In an effort to better understand the ancestral state of the human distal gut microbiome, we examine feces retrieved from archaeological contexts (coprolites). To accomplish this, we pyrosequenced the 16S rDNA V3 region from duplicate coprolite samples recovered from three archaeological sites, each representing a different depositional environment: Hinds Cave (∼8000 years B.P.) in the southern United States, Caserones (1600 years B.P.) in northern Chile, and Rio Zape in northern Mexico (1400 years B.P.). Clustering algorithms grouped samples from the same site. Phyletic representation was more similar within sites than between them. A Bayesian approach to source-tracking was used to compare the coprolite data to published data from known sources that include, soil, compost, human gut from rural African children, human gut, oral and skin from US cosmopolitan adults and non-human primate gut. The data from the Hinds Cave samples largely represented unknown sources. The Caserones samples, retrieved directly from natural mummies, matched compost in high proportion. A substantial and robust proportion of Rio Zape data was predicted to match the gut microbiome found in traditional rural communities, with more minor matches to other sources. One of the Rio Zape samples had taxonomic representation consistent with a child. To provide an idealized scenario for sample preservation, we also applied source tracking to previously published data for Ötzi the Iceman and a soldier frozen for 93 years on a glacier. Overall these studies reveal that human microbiome data has been preserved in some coprolites, and these preserved human microbiomes match more closely to those from the rural communities than to those from cosmopolitan communities. These results suggest that the modern cosmopolitan lifestyle resulted in a dramatic change to the human gut microbiome.

Interstitial cystitis/bladder pain syndrome (IC/BPS) is a syndrome of unpleasant bladder sensations and lower urinary tract symptoms. The three main proposed etiologies are bladder urothelial dysfunction, bladder inflammation (possible neurogenic), and neuropathic pain. Despite decades of basic and clinical research, IC/BPS remains difficult to treat. A variety of treatments are used, each aimed towards one etiology. For example, glycosaminoglycans are thought to improve the urothelial permeability barrier, anti-inflammatory agents are used to decrease general inflammation, and mast cell stabilizers and/or antagonists of mast cell products are used in the treatment of neurogenic inflammation. In the (unfortunately frequent) event that a treatment fails, possible reasons are that (1) the clinician is aiming towards the wrong etiology for that patient (i.e., the treatment is off target) or (2) the correct etiology is being targeted, but the treatment is not ameliorating it (i.e., the treatment is sub-therapeutic). This is a crucial distinction, because an off-target treatment should be abandoned, but a sub-therapeutic treatment should be escalated. Currently, our inability to make this crucial distinction is the greatest obstacle to effective treatment. An important future advance would be to identify urine or serum biomarkers specific to each etiologic target. Then, each biomarker could be used to select appropriate patients for each treatment and monitor the treatment's effect on its intended target.

We present the oldest genetically identified dog in the Americas, directly dated to 9,260±170 Cal. B.P. The DNA was extracted from an occipital condyle imbedded in a human paleofecal sample from Hinds Cave in southwest Texas. A 368 base pair fragment of the mitochondrial genome control region was sequenced. These data were analyzed with comparable data, which included other ancient dogs and extant dogs, wolves and coyotes from around the world. Compiled with published data, our results characterize ancient American dogs within clades rooted by Eurasian wolves. In the Americas, these data provide no evidence of local interbreeding with wolves. This is a departure from the genetic pattern in other areas of the world where interbreeding with local wolf populations is apparent. Our discovery of domestic dog bone in a human paleofecal sample provides the earliest direct evidence for human consumption of dogs in the New World. These data support the hypothesis that dogs were a food source for early Paleoamericans.

The expansion of shell disease is an emerging threat to the inshore lobster fisheries in the northeastern United States. The development of models to improve the efficiency and precision of existing monitoring programs is advocated as an important step in mitigating its harmful effects. The objective of this study is to construct a statistical model that could enhance the existing monitoring effort through (1) identification of potential disease-associated abiotic and biotic factors, and (2) estimation of spatial variation in disease prevalence in the lobster fishery. A delta-generalized additive modeling (GAM) approach was applied using bottom trawl survey data collected from 2001–2013 in Long Island Sound, a tidal estuary between New York and Connecticut states. Spatial distribution of shell disease prevalence was found to be strongly influenced by the interactive effects of latitude and longitude, possibly indicative of a geographic origin of shell disease. Bottom temperature, bottom salinity, and depth were also important factors affecting the spatial variability in shell disease prevalence. The delta-GAM projected high disease prevalence in non-surveyed locations. Additionally, a potential spatial discrepancy was found between modeled disease hotspots and survey-based gravity centers of disease prevalence. This study provides a modeling framework to enhance research, monitoring and management of emerging and continuing marine disease threats.