Utility of Microbiomes for Population Management (hosted by AFS)

Microbiome research is a newly emerging field that has gained a lot of attention in the areas of evolutionary biology, veterinary sciences, human medicine, and biomedical engineering. Previously, host associated microbes have mostly been studied for their negative effects on host biology as parasites and pathogens. However, recent investigations have shown that host-associated microbial communities can play beneficial roles including aiding in host adaptation to new niches, resistance to diseases, and resilience to environmental threats. Linking microbiome information and host health has initiated the use of microbiome-based solutions for population management. Applications include for example: (i) use of probiotics for disease prevention in commercial fish production; (ii) augmentation of the skin microbiome of amphibians with antifungal metabolite-producing bacteria to increase resistance to infection by the lethal fungus Bd; (iii) identification, culturing, and industrial use of fermenting bacteria from rumen; and (iv) bringing hosts into the laboratory to manipulate their microbiome and understand how host-microbiome interactions affect development and disease. We are inviting abstracts (for 20min talks) to highlight the use of host-associated microbes in population management and to provide future guidelines for studies in the wild. The symposium will be concluded with a 40-minute open discussion.

8:00AM Compute Resources, Training and Workflows Available to the Microbiome Community
  Bhavya Papudeshi, Sheri A Sanders, Carrie Ganote, Thomas Doak
Microbes play a critical role in the host’s health and ecological stability. Increasing numbers of research studies have shown the influence of the microbiome on immune response, nutrient absorption and in maintaining health: this has led to an increase in the number of sequencing projects and big data analysis has now become a biological problem. The National Center for Genome Analysis Support (NCGAS) is an organization funded by the NSF to liaison between biologists and computational resources. NCGAS provides researchers free access to the needed computational resources, and training to use these resources for analysis. We develope bioinformatic workflows – to reconstruct genomes from shotgun metagenomes, to examine the role of specific genera of interest in a community, and mining the ~14 PB Sequence Read Archive (SRA) to identify other datasets with sequences of interest. These workflows are open source and available to the community, with documentation. Additionally, we provide preconfigured virtual machines with QIIME2 and MEGAN toolkits. In this presentation, we demonstrate our microbiome workflows, nationally available computer resources, and training available to the research community. Access to computational resources and bioinformatics workflows should not be a critical bottleneck in research studies.
8:20AM Microbial Bioremediation of Crude Oil and Its Effect on Threespine Stickleback Immunity
  Kelly Ireland, Rachael Kramp, Kathryn Milligan-Myhre
Crude oil and its constituents (i.e. polycyclic aromatic hydrocarbons – PAHs) have many harmful organismal effects, both short and long-term. Of particular interest is how immunotoxic effects of PAHs increase susceptibility to pathogens causing increased mortality in some fish. Reduction of these effects could help protect fish health. Many oil spill recovery methods promote microbial bioremediation by encouraging the growth of microbes capable of PAH degradation or altering oil for easier consumption by microbes. Bioremediation methods were largely used in the 1989 Exxon Valdez oil spill clean-up efforts. Some PAH degrading (PAHD) microbes are even found living within organisms, which may benefit the host following a spill. However, the toxicity of the remaining oil and byproducts of microbial bioremediation is largely unknown. Research has yet to be conducted on the interactions between organisms exposed to PAHs and treated with PAHD microbes. We aimed to use threespine stickleback (Gasterosteus aculeatus) to determine species specific effects of crude oil and if microbial bioremediation can diminish the adverse effects of exposure. Fish with gnotobiotic microbiomes were treated with crude oil or phenanthrene (the main PAH of Alaska North Slope crude). Samples were collected for qRT-PCR of immune genes and 16S microbial community analysis.
8:40AM Maximum Exploitation: What Can Dreissenid Mussels Tell Us about Ecosystem Health?
