Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria

Understanding the relationship between the composition of the human gut microbiota and the ecological forces shaping it is of great importance; however, knowledge of the biogeographical and ecological relationships between physically interacting taxa is limited. Interbacterial antagonism may play an important role in gut community dynamics, yet the conditions under which antagonistic behaviour is favoured or disfavoured by selection in the gut are not well understood. Here, using genomics, we show that a species-specific type VI secretion system (T6SS) repeatedly acquires inactivating mutations in Bacteroides fragilis in the human gut. This result implies a fitness cost to the T6SS, but we could not identify laboratory conditions under which such a cost manifests. Strikingly, experiments in mice illustrate that the T6SS can be favoured or disfavoured in the gut depending on the strains and species in the surrounding community and their susceptibility to T6SS antagonism. We use ecological modelling to explore the conditions that could underlie these results and find that community spatial structure modulates interaction patterns among bacteria, thereby modulating the costs and benefits of T6SS activity. Our findings point towards new integrative models for interrogating the evolutionary dynamics of type VI secretion and other modes of antagonistic interaction in microbiomes.

Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria

Understanding the relationship between the composition of the human gut microbiota and the ecological forces shaping it is of high importance as progress towards therapeutic modulation of the microbiota advances. However, given the inaccessibility of the gastrointestinal tract, our knowledge of the biogeographical and ecological relationships between physically interacting taxa has been limited to date. It has been suggested that interbacterial antagonism plays an important role in gut community dynamics, but in practice the conditions under which antagonistic behavior is favored or disfavored by selection in the gut environment are not well known. Here, using phylogenomics of bacterial isolate genomes and analysis of infant and adult fecal metagenomes, we show that the contact-dependent type VI secretion system (T6SS) is repeatedly lost from the genomes of Bacteroides fragilis in adults compare to infants. Although this result implies a significant fitness cost to the T6SS, but we could not identify in vitro conditions under which such a cost manifests. Strikingly, however, experiments in mice illustrated that the B. fragilis T6SS can be favored or disfavored in the gut environment, depending on the strains and species in the surrounding community and their susceptibility to T6SS antagonism. We use a variety of ecological modeling techniques to explore the possible local community structuring conditions that could underlie the results of our larger scale phylogenomic and mouse gut experimental approaches. The models illustrate robustly that the pattern of local community structuring in space can modulate the extent of interactions between T6SS-producing, sensitive, and resistant bacteria, which in turn control the balance of fitness costs and benefits of performing contact-dependent antagonistic behavior. Taken together, our genomic analyses, in vivo studies, and ecological theory point toward new integrative models for interrogating the evolutionary dynamics of type VI secretion and other predominant modes of antagonistic interaction in diverse microbiomes.

Application of Nucleic Acid-Based Strategies to Detect Infectious Pathogens in Orthopaedic Implant-Related Infection

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Implant-associated infection in orthopaedic surgery remains an enormous and largely unsolved clinical problem with a high rate of persistent or recurrent infection. This may be due, at least in part, to the potential for underdiagnosis by traditional microbial culture or the potential for culture to incompletely identify the microbial species present.

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Nucleic acid-based diagnostic techniques, focused on using the diagnostic information contained in DNA or RNA to identify microbial species, have been developing rapidly and have garnered escalating interest for both clinical and research applications.

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Commonly applied techniques include end-point polymerase chain reaction (PCR), quantitative PCR, Sanger sequencing, and next-generation sequencing. Understanding the specific strengths and weaknesses of each technique is critical to understanding their utility, applying the correct assessment strategy, and critically understanding and interpreting research.

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The best practices for interpreting nucleic acid-based diagnostic techniques include considering positive and negative controls, reads per sample, detection thresholds (for differentiating contaminants from positive results), and the primer set or targeted regions.

