Translating Microbiome Research From and To the Clinic.

Extensive research has elucidated the influence of the gut microbiota on human health and disease susceptibility and resistance. We review recent clinical and laboratory-based experimental studies associating the gut microbiota with certain human diseases. We also highlight ongoing translational advances that manipulate the gut microbiota to treat human diseases and discuss opportunities and challenges in translating microbiome research from and to the bedside.

Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species and strain level diversity and evolution.

Species of the Bacteroidales order are among the most abundant and stable bacterial members of the human gut microbiome with diverse impacts on human health. While Bacteroidales strains and species are genomically and functionally diverse, order-wide comparative analyses are lacking. We cultured and sequenced the genomes of 408 Bacteroidales isolates from healthy human donors representing nine genera and 35 species and performed comparative genomic, gene-specific, mobile gene, and metabolomic analyses. Families, genera, and species could be grouped based on many distinctive features. However, we also show extensive DNA transfer between diverse families, allowing for shared traits and strain evolution. Inter- and intra-specific diversity is also apparent in the metabolomic profiling studies. This highly characterized and diverse Bacteroidales culture collection with strain-resolved genomic and metabolomic analyses can serve as a resource to facilitate informed selection of strains for microbiome reconstitution.

Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species- and strain-level diversity and evolution.

Species of the Bacteroidales order are among the most abundant and stable bacterial members of the human gut microbiome, with diverse impacts on human health. We cultured and sequenced the genomes of 408 Bacteroidales isolates from healthy human donors representing nine genera and 35 species and performed comparative genomic, gene-specific, metabolomic, and horizontal gene transfer analyses. Families, genera, and species could be grouped based on many distinctive features. We also observed extensive DNA transfer between diverse families, allowing for shared traits and strain evolution. Inter- and intra-species diversity is also apparent in the metabolomic profiling studies. This highly characterized and diverse Bacteroidales culture collection with strain-resolved genomic and metabolomic analyses represents a valuable resource to facilitate informed selection of strains for microbiome reconstitution.

Exposure and resistance to lantibiotics impact microbiota composition and function.

The intestinal microbiota is composed of hundreds of distinct microbial species that interact with each other and their mammalian host. Antibiotic exposure dramatically impacts microbiota compositions and leads to acquisition of antibiotic-resistance genes. Lantibiotics are ribosomally synthesized and post-translationally modified peptides produced by some bacterial strains to inhibit the growth of competing bacteria. Nisin A is a lantibiotic produced by Lactococcus lactis that is commonly added to food products to reduce contamination with Gram-positive pathogens. Little is known, however, about lantibiotic-resistance of commensal bacteria inhabiting the human intestine. Herein, we demonstrate that Nisin A administration to mice alters fecal microbiome compositions and the concentration of taurine-conjugated primary bile acids. Lantibiotic Resistance System genes (LRS) are encoded by lantibiotic-producing bacterial strains but, we show, are also prevalent in microbiomes across human cohorts spanning vastly different lifestyles and 5 continents. Bacterial strains encoding LRS have enhanced in vivo fitness upon dietary exposure to Nisin A but reduced fitness in the absence of lantibiotic pressure. Differential binding of host derived, secreted IgA contributes to fitness discordance between bacterial strains encoding or lacking LRS. Although LRS are associated with mobile genetic elements, sequence comparisons of LRS encoded by distinct bacterial species suggest they have been long-term components of their respective genomes. Our study reveals the prevalence, abundance and physiologic significance of an underappreciated subset of antimicrobial resistance genes encoded by commensal bacterial species constituting the human gut microbiome, and provides insights that will guide development of microbiome augmenting strategies.

Bifidobacteria metabolize lactulose to optimize gut metabolites and prevent systemic infection in patients with liver disease.

Progression of chronic liver disease is precipitated by hepatocyte loss, inflammation and fibrosis. This process results in the loss of critical hepatic functions, increasing morbidity and the risk of infection. Medical interventions that treat complications of hepatic failure, including antibiotic administration for systemic infections and lactulose treatment for hepatic encephalopathy, can impact gut microbiome composition and metabolite production. Here, using shotgun metagenomic sequencing and targeted metabolomic analyses on 847 faecal samples from 262 patients with acute or chronic liver disease, we demonstrate that patients hospitalized for liver disease have reduced microbiome diversity and a paucity of bioactive metabolites, including short-chain fatty acids and bile acid derivatives, that impact immune defences and epithelial barrier integrity. We find that patients treated with the orally administered but non-absorbable disaccharide lactulose have increased densities of intestinal bifidobacteria and reduced incidence of systemic infections and mortality. Bifidobacteria metabolize lactulose, produce high concentrations of acetate and acidify the gut lumen in humans and mice, which, in combination, can reduce the growth of antibiotic-resistant bacteria such as vancomycin-resistant Enterococcus faecium in vitro. Our studies suggest that lactulose and bifidobacteria serve as a synbiotic to reduce rates of infection in patients with severe liver disease.

Protein Aggregation is Associated with Acinetobacter baumannii Desiccation Tolerance.

