Symbiotic Human Gut Bacteria with Variable Metabolic Priorities for Host Mucosal Glycans.

UnlabelledMany symbiotic gut bacteria possess the ability to degrade multiple polysaccharides, thereby providing nutritional advantages to their hosts. Like microorganisms adapted to other complex nutrient environments, gut symbionts give different metabolic priorities to substrates present in mixtures. We investigated the responses of Bacteroides thetaiotaomicron, a common human intestinal bacterium that metabolizes more than a dozen different polysaccharides, including the O-linked glycans that are abundant in secreted mucin. Experiments in which mucin glycans were presented simultaneously with other carbohydrates show that degradation of these host carbohydrates is consistently repressed in the presence of alternative substrates, even by B. thetaiotaomicron previously acclimated to growth in pure mucin glycans. Experiments with media containing systematically varied carbohydrate cues and genetic mutants reveal that transcriptional repression of genes involved in mucin glycan metabolism is imposed by simple sugars and, in one example that was tested, is mediated through a small intergenic region in a transcript-autonomous fashion. Repression of mucin glycan-responsive gene clusters in two other human gut bacteria, Bacteroides massiliensis and Bacteroides fragilis, exhibited variable and sometimes reciprocal responses compared to those of B. thetaiotaomicron, revealing that these symbionts vary in their preference for mucin glycans and that these differences occur at the level of controlling individual gene clusters. Our results reveal that sensing and metabolic triaging of glycans are complex processes that vary among species, underscoring the idea that these phenomena are likely to be hidden drivers of microbiota community dynamics and may dictate which microorganisms preferentially commit to various niches in a constantly changing nutritional environment.ImportanceHuman intestinal microorganisms impact many aspects of health and disease, including digestion and the propensity to develop disorders such as inflammation and colon cancer. Complex carbohydrates are a major component of the intestinal habitat, and numerous species have evolved and refined strategies to compete for these coveted nutrients. Our findings reveal that individual bacteria exhibit different preferences for carbohydrates emanating from host diet and mucosal secretions and that some of these prioritization strategies are opposite to one another. Thus, we reveal new aspects of how individual bacteria, some with otherwise similar metabolic potential, partition to "preferred niches" in the complex gut ecosystem, which has important and immediate implications for understanding and predicting the behavioral dynamics of this community

Phenotypic and Genomic Diversification in Complex Carbohydrate-Degrading Human Gut Bacteria

Symbiotic bacteria are responsible for the majority of complex carbohydrate digestion in the human colon. Since the identities and amounts of dietary polysaccharides directly impact the gut microbiota, determining which microorganisms consume specific nutrients is central for defining the relationship between diet and gut microbial ecology. Using a custom phenotyping array, we determined carbohydrate utilization profiles for 354 members of the Bacteroidetes, a dominant saccharolytic phylum. There was wide variation in the numbers and types of substrates degraded by individual bacteria, but phenotype-based clustering grouped members of the same species indicating that each species performs characteristic roles. The ability to utilize dietary polysaccharides and endogenous mucin glycans was negatively correlated, suggesting exclusion between these niches. By analyzing related Bacteroides ovatus/Bacteroides xylanisolvens strains that vary in their ability to utilize mucin glycans, we addressed whether gene clusters that confer this complex, multilocus trait are being gained or lost in individual strains. Pangenome reconstruction of these strains revealed a remarkably mosaic architecture in which genes involved in polysaccharide metabolism are highly variable and bioinformatics data provide evidence of interspecies gene transfer that might explain this genomic heterogeneity. Global transcriptomic analyses suggest that the ability to utilize mucin has been lost in some lineages of B. ovatus and B. xylanisolvens, which harbor residual gene clusters that are involved in mucin utilization by strains that still actively express this phenotype. Our data provide insight into the breadth and complexity of carbohydrate metabolism in the microbiome and the underlying genomic events that shape these behaviors

Experimental evaluation of ecological principles to understand and modulate the outcome of bacterial strain competition in gut microbiomes

