Sponge Microbiota are a Reservoir of Functional Antibiotic Resistance Genes

Wide application of antibiotics has contributed to the evolution of multi-drug resistant human pathogens, resulting in poorer treatment outcomes for infections. In the marine environment, seawater samples have been investigated as a resistance reservoir; however, no studies have methodically examined sponges as a reservoir of antibiotic resistance. Sponges could be important in this respect because they often contain diverse microbial communities that have the capacity to produce bioactive metabolites. Here, we applied functional metagenomics to study the presence and diversity of functional resistance genes in the sponges Aplysina aerophoba, Petrosia ficiformis and Corticium candelabrum. We obtained 37 insert sequences facilitating resistance to D-cycloserine (n=6), gentamicin (n=1), amikacin (n=7), trimethoprim (n=17), chloramphenicol (n=1), rifampicin (n=2) and ampicillin (n=3). Fifteen of 37 inserts harboured resistance genes that shared <90% amino acid identity with known gene products, whereas on 13 inserts no resistance gene could be identified with high confidence, in which case we predicted resistance to be mainly mediated by antibiotic efflux. One marine-specific ampicillin-resistance-conferring β-lactamase was identified in the genus Pseudovibrio with 41% global amino acid identity to the closest β-lactamase with demonstrated functionality, and subsequently classified into a new family termed PSV. Taken together, our results show that sponge microbiota host diverse and novel resistance genes that may be harnessed by phylogenetically distinct bacteria

The application of molecular based tools for bioaerosol source tracking and disinfection assessment

Airborne microorganisms play a pivotal role in public health, national security, economic, and agricultural matters, yet our understanding of their identity, distribution and abundance is limited. Employment of molecular based detection and enumeration methods to the study of aerobiology would improve our understanding of commonly encountered microorganisms, as well as establish baseline information for surveillance efforts. This dissertation uses such methods to examine several environments of public health interest. The first case investigated was the potential partitioning of waterborne microorganisms into the atmosphere by massive pumping and aeration operations of floodwaters in New Orleans following Hurricanes Katrina and Rita. To determine if remediation efforts significantly impacted airborne microbe populations, or resulted in aerosolization of potentially pathogenic microorganisms, paired air and water samples were collected in the immediate vicinity of turbulent pumping and aeration operations and analyzed. Remediation activities were found not to significantly impact the bioaerosol ecology proximal to large engineering works. No pathogenic species were detected in the aerosol samples. Airborne ecology results were consistent with phylum level taxonomic patterns emerging from observations of outdoor bioaerosol communities. The second scenario examined was worker exposure to harmful bioaerosols within concentrated animal feeding operations (CAFOs). The recovered ecology was more diverse than previously reported and dominated by organisms associated with animal gut microbiota. No respiratory pathogens of concern were observed; however, the potentially pathogenic species Aerococcus viridans was present in several samples. Fungal species were not recovered from indoor samples. The third situation reviewed was indoor airborne ecology of flood impacted and subsequently remediated homes in New Orleans. Observed fungal populations were substantially different from those commonly recovered using traditional culture methods from water-damaged homes. Wallemia sebi was the only potential respiratory pathogen observed in significant abundance and was found in both indoor and outdoor environments. Finally quantitative PCR was explored as a tool to assess aerosol disinfection efficiency. Bench scale experiments revealed that UV exposure did not impact recovery of QPCR at doses germane to airborne microbial inactivation

Adaptive laboratory evolution to hypersaline conditions, of lactic acid bacteria isolated from seaweed

Seaweed biomass has been proposed as a promising alternative carbon source for fermentation processes using microbial factories. However, the high salinity content of seaweed biomass is a limiting factor in large scale fermentation processes. To address this shortcoming, three bacterial species (Pediococcus pentosaceus, Lactobacillus plantarum, and Enterococcus faecium) were isolated from seaweed biomass and evolved to increasing concentrations of NaCl. Following the evolution period, P. pentosaceus reached a plateau at the initial NaCl concentration, whereas L. plantarum, and E. faecium showed a 1.29 and 1.75-fold increase in their salt tolerance, respectively. The impact that salt evolution had on lactic acid production using hypersaline seaweed hydrolysate was investigated. Salinity evolved L. plantarum produced 1.18-fold more lactic acid than the wild type, and salinity evolved E. faecium was able to produce lactic acid, while the wild type could not. No differences in lactic acid production were observed between the P. pentosaceus salinity evolved and wild type strains. Evolved lineages were analyzed for the molecular mechanisms underlying the observed phenotypes. Mutations were observed in genes affecting the ion balance in the cell, the composition of the cell membrane and proteins acting as regulators. This study demonstrates that bacterial isolates from saline niches are promising microbial factories for the fermentation of saline substrates, without the requirement of previous desalination steps, while preserving high final product yields

Transcriptional interactions suggest niche segregation among microorganisms in the human gut

The human gastrointestinal (GI) tract is the habitat for hundreds of microbial species, of which many cannot be cultivated readily, presumably because of the dependencies between species(1). Studies of microbial co-occurrence in the gut have indicated community substructures that may reflect functional and metabolic interactions between cohabiting species(2,3). To move beyond species co-occurrence networks, we systematically identified transcriptional interactions between pairs of coexisting gut microbes using metagenomics and microarray-based metatranscriptomics data from 233 stool samples from Europeans. In 102 significantly interacting species pairs, the transcriptional changes led to a reduced expression of orthologous functions between the coexisting species. Specific species-species transcriptional interactions were enriched for functions important for H-2 and CO2 homeostasis, butyrate biosynthesis, ATP-binding cassette (ABC) transporters, flagella assembly and bacterial chemotaxis, as well as for the metabolism of carbohydrates, amino acids and cofactors. The analysis gives the first insight into the microbial community-wide transcriptional interactions, and suggests that the regulation of gene expression plays an important role in species adaptation to coexistence and that niche segregation takes place at the transcriptional level