Desiccation tolerance has been implicated as an important characteristic that potentiates the spread of the bacterial pathogen Acinetobacter baumannii on dry surfaces. Here we explore several factors influencing desiccation survival of A. baumannii. At the macroscale level, we find that desiccation tolerance is influenced by cell density and growth phase. A transcriptome analysis indicates that desiccation represents a unique state for A. baumannii compared to commonly studied growth phases and strongly influences pathways responsible for proteostasis. Remarkably, we find that an increase in total cellular protein aggregates, which is often considered deleterious, correlates positively with the ability of A. baumannii to survive desiccation. We show that inducing protein aggregate formation prior to desiccation increases survival and, importantly, that proteins incorporated into cellular aggregates can retain activity. Our results suggest that protein aggregates may promote desiccation tolerance in A. baumannii through preserving and protecting proteins from damage during desiccation until rehydration occurs.

The effects of prolonged exposure to hypoxia and Florida red tide (Karenia brevis) on the survival and activity of stone crabs.

Florida red tides are harmful algae blooms caused by the dinoflagellate Karenia brevis, which occur along Florida's gulf coast almost annually. In recent years Florida red tide blooms have become more common, frequent, and intense. Florida's southwest coast, from Manatee to Collier County, has experienced repeated and prolonged K. brevis blooms since 2011 with the most recent bloom in 2017 lasting 17 months and resulting in both hypoxic and anoxic events. We therefore determined the survival and level of lethargy (e.g., lack of responsiveness or reduction in behavioral reactions) of sublegal stone crabs to K. brevis and hypoxia as both singular and simultaneous stressors. Crabs were randomly assigned to one of six treatments that included: 1) high concentration of toxic K. brevis (> 1 million cells L-1) maintained at normoxic levels (7.2 mg L-1 ± S.D. 0.47 dissolved oxygen), 2) moderate hypoxia (1.6 mg L-1 ± S.D. 0.42 dissolved oxygen) with no K. brevis, 3) moderate hypoxia (1.5 mg L-1 ± S.D. 0.43 dissolved oxygen) with a high concentration of K. brevis, 4) severe hypoxia with no K. brevis (0.69 mg L-1 ± S.D. 0.36 dissolved oxygen), 5) severe hypoxia (0.63 mg L-1 ± S.D. 0.40 dissolved oxygen) with a high concentration of K. brevis, and 6) a normoxic control (7.3 mg L-1 ± S.D. 0.61 dissolved oxygen) with no K. brevis. Survival and stone crab lethargy or responsiveness was monitored every 10-12 h for six days. Crabs simultaneously exposed to K. brevis and severe hypoxia exhibited a 43% decrease in survival and experienced increased lethargy within 24 h relative to the control (7% decrease in survival, no increase in lethargy). The increase in stress level and sluggish behavior during exposure to hypoxia was evident by a general lack of responsiveness or movement which indicates that nearshore populations of stone crabs are unlikely to emigrate away from such conditions suggesting that future harvests may be reduced following prolonged K. brevis blooms and hypoxic events.

Karenia brevis causes high mortality and impaired swimming behavior of Florida stone crab larvae.

The dinoflagellate Karenia brevis causes harmful algal blooms commonly referred to as red tides that are prevalent along Florida's gulf coast. Severe blooms often cause fish kills, turbid water, and hypoxic events all of which can negatively impact local fisheries. The stone crab, Menippe mercenaria, is a ˜$25 million per year fishery that occurs primarily along Florida's gulf coast. On the west Florida shelf, red tides occur from fall through spring, although severe blooms can occur during the summer. During the summer, stone crabs are reproductive and release larvae that are transported offshore where K. brevis blooms originate. This study determined the effects of K. brevis exposure on the survivorship, vertical swimming behavior, and oxygen consumption of stage-1 larval stone crabs. Survivorship was determined by exposing larvae to high (> 1 × 106 cells L-1) and medium (˜1 × 105 cells L-1) K. brevis concentrations for 96-hrs and were compared to controls that had no algae present. Larval swimming behavior (i.e., geotaxis) and oxygen consumption were monitored after 6-hr exposure to K. brevis. After 96-hrs of exposure, mortality was 100% and 30% for larvae in the high and medium concentrations of K. brevis, respectively, relative to the control. Larval swimming behavior was reversed in the K. brevis treatment; however oxygen consumption rates did not differ among treatments. These results suggest that severe blooms during the summer may reduce larval supply and serve as a potential bottleneck for new individuals recruiting into the fishery in years following a K. brevis bloom.

The effects of red tide (Karenia brevis) on reflex impairment and mortality of sublegal Florida stone crabs, Menippe mercenaria.

The Florida stone crab, Menippe mercenaria, is a major commercial fishery that occurs primarily along Florida's west coast, where harmful algal blooms of Karenia brevis frequently develop. To determine sublethal and lethal effects of K. brevis on M. mercenaria, we exposed sublegal stone crabs to three seawater treatments in laboratory conditions: no K. brevis (control), a low-toxin K. brevis strain (Wilson LT), and a toxic K. brevis (New Pass strain). Total food consumed, reflex impairment and survivorship of each crab was monitored throughout the nine-day experiment. Crabs in the toxic treatment consumed 67% less food. The probability of an individual losing a reflex significantly increased with time (days), and there was a 42% decrease in survivorship in the toxic treatment. This is the first study to demonstrate negative effects of K. brevis on the stone crab, presenting the critical need of further investigation to fully understand how red tide may impact sustainability of the fishery.