It is unclear if coexistence theory can be applied to gut microbiomes to understand their characteristics and modulate their composition. Through experiments in gnotobiotic mice with complex microbiomes, we demonstrated that strains of Akkermansia muciniphila and Bacteroides vulgatus could only be established if microbiomes were devoid of these species. Strains of A. muciniphila showed strict competitive exclusion, while B. vulgatus strains coexisted but populations were still influenced by competitive interactions. These differences in competitive behavior were reflective of genomic variation within the two species, indicating considerable niche overlap for A. muciniphila strains and a broader niche space for B. vulgatus strains. Priority effects were detected for both species as strains’ competitive fitness increased when colonizing first, which resulted in stable persistence of the A. muciniphila strain colonizing first and competitive exclusion of the strain arriving second. Based on these observations, we devised a subtractive strategy for A. muciniphila using antibiotics and showed that a strain from an assembled community can be stably replaced by another strain. By demonstrating that competitive outcomes in gut ecosystems depend on niche differences and are historically contingent, our study provides novel information to explain the ecological characteristics of gut microbiomes and a basis for their modulation

Inherited selective cobalamin malabsorption in Komondor dogs associated with a CUBN splice site variant

Background Three Komondor dogs in a small family and 3 sporadic cases exhibited a constellation of signs that included juvenile-onset of failure-to-thrive, inappetence, vomiting and/or diarrhea, and weakness. In each we documented dyshematopoiesis, increased anion gap, methylmalonic acidemia/-uria, and serum cobalamin deficiency. Urine protein electrophoresis demonstrated excretion of cubam ligands. All clinical signs and metabolic abnormalities, except proteinuria, were reversed by regular parenteral cobalamin administration. The pattern of occurrence and findings in the disorder suggested an autosomal recessive inheritance of cobalamin malabsorption with proteinuria, a condition in humans called Imerslund-Gräsbeck syndrome. The purpose of this study was to determine the molecular cause of this disorder in Komondors. Results Whole genome sequencing of two affected Komondor dogs of unknown relatedness and one parent and a clinically-normal littermate of an affected dog revealed a pathogenic single-base change in the CUBN intron 55 splice donor consensus sequence (NM_001003148.1: c.8746 + 1G > A) that was homozygous in affected dogs and heterozygous in the unaffected parents. Alleles of the variant co-segregated with alleles of the disease locus in the entire family and all more distantly-related sporadic cases. A population study using a simple allele-specific DNA test indicated mutant allele frequencies of 8.3 and 4.5% among North American and Hungarian Komondors, respectively. Conclusions DNA testing can be used diagnostically in Komondors when clinical signs are suggestive of cobalamin deficiency or to inform Komondor breeders prospectively and prevent occurrence of future affected dogs. This represents the third cubilin variant causing inherited selective cobalamin malabsorption in a large animal ortholog of human Imerslund-Gräsbeck syndrome

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism

Yeasts, which have been a component of the human diet for at least 7000 years, possess an elaborate cell wall α-mannan. The influence of yeast mannan on the ecology of the human microbiota is unknown. Here we show that yeast α-mannan is a viable food source for Bacteroides thetaiotaomicron (Bt), a dominant member of the microbiota. Detailed biochemical analysis and targeted gene disruption studies support a model whereby limited cleavage of α-mannan on the surface generates large oligosaccharides that are subsequently depolymerized to mannose by the action of periplasmic enzymes. Co-culturing studies showed that metabolism of yeast mannan by Bt presents a ‘selfish’ model for the catabolism of this recalcitrant polysaccharide. This report shows how a cohort of highly successful members of the microbiota has evolved to consume sterically-restricted yeast glycans, an adaptation that may reflect the incorporation of eukaryotic microorganisms into the human diet

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism

Yeasts, which have been a component of the human diet for at least 7,000 years, possess an elaborate cell wall α-mannan. The influence of yeast mannan on the ecology of the human microbiota is unknown. Here we show that yeast α-mannan is a viable food source for the Gram-negative bacterium Bacteroides thetaiotaomicron, a dominant member of the microbiota. Detailed biochemical analysis and targeted gene disruption studies support a model whereby limited cleavage of α-mannan on the surface generates large oligosaccharides that are subsequently depolymerized to mannose by the action of periplasmic enzymes. Co-culturing studies showed that metabolism of yeast mannan by B. thetaiotaomicron presents a ‘selfish’ model for the catabolism of this difficult to breakdown polysaccharide. Genomic comparison with B. thetaiotaomicron in conjunction with cell culture studies show that a cohort of highly successful members of the microbiota has evolved to consume sterically-restricted yeast glycans, an adaptation that may reflect the incorporation of eukaryotic microorganisms into the human diet

