Host-specific Characteristics Research Articles

Understanding the role of the human gut microbiome in overweight and obesity.

The gut microbiome may be related to the prevalence of overweight and obesity, but high interindividual variability of the human microbiome complicates our understanding. Obesity often occurs concomitantly with micronutrient deficiencies that impair energy metabolism. Microbiota composition is affected by diet. Host-microbiota interactions are bidirectional. We propose three pathways whereby these interactions may modulate the gut microbiome and obesity: (1) ingested compounds or derivatives affecting small intestinal transit, endogenous secretions, digestion, absorption, microbiome balance, and gut barrier function directly affect host metabolism; (2) substrate availability affecting colonic microbial composition and contact with the gut barrier; and (3) microbial end products affecting host metabolism. The quantity/concentration, duration, and/or frequency (circadian rhythm) of changes in these pathways can alter the gut microbiome, disrupt the gut barrier, alter host immunity, and increase the risk of and progression to overweight and obesity. Host-specific characteristics (e.g., genetic variations) may further affect individual sensitivity and/or resilience to diet- and microbiome-associated perturbations in the colonic environment. In this narrative review, the effects of selected interventions, including fecal microbiota transplantation, dietary calorie restriction, dietary fibers and prebiotics, probiotics and synbiotics, vitamins, minerals, and fatty acids, on the gut microbiome, body weight, and/or adiposity are summarized to help identify mechanisms of action and research opportunities.

Boreal moss-microbe interactions are revealed through metagenome assembly of novel bacterial species

Moss-microbe interactions contribute to ecosystem processes in boreal forests. Yet, how host-specific characteristics and the environment drive the composition and metabolic potential of moss microbiomes is still poorly understood. In this study, we use shotgun metagenomics to identify the taxonomy and metabolic potential of the bacteria of four moss species of the boreal forests of Northern Québec, Canada. To characterize moss bacterial community composition and diversity, we assembled the genomes of 110 potentially novel bacterial species. Our results highlight that moss genus, species, gametophyte section, and to a lesser extent soil pH and soil temperature, drive moss-associated bacterial community composition and diversity. In the brown gametophyte section, two Stigonema spp. showed partial pathway completeness for photosynthesis and nitrogen fixation, while all brown-associated Hyphomicrobiales had complete assimilatory nitrate reduction pathways and many nearly complete carbon fixation pathways. Several brown-associated species showed partial to complete pathways for coenzyme M and F420 biosynthesis, important for methane metabolism. In addition, green-associated Hyphomicrobiales (Methylobacteria spp.) displayed potential for the anoxygenic photosystem II pathway. Overall, our findings demonstrate how host-specific characteristics and environmental factors shape the composition and metabolic potential of moss bacteria, highlighting their roles in carbon fixation, nitrogen cycling, and methane metabolism in boreal forests.

Clustered Regularly Interspaced Short Palindromic Repeat-1 (CRISPR-1) Locus as a Tool for Tracing the Zoonotic History of Salmonella enterica Strains.

Background Salmonella enterica is a significant foodborne pathogen that causes considerable illness and death in humans and animals. The clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein (Cas) system in bacteria acts as an adaptive immune defense against invasive genetic elements by incorporating short intergenic spacers (IGSs) into CRISPR loci. These loci serve as molecular records of past interactions with phages and plasmids, providing insights into the transmission and evolution of bacterial strains across different hosts. Aim This study aimed to investigate the diversity of IGSs in the CRISPR-1 locus of S. enterica isolates from humans and camels. The objective was to assess the potential of IGSs to distinguish strains, track sources, and understand patterns of zoonotic transmission. Materials and methods Genomic DNA was extracted from multiple strains of S. enterica, and the CRISPR-1 locus was polymerase chain reaction (PCR) amplified and sequenced. The sequences were compared to identify distinct patterns of IGSs and potential host-specific characteristics. Sanger sequencing and bioinformatics tools were used to classify the IGSs and determine their similarity to known sequences in the National Center for Biotechnology Information (NCBI) database. Results Sequence analysis revealed five distinct CRISPR-1 types among S. enterica isolates from humans and three among camel isolates. The presence of shared IGSs between human and camel S. entericaisolates suggested zoonotic or reverse-zoonotic transmission events. Additionally, host-specific unknown IGSs (UIGS) were identified. Importantly, camel isolates initially identified as S. enterica subspeciesenterica serovar Enteritidis based on rrnH gene sequencing were reclassified as S. enterica serovar Enteritidis based on CRISPR-1 profiling, demonstrating the higher resolution of CRISPR-based genotyping. Conclusion The diversity of IGSs in the CRISPR-1 locus effectively differentiated S. enterica strains and provided insights into their evolutionary origins and transmission dynamics. CRISPR-based genotyping proves to be a promising tool to complement traditional serotyping methods, enhancing the molecular epidemiology of salmonellosis and potentially leading to better management and control strategies for this pathogen.

