comparisons of temporal datasets with the purpose of examining hybrid zone characteristics over multiple generations

Mauldin et al Microsatellite Data Dryad

This file contains all microsatellite data examined in the study. The first row contains column headers. The first column contains museum ID numbers. All following columns indicate allele sizes for the animal indicated at the beginning of the row. Missing data value is coded as "0