Detecting Flavobacterial Fish Pathogens in the Environment via High-Throughput Community Analysis

Diseases caused by the fish pathogens Flavobacterium columnare and Flavobacterium psychrophilum are major contributors of preventable losses in the aquaculture industry. The persistent and difficult-to-control infections caused by these bacteria make timely intervention and prophylactic elimination of pathogen reservoirs important measures to combat these disease-causing agents. In this study, we present two independent assays for detecting these pathogens in a range of environmental samples. Natural water samples were inoculated with F. columnare and F. psychrophilum over 5 orders of magnitude, and pathogen levels were detected using Illumina MiSeq sequencing and droplet digital PCR. Both detection methods accurately identified pathogen-positive samples and showed good agreement in quantifying each pathogen. Additionally, the real-world application of these approaches was demonstrated using environmental samples collected at a rainbow trout (Oncorhynchus mykiss) aquaculture facility. These results show that both methods can serve as useful tools for surveillance efforts in aquaculture facilities, where the early detection of these flavobacterial pathogens may direct preventative measures to reduce disease occurrence. IMPORTANCE Early detection of a deadly disease outbreak in a population can be the difference between mass mortality or mitigated effects. In the present study, we evaluated and compared two molecular techniques for detecting economically impactful aquaculture pathogens. We demonstrate that one of these techniques, 16S rRNA gene sequencing using Illumina MiSeq technology, provides the ability to accurately detect two freshwater fish pathogens, F. columnare and F. psychrophilum, while simultaneously profiling the native microbial community. The second technique, droplet digital PCR, is commonly used for pathogen detection, and the results obtained using the assays we designed with this method served to validate those obtained using the MiSeq method. These two methods offer distinct advantages. The MiSeq method pairs pathogen detection and microbial community profiling to answer immediate and long-term fish health concerns, while the droplet digital PCR method provides fast and highly sensitive detection that is useful for surveillance and rapid clinical responses.

Role of Gut Microbiota and Short Chain Fatty Acids in Modulating Energy Harvest and Fat Partitioning in Youth

OBJECTIVE

We aimed at determining the relationship of the gut microbiota and short chain fatty acids with obesity and fat partitioning and at testing potential differences in the ability of gut microbiota to ferment equal amounts of carbohydrates (CHO) between lean and obese youth.

RESEARCH DESIGN AND METHODS

We analyzed the gut microbiota of 84 youth in whom body fat distribution was measured by fast-magnetic resonance imaging, de novo lipogenesis (DNL) quantitated using deuterated water, and the capability of gut flora to ferment CHO was assessed by ¹³C-fructose treatment in vitro.

RESULTS

A significant association was found between the Firmicutes to Bacteroidetes ratio, and the abundance of Bacteroidetes and Actinobacteria with body mass index, visceral and SC fat (all P < .05). Plasma acetate, propionate, and butyrate were associated with body mass index and visceral and SC fat (all P < .05) and with hepatic DNL (P = .01, P = .09, P = .04, respectively). Moreover, the rate of CHO fermentation from the gut flora was higher in obese than in lean subjects (P = .018).

CONCLUSIONS

These data demonstrate that obese youth show a different gut flora composition than lean and that short chain fatty acids are associated with body fat partitioning and DNL. Also, the gut microbiota of obese youth have a higher capability than the gut flora of lean to oxidize CHO.

Metagenomic analysis of the medicinal leech gut microbiota

There are trillions of microbes found throughout the human body and they exceed the number of eukaryotic cells by 10-fold. Metagenomic studies have revealed that the majority of these microbes are found within the gut, playing an important role in the host's digestion and nutrition. The complexity of the animal digestive tract, unculturable microbes, and the lack of genetic tools for most culturable microbes make it challenging to explore the nature of these microbial interactions within this niche. The medicinal leech, Hirudo verbana, has been shown to be a useful tool in overcoming these challenges, due to the simplicity of the microbiome and the availability of genetic tools for one of the two dominant gut symbionts, Aeromonas veronii. In this study, we utilize 16S rRNA gene pyrosequencing to further explore the microbial composition of the leech digestive tract, confirming the dominance of two taxa, the Rikenella-like bacterium and A. veronii. The deep sequencing approach revealed the presence of additional members of the microbial community that suggests the presence of a moderately complex microbial community with a richness of 36 taxa. The presence of a Proteus strain as a newly identified resident in the leech crop was confirmed using fluorescence in situ hybridization (FISH). The metagenome of this community was also pyrosequenced and the contigs were binned into the following taxonomic groups: Rikenella-like (3.1 MB), Aeromonas (4.5 MB), Proteus (2.9 MB), Clostridium (1.8 MB), Eryspelothrix (0.96 MB), Desulfovibrio (0.14 MB), and Fusobacterium (0.27 MB). Functional analyses on the leech gut symbionts were explored using the metagenomic data and MG-RAST. A comparison of the COG and KEGG categories of the leech gut metagenome to that of other animal digestive-tract microbiomes revealed that the leech digestive tract had a similar metabolic potential to the human digestive tract, supporting the usefulness of this system as a model for studying digestive-tract microbiomes. This study lays the foundation for more detailed metatranscriptomic studies and the investigation of symbiont population dynamics.