Bacterial Adaptive Memory in Methicillin-Resistant Staphylococcus aureus from Endotracheal Tubes.

To evaluate the expression dynamics of biofilm genes in methicillin-resistant Staphylococcus aureus (MRSA) retrieved from endotracheal tubes (ETT) and to determine how gene regulation is attenuated in vitro where host-environmental factors are no longer present. Biofilm was grown (24 h) in tryptic broth soy plus 0.25% glucose for a clinical MRSA isolate in planktonic state and after sessile growth named ETT-MRSA (S2, S3, S4, S5, S6, S7). Gene expression of five biofilm-related genes (icaC, clfB, ebps, fnbB, and RNA III) was assessed consecutively from day 1 to day 4 after ETT growth through real-time PCR. 16S rRNA was used as a control. The MRSA isolates retrieved from ETT were capable of producing biofilms dependent on ica. The gene expression dynamics of ETT-MRSA changed progressively compared to planktonic MRSA gene expression under both ambient air (p < 0.001) and ambient air with 5% CO2 (p < 0.001). Dynamic assessment of icaC expression in both atmospheric conditions showed progressive downregulation in vitro compared to in vivo ETT biofilms. The expression patterns of clfB and ebps genes were similar to icaC. In contrast, the expression of the RNA III gene showed progressive upregulation from day 1 to day 4 (p < 0.001). MRSA loses its biofilm gene expression in vitro, by adaptive features across multiple generations, as evidenced by the progressive downregulation of icaC and upregulation of RNA III. These findings underscore the significance of host-environment dependence in regulating bacterial biofilm genes, highlighting its importance in diagnostics. Bacterial strains lose their host-specific characteristics as they are cultured in vitro.

Comprehensive Linear Epitope Prediction System for Host Specificity in Nodaviridae

Background: Nodaviridae infection is one of the leading causes of death in commercial fish. Although many vaccines against this virus family have been developed, their efficacies are relatively low. Nodaviridae are categorized into three subfamilies: alphanodavirus (infects insects), betanodavirus (infects fish), and gammanodavirus (infects prawns). These three subfamilies possess host-specific characteristics that could be used to identify effective linear epitopes (LEs). Methodology: A multi-expert system using five existing LE prediction servers was established to obtain initial LE candidates. Based on the different clustered pathogen groups, both conserved and exclusive LEs among the Nodaviridae family could be identified. The advantages of undocumented cross infection among the different host species for the Nodaviridae family were applied to re-evaluate the impact of LE prediction. The surface structural characteristics of the identified conserved and unique LEs were confirmed through 3D structural analysis, and concepts of surface patches to analyze the spatial characteristics and physicochemical propensities of the predicted segments were proposed. In addition, an intelligent classifier based on the Immune Epitope Database (IEDB) dataset was utilized to review the predicted segments, and enzyme-linked immunosorbent assays (ELISAs) were performed to identify host-specific LEs. Principal findings: We predicted 29 LEs for Nodaviridae. The analysis of the surface patches showed common tendencies regarding shape, curvedness, and PH features for the predicted LEs. Among them, five predicted exclusive LEs for fish species were selected and synthesized, and the corresponding ELISAs for antigenic feature analysis were examined. Conclusion: Five identified LEs possessed antigenicity and host specificity for grouper fish. We demonstrate that the proposed method provides an effective approach for in silico LE prediction prior to vaccine development and is especially powerful for analyzing antigen sequences with exclusive features among clustered antigen groups.

