Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness.

UnlabelledWe analyzed the 16S rRNA amplicon composition in fecal samples of selected patients during their prolonged stay in an intensive care unit (ICU) and observed the emergence of ultra-low-diversity communities (1 to 4 bacterial taxa) in 30% of the patients. Bacteria associated with the genera Enterococcus and Staphylococcus and the family Enterobacteriaceae comprised the majority of these communities. The composition of cultured species from stool samples correlated to the 16S rRNA analysis and additionally revealed the emergence of Candida albicans and Candida glabrata in ~75% of cases. Four of 14 ICU patients harbored 2-member pathogen communities consisting of one Candida taxon and one bacterial taxon. Bacterial members displayed a high degree of resistance to multiple antibiotics. The virulence potential of the 2-member communities was examined in C. elegans during nutrient deprivation and exposure to opioids in order to mimic local conditions in the gut during critical illness. Under conditions of nutrient deprivation, the bacterial members attenuated the virulence of fungal members, leading to a "commensal lifestyle." However, exposure to opioids led to a breakdown in this commensalism in 2 of the ultra-low-diversity communities. Application of a novel antivirulence agent (phosphate-polyethylene glycol [Pi-PEG]) that creates local phosphate abundance prevented opioid-induced virulence among these pathogen communities, thus rescuing the commensal lifestyle. To conclude, the gut microflora in critically ill patients can consist of ultra-low-diversity communities of multidrug-resistant pathogenic microbes. Local environmental conditions in gut may direct pathogen communities to adapt to either a commensal style or a pathogenic style.ImportanceDuring critical illness, the normal gut microbiota becomes disrupted in response to host physiologic stress and antibiotic treatment. Here we demonstrate that the community structure of the gut microbiota during prolonged critical illness is dramatically changed such that in many cases only two-member pathogen communities remain. Most of these ultra-low-membership communities display low virulence when grouped together (i.e., a commensal lifestyle); individually, however, they can express highly harmful behaviors (i.e., a pathogenic lifestyle). The commensal lifestyle of the whole community can be shifted to a pathogenic one in response to host factors such as opioids that are released during physiologic stress and critical illness. This shift can be prevented by using compounds such as Pi-PEG15-20 that interrupt bacterial virulence expression. Taking the data together, this report characterizes the plasticity seen with respect to the choice between a commensal lifestyle and a pathogenic lifestyle among ultra-low-diversity pathogen communities that predominate in the gut during critical illness and offers novel strategies for prevention of sepsis

Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone

The deep subsurface soil microbiome encompasses a vast amount of understudied phylogenetic diversity and metabolic novelty, and the metabolic capabilities and ecological roles of these communities remain largely unknown. We observed a widespread and relatively abundant bacterial phylum (CSP1-3) in deep soils and evaluated its phylogeny, ecology, metabolism, and evolutionary history. Genome analysis indicated that members of CSP1-3 were actively replicating in situ and were widely involved in the carbon, nitrogen, and sulfur cycles. We identified potential adaptive traits of CSP1-3 members for the oligotrophic deep soil environments, including a mixotrophic lifestyle, flexible energy metabolisms, and conservation pathways. The ancestor of CSP1-3 likely originated in an aquatic environment, subsequently colonizing topsoil and, later, deep soil environments, with major CSP1-3 clades adapted to each of these distinct niches. The transition into the terrestrial environment was associated with genome expansion, including the horizontal acquisition of a range of genes for carbohydrate and energy metabolism and, in one lineage, high-affinity terminal oxidases to support a microaerophilic lifestyle. Our results highlight the ecology and genome evolution of microbes in the deep Critical Zone

THE ADAPTIVE SIGNIFICANCE OF SHELL MORPHOLOGY AND COLOR IN CERION (MOLLUSCA, GASTROPODA, PULMONATA)

Cerion is a morphologically diverse genus of land snails inhabiting Cuba, the Cayman Islands, Bahama Islands, Hispanola, Virgin Islands, Dutch Antilles, and the Florida Keys. Due to extensive interpopulational variation over 600 species have been described, but nearly all hybridize freely, and only one case of sympatry is known. Morphological variation within populations is much more moderate. The distribution of morphological types has been explained as the result of hurricanes casting ashore lone propagules which founded new populations. But more recent work indicates there is a systematic pattern to the distribution of morphological types. Literature on the adaptive morphology of snail shells is reviewed and applied to Cerion. Specifically considered are shell size, color, strength of ribbing, and resistance to crushing. Experiments demonstrating the possible adaptive value of variation in each of these traits were performed and correlations between morphology and habitat were noted. The force necessary to crush shells of seven species and ten populations of Cerion was determined using a mechanical crab claw. The populations sampled represent a variety of degrees of shell thickness, ribbiness, shape, and overall size. Models predicting shell strength from measures of shell height, breadth, thickness, and rib height were developed. Predictions of shell strength are consistent with determinations of snails\u27 susceptibility to being crushed by the land crab Gecarcinus lateralis, a predator of Cerion. The color of different Cerion ranges from white to almost solid dark brown. It has been demonstrated for other snail species that more darkly pigmented shells absorb more radiant energy, and correlations between color and climate have been noted. Differences in the temperatures of Cerion shells of different degrees of mottling were estimated by measuring the temperatures of shells exposed to direct sunlight. Comparisons were also made between shells of different surface textures and ribbiness. The maximum difference between hourly mean temperatures was 3.1(DEGREES)C, between white and heavily mottled shells. The maximum shell temperatures of pigmented shells (48(DEGREES)C) was below the lethal temperture determined in the laboratory when snails were exposed to elevated temperatures for 5 hours (52.5(DEGREES)C). But snails exposed to 42.5(DEGREES)C for one week died of dehydration. It is concluded that white shells should be favored in habitats where there is little or no shade. Nine morphospecies of Cerion were collected from Abaco Island and Long Island in the Bahamas and from the Florida Keys. Habitat data for each collection site were recorded and included location, elevation, substrate type, shade, predominant vegetation, presence of other snail species, and evidence of predators. Notes were also made of the estivation position at each site, i.e., whether the snails were in leaf litter or above ground on plants or rocks. Snails with stronger shell types, as determined by experimental means, were more commonly found where there were signs of potential predators, especially Gecarcinus lateralis. Pigmented snails were more often found in shaded habitats, and white snails in habitats where they were exposed to direct sunlight. Snails at the most exposed sites had a lower height to breadth ratio, and small adult snails and juveniles behaviorally compensate for their greater susceptibility to desiccation by estivating in leaf litter rather than above ground. Thus, the distribution of different Cerion shell morphologies is consistent with functional adaptations to local habitat