  Ammar Hanif, Edward Johnson, Ashley Elgin
Two species of invasive dreissenid mussels (Dreissena polymorpha and Dreissena bugensis) have become a major problem within the Laurentian Great Lakes drastically changing the ecosystem. Most studies involving these mussels throughout the Laurentian Great Lakes have focused on organism physiology, distribution, ecological effects, and genetics. Winters et al (2011) mentioned the need to study the microbiome of dreissenid mussels given the increasing interest in studies focusing on the changing benthic microbial community. The recent development of high-throughput sequencing has given deeper insights into an organism’s microbial community. As part of NOAA’s long standing Mussel Watch program dreissenid mussels have been collected and monitored for chemicals of emerging concern, polycyclic aromatic hydrocarbons (PAH), and health metrics (metabolomics, DNA damage, cellular biomarkers for stress) from the Laurentian Great Lakes. In 2018 we conducted a temporal study (May – Nov) to characterize the microbial community of the invasive dreissenid mussels collected from a single site in Lake Michigan. Here we describe the method, microbial community and inferences to ecosystem health. This study is a collaboration between NOAA’s Mussel Watch program within the Great Lakes and NOAA’s Great Lakes Research Laboratory and will augment their studies of ecosystem health, mussel physiology, and benthic ecology.
9:00AM Comparative Genomic Analysis of Metagenome-Assembled Genomes from Feces of Antibiotic Treated Koalas after Chlamydia Infection
  Laetitia Wilkins, Katherine Dahlhausen, Guillaume Jospin, Jonathan Eisen
Koala (Phascolarctos cinereus) populations in Queensland and New South Wales, Australia are listed as vulnerable. The biggest threats to their existence include overhunting, habitat destruction, and chlamydia infections caused by Chlamydia pecorum and pneumoniae. For over two decades, infected koalas have been brought to wildlife hospitals to treat their chlamydia with antibiotics. Unfortunately, antibiotic treatment also affects their natural gut microbiome. The microbial communities in koala intestines help break down toxic compounds from eucalyptus leaves. Dahlhausen et al. (2018) characterized shifts of koala intestinal microbial communities associated with antibiotic treatment. They identified bacteria that correlate with koala health after antibiotic treatment. This included several taxa within Ruminococcus, Cloacibacillus, and Lonepinella koalarum, that was subsequently cultured and sequenced (publication in preparation). Here we used metagenomic shotgun sequencing of feces collected for the original study from a koala that survived treatment and one that deceased shortly after collection. We performed a comparative genomic analysis of metagenome-assembled genomes (MAGs) and closely related publicly available genomes to look for evidence in koala feces for degradation of toxins found in eucalyptus leaves. Moreover, we searched the MAGs in koala feces for antibiotic resistance genes to guide future treatment of chlamydia.
9:20AM Moose Rumen Microbes and Their Relevance to Agriculture and Health
  Suzanne Ishaq
Moose (Alces alces) have an intractability to captive management that largely stems from digestive tract dysbiosis; mediated by modified diet and shifts in the gut microbiota. Moose may seem a dubious source for information about gut health and livestock production, yet this intractability and lack of integration into human populations centers left their diet and rumen microbial community effectively unaltered by human influence. They model a natural gut ecosystem which processes large inputs of complex carbohydrates and supports a diverse and functional microbial community. Diet, social interactions, environmental conditions, stress, immune function and challenges, and a number of lifestyle factors alter gut microbiota, such that domesticated livestock and research animals no longer represent a true gut wildtype. In the age of “missing microbes” and growing concern around host microbiota and health, the ability to study a true wildtype microbial ecosystem can offer many insights. Further, their rumen is smaller relative to body size than other ruminants, and the reticulum larger; with a large body size and low caloric content of their diet. Collectively, this speaks to the efficiency of their gut microbiota, which has implications for livestock production as well as industry, including biomass digesters, manure fertilization, of feed pre-treatment.
09:40AM Break
10:10AM Bacterial Adaptation to the Zebrafish Gut: Dissecting a Mechanism of Host Colonization
  Catherine Robinson
Animals are colonized by microorganisms that profoundly impact their health and development. A consequence of this intimate relationship is that changes in the composition or function of the microbiota can incite disease. However, developing approaches to restore healthy function of dysbiotic communities requires a deeper understanding of the host-microbe interactions that govern community structure and function. The zebrafish has emerged recently as a powerful model for studying host-microbe systems. In order to investigate bacterial traits that are important for host colonization, we evolutionarily adapted a zebrafish bacterial isolate, Aeromonas veronii, to the germ-free larval zebrafish gut. Strikingly, the initial adaptations did not increase within-host fitness, but rather enhanced transmission into the fish from the environment. Genomic analysis showed that mutations in the same gene arose independently across replicate evolving populations. This gene encodes a protein that modulates bacterial motility in response to specific extracellular amino acids. In the context of the zebrafish, these amino acids both increase immigration into the host and modulate competition outcome between the wild type and ΔspdE strains. Combined, this work contributes important insights into the selective forces in host-microbe systems and provides a specific mechanism of host colonization by a bacterial symbiont.