Human Colonoids Enable the Study of Host‐Specific Infectivity and Proteomic Responses to Campylobacter jejuni Infection

BackgroundImmortalized cell lines are conventionally used to examine bacterial virulence and host responses. These models lack heterogeneity, complexity and do not allow interrogation of host specific characteristics. Human intestinal organoids provide a model of human epithelium and allow determination of whether bacterial infections elicit host dependent responses.ObjectiveDetermine how gender and stress influence responses to Campylobacter infection using human colonic organoids.MethodsColonic biopsies were collected from 20 volunteers (10/sex), with Hospital Anxiety and Depression Score of &lt;4 (low stress) or &gt;14 (high stress). Crypts were isolated from biopsies. Monolayers were generated, experimentally infected with 3 different clinical isolates of C. jejuni (OD600 1) and averaged. Bacterial virulence and transepithelial resistance (TER) was measured throughout infection. Proteomics was done 24h post‐infection, with analysis via 1D‐LC‐MS using an Orbitrap Eclipse. Data was processed with MS2 ID pipeline MyriMatch‐IDPicker and proteins FDR&lt;0.1 considered significant.ResultsColonoid cultures were generated from 75% of volunteers. C. jejuni strains attachmed and invaded all colonoids. Greater bacterial attachment was seen on high stress volunteer colonoids compared low stress (0.08 ± 0.11 vs. 0.03 ± 0.08 CFU/starting inoculum for males, 0.015 ± 0.036 vs. 0.014 ± 0.014 for females, p&lt;0.05 for both) and on high stress males compared to females (p&lt;0.001). Colonoids from high stress volunteers had a significant drop in TER 24h post‐infection compared to non‐infected controls (42.1 ± 30.7 vs 125.2 ± 62.4, % baseline, p&lt;0.05). Proteomic analysis showed minimal differences between high and low stress or between female and male colonoids at baseline (4 and 9 proteins respectively). Upon infection 195 proteins were differentially abundant with 161 increased in stressed organoids (FDR&lt;0.1). Increased apoptotic pathway activation and cellular reorganization; pro‐apoptotic death‐associated protein‐kinase 3 (DAPK3), and DNA damage response serine/threonine‐protein kinase protein (TAOK3) were seen. Gene set enrichment analysis (GSEA) showed increased interferon alpha and beta signaling, IL‐1 and IL‐17 responses and MHC1/2 antigen processing in high stress infected monolayers (FDR&lt;0.1). No differences between male high and low stress organoids post infection. In contrast, 1289 proteins were differentially abundant between high and low stress females with 84% up in stressed organoids. IL‐1 and IL‐12 signaling was up in high stress female organoids (FDR&lt;0.1).ConclusionsColonoid monolayers can be developed from human volunteers and used to evaluate host pathogen interactions. Colonoid cultures highlight variability in C. jejuniinfectivity and host responses; with robust C. jejunivirulence seen with high stress male individuals and the greatest change in proteomic profile in response to infection in high stress females. These findings demonstrate utility of colonoids and provide a platform to study personalized host responses to infection.

박테리오파지를 이용한 병원성 세균의 억제

Excessive use of antibiotics in various industries including agriculture, fisheries, and pharmaceutical industry has led to the emergence of superbacteria which is antibiotic resistant pathogenic bacteria. For that reason, alternative antibiotics have been researched and developed to replace the drugs. Bacteriophage, which is human-friendly and has host-specific characteristics, is one of the alternative antibiotics candidates and can effectively inhibit the growth of pathogenic bacteria such as Staphylococcus aureus, Salmonella, Bacillus cereus, Escherichia coli, and Listeria monocytogenes. In this paper, status of antibiotic resistant pathogenic bacteria and treatment of bacteriophages for the control of the pathogenic bacteria are shortly reviewed.