SEARCHING ENCRYPTED CLOUD DATA

The major setback of the cloud is its inability to induce strong trust in its users. For us, the users of the cloud, to be sure of the security of the data from other users, we have to trust cloud. In most of the cases, say if the data were to be hosted on Microsoft’s servers, we can trust Microsoft in its policies to prevent unauthorized access to it from other users (via hacking). But, the issue that is haunting the cloud is this - ”How can we be sure that our data is safe from Cloud service providers themselves?” The most intuitive solution for the cloud service provider to gain trust is to insist we encrypt our data. That is an irrefutable act of honesty from the cloud. But this has some obvious setbacks, few of which would negate the very advantages of cloud. One such issue that dictates the scope of this thesis is this - Typical cryptographic algorithms are not amenable to search. Now, if we were to implement a search engine on cloud (which has the data encrypted), the native search techniques have to be extended on to the cryptographic domain so that the cloud can perform the tasks of a search engine. This thesis explores the solutions to the above mentioned problem of searching over encrypted data, specifically using a secure pre-processed index approach. Though significant ideas have been proposed in the area, there is no concrete implementation to analyze if it can be used in the industrial setting. The main goal of the thesis is to implement a system which supports a variety of searching techniques. We make use of Amazon EC2 and test out the designed systems to evaluate how feasible they are for immediate consumption by the industry.M.S. in Computer Engineering, May 201

Optimizing LaneSegNet for Real-Time Lane Topology Prediction in Autonomous Vehicles

With the increasing prevalence of autonomous vehicles, it is essential for computer vision algorithms to accurately assess road features in real-time. This study explores the LaneSegNet architecture, a new approach to lane topology prediction which integrates topological information with lane-line data to provide a more contextual understanding of road environments. The LaneSegNet architecture includes a feature extractor, lane encoder, lane decoder, and prediction head, leveraging components from ResNet-50, BEVFormer, and various attention mechanisms. We experimented with optimizations to the LaneSegNet architecture through feature extractor modification and transformer encoder-decoder stack modification. We found that modifying the encoder and decoder stacks offered an interesting tradeoff between training time and prediction accuracy, with certain combinations showing promising results. Our implementation, trained on a single NVIDIA Tesla A100 GPU, found that a 2:4 ratio reduced training time by 22.3% with only a 7.1% drop in mean average precision, while a 4:8 ratio increased training time by only 11.1% but improved mean average precision by a significant 23.7%. These results indicate that strategic hyperparameter tuning can yield substantial improvements depending on the resources of the user. This study provides valuable insights for optimizing LaneSegNet according to available computation power, making it more accessible for users with limited resources and increasing the capabilities for users with more powerful resources.Comment: 18 pages, 16 figure

Catheter associated urinary tract infections due to Trichosporon asahii

Urinary tract infections (UTIs) caused by fungi, frequently associated with medical devices, have increased and caused great morbidity and mortality among hospitalized patients. Difficulties on different species identification as well as the lack of standardized sensitivity tests in vitro, contribute to the limited information available on epidemiology, diagnosis, and therapeutics of Trichosporon infections. There are only sporadic reports of UTI caused by Trichosporon asahii reported from India. We report six cases of UTI caused by T. asahii in severely ill patients in a tertiary care setup. Among six positive T. asahii UTI, four were found in female patients with a mean age of 60 years. We observed that all patients were on indwelling urinary catheter, broad-spectrum antibiotics, and with other comorbid conditions. With regard to the antifungal susceptibility testing, all the isolates were resistant to amphotericin B and sensitive to voriconazole. Majority of them were sensitive to Itraconazole, half of them were sensitive to fluconazole. The ubiquity and biofilm formation poses difficulty in establishing pathogenicity and delineating environmental or nosocomial infections. Risk factors such as use of antibiotics, indwelling catheter, and comorbidities such as hypertension, diabetes, anemia, and chronic kidney disease predispose for the development of UTI by T. asahii. Isolation of the same yeast in three consecutive urine samples with significant counts, along with significant number of pus cells establishes T. asahii as an etiological agent of UTI. Furthermore, the clearance of the fungus from the urinary tract with the recovery of the patient following catheter removal and antifungal therapy further confirms T. asahii as the cause of UTI