10:30AM Skin Microbiome of Sierra Nevada Yellow-legged Frogs: Population Biology and its Role in Fungal Infections and Restorations Efforts
  Sonia Lorraine Ghose, Jonathan Eisen
The Sierra Nevada yellow-legged frog, Rana sierrae, has been driven close to extinction in part by the amphibian fungal pathogen Batrachochytrium dendrobatidis (Bd). Skin-associated microbes can inhibit Bd infection, and several studies have shown that differences in overall microbial community structure may result in distinct disease outcomes for hosts. I am collaborating with the San Francisco Zoo and the Sierra Nevada Aquatic Research Laboratory to incorporate an examination of the skin microbiome into recent population restoration efforts for this species. This has involved sampling the skin microbiome of frogs in captivity, during experimental Bd infection treatment, and in the field. This ongoing work will provide context for incorporating microorganisms into restoration efforts, a widely overlooked method for promoting organismal health.
10:50AM Captivity-Induced Changes in the Skin Microbial Communities of Hellbenders (Cryptobranchus alleganiensis)
  Obed Hernandez-Gomez, Erin Kenison, Jeffrey Briggler, Rod Williams
Captive environments are maintained in hygienic ways to prevent the spread of infectious disease. Aseptic conditions can affect the establishment and maintenance of “wild-type” microbiotas. Alternative microbiomes can result in the proliferation of disease among captive stock or upon reintroduction. Hellbenders (Cryptobranchus alleganiensis) are a threatened salamander for which captive management is currently employed. We characterized the skin microbiota of wild and captive-reared hellbenders from two subspecies, the eastern (C. a. alleganiensis) and the Ozark hellbender (C. a. bishopi). We also tracked changes in the skin microbiota of captive-reared eastern hellbenders exposed to river water from an intended re-introduction site. Captive eastern hellbenders possessed richer communities than wild cohorts, whereas the opposite pattern was observed within the Ozark subspecies. We found microbial community structure between wild and captive individuals. Captive eastern hellbenders exposed to river water had higher skin microbial diversity and distinct community composition, compared to control hellbenders. Exposing hellbenders to river water in captivity was an effective method to increase bacterial colonization and produced similar changes as release into the river. Our study provides a baseline for the effect of captivity on the skin microbiotas of hellbenders and highlights the need to incorporate microbial management in captive-rearing programs.
11:10AM Comparison of Methods for the Inhibition of a Virulent Strain of Chytrid Fungus, Batrachochytrium Dendrobatidis
  Marina De León, Wei-Jen Lin, Jill Adler-Moore
A virulent genotype of Batrachochytrium dendrobatidis (Bd), the Global Panzootic Lineage (Bd-GPL), is implicated as the cause of global amphibian population declines. Bd-GPL strain JEL274 was isolated from Anaxyrus boreas toads in Colorado, USA where populations are in decline due to chytridiomycosis, the disease caused by Bd. We show the difficulty in attempting to control JEL274 by challenging the genotype against three methods of inhibition; exposure to amphotericin B, recombinant E. coli-violacein, and A. boreas skin-associated bacteria. The Minimum Inhibitory Concentration of amphotericin B on JEL274 was 10-fold higher than previously tested genotypes suggesting that JEL274 is remarkably drug resistant. Violacein, a metabolite expressed by some proteobacteria has been shown to inhibit growth of the fungus. We explored the difference in fungal inhibition between recombinant E. coli-violacein and natural antifungal activity of bacteria isolated from A. boreas skin. Plasmid vectors containing the violacein genes were transformed into NEB5-alpha E. coli and the transformants expressed the characteristic deep violet pigment of violacein. Toad skin bacterial isolates were identified using 16S rRNA gene sequencing. Chryseobacterium indologenes inhibited JEL274 significantly better than recombinant E. coli-violacein and we postulate that this bacterium may be involved with the clearing of Bd infections of the toads.
11:30AM Discussion

Organizers: Obed Hernandez-Gomez, Laetitia Wilkins
Supported by: Dr. Laetitia Wilkins & Dr. Obed Hernandez-Gomez

Location: Reno-Sparks CC Date: October 2, 2019 Time: 8:00 am - 11:50 am