A voting mechanism-based linear epitope prediction system for the host-specific Iridoviridae family

BackgroundThe Iridoviridae family is categorized into five genera and clustered into two subfamilies: Alphairidovirinae includes Lymphocystivirus, Ranavirus (GIV), and Megalocystivirus (TGIV), which infect vertebrate hosts and Betairidovirinae includes Iridovirus and Chloriridovirus, which infect invertebrate hosts. Clustered Iridoviridae subfamilies possess host-specific characteristics, which can be considered as exclusive features for in-silico prediction of effective epitopes for vaccine development. A voting mechanism-based linear epitope (LE) prediction system was applied to identify and endorse LE candidates with a minimum length requirement for each clustered subfamilyResultsThe experimental results showed that four conserved epitopes among the Iridovirideae family, one exclusive epitope for invertebrate subfamily and two exclusive epitopes for vertebrate family were predicted. These predicted LE candidates were further validated by ELISA assays for evaluating the strength of antigenicity and cross antigenicity. The conserved LEs for Iridoviridae family reflected high antigenicity responses for the two subfamilies, while exclusive LEs reflected high antigenicity responses only for the host-specific subfamilyConclusionsHost-specific characteristics are important features and constraints for effective epitope prediction. Our proposed voting mechanism based system provides a novel approach for in silico LE prediction prior to vaccine development, and it is especially powerful for analyzing antigen sequences with exclusive features between two clustered groups.

Spatial clustering of Borrelia burgdorferi sensu lato within populations of Allen's chipmunks and dusky-footed woodrats in northwestern California.

The ecology of Lyme borreliosis is complex in northwestern California, with several potential reservoir hosts, tick vectors, and genospecies of Borrelia burgdorferi sensu lato. The primary objective of this study was to determine the fine-scale spatial distribution of different genospecies in four rodent species, the California ground squirrel (Otospermophilus beecheyi), northern flying squirrel (Glaucomys sabrinus), dusky-footed woodrat (Neotoma fuscipes), and Allen’s chipmunk (Neotamias senex). Rodents were live-trapped between June 2004 and May 2005 at the Hoopa Valley Tribal Reservation (HVTR) in Humboldt County, California. Ear-punch biopsies obtained from each rodent were tested by polymerase chain reaction (PCR) and sequencing analysis. The programs ArcGIS and SaTScan were used to examine the spatial distribution of genospecies. Multinomial log-linear models were used to model habitat and host-specific characteristics and their effect on the presence of each borrelial genospecies. The Akaike information criterion (AICc) was used to compare models and determine model fit. Borrelia burgdorferi sensu stricto was primarily associated with chipmunks and B. bissettiae largely with woodrats. The top model included the variables “host species”, “month”, and “elevation” (weight = 0.84). Spatial clustering of B. bissettiae was detected in the northwestern section of the HVTR, whereas B. burgdorferi sensu stricto was clustered in the southeastern section. We conclude that the spatial distribution of these borreliae are driven at least in part by host species, time-of-year, and elevation.

First case report of Eustrongylidosis in eel (Anguilla anguilla) populations inhabiting Danube Delta lakes

Abstract Fish eustrongylidosis is a parasitic disease involving 3 rd and 4 th stages larvae of the Eustrongylides nematode (Ph: Nemathelminthes). Over the past 20 years, the number of case reportings on fish eustrongylidosis has increased, especially within industrial fisheries and amongst fishermen. Recent data have confirmed the tendency of a spatial extension of the parasite distribution area towards the Danubian shores of Oltenia and Calarasi, as well as a progressive increase of affected fish host species into natural environments. During the study, the infested fish underwent parasitological and anatomopathological examinations, with the aim to identify the nematode (genus level) and the pathological effects of the parasite over its host. In Romania, this is the first report on eustrongylidosis in eel, detected within fish populations inhabiting some Danubian Delta lakes. This case comes to confirm the low host specificity characteristics of this parasite and its spreading tendency towards new environments.

Light respiratory processes and gross photosynthesis in two scleractinian corals.

