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

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

Dechlorination of Four Commercial Polychlorinated Biphenyl Mixtures (Aroclors) by Anaerobic Microorganisms from Sediments

The rate, extent, and pattern of dechlorination of four Aroclors by inocula prepared from two polychlorinated biphenyl (PCB)-contaminated sediments were compared. The four mixtures used, Aroclors 1242, 1248, 1254, and 1260, average approximately three, four, five, and six chlorines, respectively, per biphenyl molecule. All four Aroclors were dechlorinated with the loss of meta plus para chlorines ranging from 15 to 85%. Microorganisms from an Aroclor 1242-contaminated site in the upper Hudson River dechlorinated Aroclor 1242 to a greater extent than did microorganisms from Aroclor 1260-contaminated sediments from Silver Lake, Mass. The Silver Lake inoculum dechlorinated Aroclor 1260 more rapidly than the Hudson River inoculum did and showed a preferential removal of meta chlorines. For each inoculum the rate and extent of dechlorination tended to decrease as the degree of chlorination of the Aroclor increased, especially for Aroclor 1260. The maximal observed dechlorination rates were 0.3, 0.3, and 0.2 μg-atoms of Cl removed per g of sediment per week for Aroclors 1242, 1248, and 1254, respectively. The maximal observed dechlorination rates for Hudson River and Silver Lake organisms for Aroclor 1260 were 0.04 and 0.21 μg-atoms of Cl removed per g of sediment per week, respectively. The dechlorination patterns obtained suggested that the Hudson River microorganisms were more capable than the Silver Lake organisms of removing the last para chlorine. These results suggest that there are different PCB-dechlorinating microorganisms at different sites, with characteristic specificities for PCB dechlorination

Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter

Targeting sequencing to genes involved in key environmental processes, i.e. ecofunctional genes, provides an opportunity to sample nature’s gene guilds to greater depth and help link community structure to process-level outcomes. Vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. The overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknown diversity. To illustrate current issues surrounding amplicon read processing we provide examples for three ecofunctional gene groups. A combination of in-silico, environmental and cultured strain sequences was used to test new primers targeting the dioxin and dibenzofuran degrading genes dxnA1, dbfA1, and carAa. The majority of obtained environmental sequences were classified into novel sequence clusters, illustrating the discovery value of the approach. For the nitrite reductase step in denitrification, the well-known nirK primers exhibited deficiencies in reference database coverage, illustrating the need to refine primer-binding sites and/or to design multiple primers, while nirS primers exhibited bias against five phyla. Amino acid-based OTU clustering of these two N-cycle genes from soil samples yielded only 114 unique nirK and 45 unique nirS genus-level groupings, likely a reflection of constricted primer coverage. Finally, supervised and non-supervised OTU analysis methods were compared using the nifH gene of nitrogen fixation, with generally similar outcomes, but the clustering (non-supervised) method yielded higher diversity estimates and stronger site-based differences. High throughput amplicon sequencing can provide inexpensive and rapid access to nature’s related sequences by circumventing the culturing barrier, but each unique gene requires individual considerations in terms of primer design and sequence processing and classification