Effects of D-amphetamine on temporal discrimination in pigeons

Two experiments used a matching to sample of durations procedure to examine changes in temporal discrimination evoked by D-amphetamine (0.75, 1.50, 2.25 and 3.0 mg/kg i.m.) in pigeons. Responses to one key color were reinforced after long (8-s) stimuli: responses to the alternative key color were reinforced after short (2-s) stimuli. Stimuli of intermediate duration were reinforced in Experiment 1 and were not reinforced in Experiment 2. Sigmoid functions relating percent of choices of the key reinforced after long-duration stimuli to the duration of stimulus presented were fit by a cumulative normal function. In addition to a parameter giving the left/right position of the sigmoid curves (which indexes temporal perception), this function also provided estimates of the range and slope of the curve (measures of stimulus control). The results showed that, contrary to many published reports, amphetamine had no effect on the left/right positioning of the sigmoid curve. There was, however, an effect of amphetamine on stimulus control, as shown by the general flattening of the psychophysical functions. Little evidence of tolerance to the drug's behavioral effects was found after 30 consecutive days of behavioral testing under amphetamine.

Objective detection of hemifield and quadrantic field defects by visual evoked cortical potentials

AIMS/BACKGROUND

An objective method for detecting hemifield and quadrantic visual field defects has been developed using steady state visual evoked cortical potentials (VECPs), an adaptive noise canceller (ANC), and Hotelling's t2 statistic. The purpose of this study was to determine the sensitivity and specificity of the technique.

METHODS

Nine subjects (mean age 44 years) were investigated with field loss due to a variety of causes including both anterior and posterior visual pathway lesions. Dynamic perimetry was performed by means of a Goldmann or Tübingen perimeter. VECP recordings were made from each visual field quadrant (23 degrees X 23 degrees) by means of a steady state reversing checkerboard (7.7 rev/s). The central 5 degrees of the visual field and the vertical and horizontal meridians were masked during these measurements. Recordings were made from three electrode sites, positioned over the visual cortex, relative to a mid frontal electrode. Each recording lasted 2 minutes, during which time fixation was monitored. The data from each recording were divided into 4 second segments, and the amplitude and phase of the VECP signal measured using the ANC. Hotelling's t2 statistic was applied to determine the probability of signal detection. Receiver operating characteristic curves were used to find the optimum signal detection threshold for identification of the visual field defects.

RESULTS

The results of the study confirmed patterns of subjective visual field loss. The technique had a sensitivity and a specificity of 81% and 85%, respectively, for detecting 'non-seeing' areas in the inferior visual field, and 82% and 89%, respectively, for detecting 'non-seeing' areas in the superior visual field.

CONCLUSION

These results demonstrate that the technique is of potential clinical value to ophthalmologists and neurologists when subjective perimetry is not possible.

Prostanoids inhibit Kupffer cell nitric oxide synthesis

Kupffer cells are the largest population of fixed tissue macrophages in the body and produce a number of mediators that are involved in host defense. These mediators include cytokines such as tumor necrosis factor-alpha and interleukin-1, prostaglandins, oxygen radicals, and nitric oxide. Prostaglandins are produced by adjacent endothelial cells in addition to Kupffer cells and regulate a number of cellular functions in a wide array of cells, but their role in nitric oxide synthesis is controversial. We studied the role of prostaglandins in regulating lipopolysaccharide (LPS)-induced nitric oxide synthesis in cultured rat Kupffer cells. Prostaglandin E2 (PGE2) inhibited Kupffer cell nitric oxide synthesis in a dose-dependent fashion in both 24- and 48-hr cultures. The effect of PGE2 persisted at low and high LPS concentrations. Prostaglandin analogues as well as other prostanoids also inhibited Kupffer cell nitric oxide synthesis. These data show that exogenous prostaglandins suppress Kupffer cell nitric oxide synthesis and may represent an important endogenous regulator of nitric oxide production.

Etretinate and visual function: a 1-year follow-up study

Concern has been expressed in the literature that the drug etretinate may be potentially retinotoxic. Four patients are reported who have received long-term treatment with etretinate and who have undergone detailed evaluation for the development of visual dysfunction over a 1-year period. Despite prolonged treatment and high total doses no evidence of ocular toxicity attributable to the drug was found in any of the patients.