The light dependency of respiratory activity of two scleractinian corals was examined using O2 microsensors and CO2 exchange measurements. Light respiration increased strongly but asymptotically with elevated irradiance in both species. Light respiration in Pocillopora damicornis was higher than in Pavona decussata under low irradiance, indicating species-specific differences in light-dependent metabolic processes. Overall, the coral P. decussata exhibited higher CO2 uptake rates than P. damicornis over the experimental irradiance range. P. decussata also harboured twice as many algal symbionts and higher total protein biomass compared to P. damicornis, possibly resulting in self-shading of the symbionts and/or changes in host tissue specific light distribution. Differences in light respiration and CO2 availability could be due to host-specific characteristics that modulate the symbiont microenvironment, its photosynthesis, and hence the overall performance of the coral holobiont.

Ecology of a corallivorous gastropod, Coralliophila abbreviata, on two scleractinian hosts. I: Population structure of snails and corals

Despite their potential importance in structuring reef communities, invertebrate corallivores and their population structures are poorly understood. We found distinct differences in the population structures (length-frequency distribution and sex ratio) of the corallivorous gastropod Coralliophila abbreviata residing on two coral-host taxa, Montastraea spp. and Acropora palmata, in the Florida Keys. In each of two survey years, around 50% of the Montastraea spp. colonies were infested, with a mean snail density of eight snails per infested colony (range 1–45), while around 20% of A. palmata colonies harbored three snails per infested colony (range 1–23). Variation in patterns of snail occurrence was also observed within a host taxon. A. palmata occurred in low- and high-density stands (0.4 and 1 colony m–2, respectively, at the initial survey) at different sites. Hurricane Georges struck the area in September 1998. When resurveyed in 1999, density of colonies in low-density stands had decreased by 75% to 0.1 colonies m–2. This decrease was accompanied by a doubling in the proportion of colonies infested with snails (from 19% to 46%) and an increase in snail density per infested colony (from 3.7±3.3 SD to 5.4±4.6 SD) as snails apparently concentrated on surviving A. palmata. In contrast, sites with high density A. palmata stands (thickets) retained colony densities of about ~1 colony m–2 among years, while snail infestation increased only from 9% to 14% of colonies surveyed and snail density essentially remained unchanged (from 2.7±1.8 to 2.9±1.9 snails per infested colony). Snails collected from Montastraea spp. were shorter than those from A. palmata in low-density stands and were longest on A. palmata in thickets. On both host taxa, female snails were longer than males. The sex ratio of snails on Montastraea spp. hosts was even (1:1), while that of snails on A. palmata was skewed (70% males). Factors that could explain observed differences in size structure and sex ratio between Coralliophila populations on the two coral host taxa include: differential susceptibility to predators, influence of host tissue nutritional quality and/or secondary metabolite content, and genetic differences (cryptic species). The host-specific characteristics of C. abbreviata populations imply that the impact of gastropods on reef communities will vary with the coral species composition.

Phylogenetic relationships among Hepatozoon species from snakes, frogs and mosquitoes of Ontario, Canada, determined by ITS-1 nucleotide sequences and life-cycle, morphological and developmental characteristics

The molecular biological characteristics of Hepatozoon species infecting various species of snakes, frogs and mosquitoes were investigated by determining the nucleotide sequences of the first internal transcribed spacer region. A phylogenetic analysis was performed on seven isolates of Hepatozoon infecting snakes, including Hepatozoon sipedon and four morphologically similar but not identical forms, and two isolates of Hepatozoon catesbianae infecting Green frogs ( Rana clamitans melanota). This analysis, which utilised data from first internal transcribed spacer nucleotide sequences, morphological and morphometric features of gamonts, oocysts and sporocysts, and previously determined life-cycle and host-specificity characteristics, revealed that H. sipedon is a polymorphic species with a wide host and geographic range. Four synapomorphies, including two nucleotide substitutions and two morphological character state changes, supported a monophyletic group of six isolates of H. sipedon from the central region of Ontario which was the sister group for an isolate (HW1) from the southern part of the province. Based on the results of this study, an evaluation of which criteria are useful for describing species of Hepatozoon is presented, with the intent of curtailing the practice of naming species based on morphological features of gamonts or on incomplete life-cycle data.

Nodulation genes in the Rhizobium--plant signal exchange.

The process of the host-plant recognition by rhizobia is complex and multi-step. The interaction between legumes and microorganisms results in the induction of the root nodule. This symbiotic interaction is highly host-specific. Bacteria within nodules fix atmospheric nitrogen. This process is of immense ecological and economic significance. The subject of this presentation is the molecular mechanism by which the bacterium determines its host-specific characteristics. First flavonoids secreted by the plant roots induce the transcription of bacterial genes involved in nodulation, the so-called nod genes. This leads to the next step of the signalling system, i.e. the production and secretion of lipo-oligosaccharide molecules by rhizobia. These signal molecules have various discernible effects on the roots of the host leguminous plants. The bacterial nodulation factors were isolated and structurally identified as substituted and N-acylated chitin oligosaccharides. These prokaryotic signals play a key role in the symbiosis by controlling the host specificity of the bacteria. They constitute a new class of signalling molecules able to elicit nodule organogenesis in leguminous plants in the absence of bacteria. More recent studies implicate involvement of root cell membrane depolarization and ion selective channels in the communication processes that initiate nodule formation.

The molecular basis of the host specificity of the Rhizobium bacteria

The interaction between soil bacteria belonging to the genera Rhizobium, Bradyrhizobium and Azorhizobium and leguminous plants results in the induction of a new plant organ, the root nodule. After invading these root nodules via infection threads the bacteria start to fix atmospheric nitrogen into ammonia which is beneficial for the host plant. This symbiotic interaction is highly host-specific in that each rhizobial strain is able to associate with only a limited number of host plant species. The subject of this presentation is the molecular mechanism by which the bacterium determines its host-specific characteristics. This mechanism appears to be based on at least two stages of molecular signaling between the bacterium and the plant host. In the first stage, flavonoids secreted by the plant root induce, in a host specific way, the transcription of bacterial genes which are involved in nodulation, the so-called nod genes. This leads to the second step of the signaling system: the production and secretion of lipo-oligosaccharide molecules by the Rhizobium bacteria. These signal molecules, which are acylated forms of small fragments of chitin, have various discernable effects on the roots of the host plants. One of these effects is the dedifferentiation of groups of cells located in the cortex which leads to the formation of nodule meristems. In their mitogenic activity the bacterial signals resemble several well-known plant hormones like auxins and cytokinins. However, there are two major differences: (i) the bacterial signals lead to the induction of a specific organ and (ii) they are host-specific in that only the signals produced by compatible bacteria are able to induce meristems. The nod genes determine this stage of host specificity by their essential role in the biosynthesis of the signal molecules. They appear to encode enzymes which are involved in the processes of fatty acid biosynthesis, fatty acid transfer, chitin synthesis and chitin modification. I will illustrate the statement that the nod gene products are ideal model enzymes for the study of these important processes because they are not needed in the free-living state of the bacteria.

Genetic analysis and cellular localization of the Rhizobium host specificity-determining NodE protein.

The nucleotide sequence of the nodE gene of Rhizobium trifolii strain ANU843 was determined. Like the nodE gene of R. leguminosarum strain 248 it encodes a protein with a predicted mol. wt of 42.0 kd. The predicted NodE proteins of R.trifolii and R.leguminosarum have a homology of 78%. Using antibodies raised against the NodE protein of R.trifolii it was shown that the NodE products of R.leguminosarum and R.trifolii are localized in the cytoplasmic membrane. Furthermore, these NodE proteins are predicted to contain at least two non-polar transbilayer alpha-helices. The nodE genes of R.trifolii and R.leguminosarum were separated from the nodF genes that precede them in the respective nodFE operons. Using the resulting clones, in which NodE was produced under control of the flavonoid-inducible nodABCIJ promoter of R.leguminosarum, it was shown that the NodE product is the main factor that distinguishes the host range of nodulation of R.trifolii and R.leguminosarum. Hybrid nodE genes, which consist of a 5' part of the R.leguminosarum nodE gene and a 3' part of the R.trifolii gene, were constructed. From the properties of these hybrid genes it was concluded that a central region of 185 amino acids at the most, containing only 44 non-identical amino acids, determines the difference in the host-specific characteristics of the two NodE proteins.