Microorganisms, Volume 7, Issue 3 (March 2019) – 31 articles

The experiment was to determine the chronic effects of two transgenic maize lines that contained the mCry1Ac gene from the Bacillus thuringiensis strain (BT) and the maroACC gene from Agrobacterium tumefaciens strain (CC), respectively, on ileal microbiota of laying hens. Seventy-two laying hens were randomly assigned to one of the three dietary treatments for 12 weeks, as follows: (1) nontransgenic near-isoline maize-based diet (CT diet), (2) BT maize-based diet (BT diet), and (3) CC maize-based diet (CC diet). Ileum histological examination did not indicate a chronic effect of two transgenic maize diets. Few differences were observed in any bacterial taxa among the treatments that used high-throughput 16S rRNA gene sequencing. The only differences that were observed for bacterial genera were that Bifidobacterium belong within the Bifidobacteriaceae family tended to be greater (p = 0.114) abundant in hens fed the transgenic maize-based diet than in hens fed the CT diet. Birds that consumed the CC maize diet tended to have less abundance (p = 0.135) of Enterobacteriaceae family in the ileum than those that consumed the CT maize diet. These results indicate the lack of adverse effects of the BT maize and the CC maize lines on the ileal microbiota of hens for long term and provide important data regarding biosafety assessment of the transgenic maize lines. Full article

Minimally processed and ready-to-eat (RTE) seafood products are gaining popularity because of their availability in retail stores and the consumers’ perception of convenience. Products that are subjected to mild processing and products that do not require additional heating prior to consumption are eaten by an increasing proportion of the population, including people that are more susceptible to foodborne disease. Worldwide, seafood is an important source of foodborne outbreaks, but the exact burden is not known. The increased interest in seafood products for raw consumption introduces new food safety issues that must be addressed by all actors in the food chain. Bacteria belonging to genus Aeromonas are ubiquitous in marine environments, and Aeromonas spp. has held the title “emerging foodborne pathogen” for more than a decade. Given its high prevalence in seafood and in vegetables included in many RTE seafood meals, the significance of Aeromonas as a potential foodborne pathogen and a food spoilage organism increases. Some Aeromonas spp. can grow relatively uninhibited in food during refrigeration under a broad range of pH and NaCl concentrations, and in various packaging atmospheres. Strains of several Aeromonas species have shown spoilage potential by the production of spoilage associated metabolites in various seafood products, but the knowledge on spoilage in cold water fish species is scarce. The question about the significance of Aeromonas spp. in RTE seafood products is challenged by the limited knowledge on how to identify the truly virulent strains. The limited information on clinically relevant strains is partly due to few registered outbreaks, and to the disputed role as a true foodborne pathogen. However, it is likely that illness caused by Aeromonas might go on undetected due to unreported cases and a lack of adequate identification schemes. A rather confusing taxonomy and inadequate biochemical tests for species identification has led to a biased focus towards some Aeromonas species. Over the last ten years, several housekeeping genes has replaced the 16S rRNA gene as suitable genetic markers for phylogenetic analysis. The result is a more clear and robust taxonomy and updated knowledge on the currently circulating environmental strains. Nevertheless, more knowledge on which factors that contribute to virulence and how to control the potential pathogenic strains of Aeromonas in perishable RTE seafood products are needed. Full article

Mycobacteria are a large family of over 100 species, most of which do not cause diseases in humans. The majority of the mycobacterial species are referred to as nontuberculous mycobacteria (NTM), meaning they are not the causative agent of tuberculous (TB) or leprosy, i.e., Mycobacterium tuberculous complex and Mycobacterium leprae, respectively. The latter group is undoubtedly the most infamous, with TB infecting an estimated 10 million people and causing over 1.2 million deaths in 2017 alone TB and leprosy also differ from NTM in that they are only transmitted from person to person and have no environmental reservoir, whereas NTM infections are commonly acquired from the environment. It took until the 1950′s for NTM to be recognised as a potential lung pathogen in people with underlying pulmonary disease and another three decades for NTM to be widely regarded by the medical community when Mycobacterium avium complex was identified as the most common group of opportunistic pathogens in AIDS patients. This review focuses on an emerging NTM called Mycobacterium abscessus (M. abs). M. abs is a rapidly growing NTM that is responsible for opportunistic pulmonary infections in patients with structural lung disorders such as cystic fibrosis and bronchiectasis, as well as a wide range of skin and soft tissue infections in humans. In this review, we discuss how we came to understand the pathogen, how it is currently treated and examine drug resistance mechanisms and novel treatments currently in development. We highlight the urgent need for new and effective treatments for M. abs infection as well as improved in vivo methods of efficacy testing. Full article

Plant growth promoting rhizobacteria (PGPR) are associated with plant roots and augment plant productivity and immunity by reducing fertilizer application rates and nutrient runoff. Studies were conducted to evaluate bell pepper transplants amended with formulation of consortium of two indigenous PGPR isolates (Bacillus subtilis and Bacillus pumilus) in terms of increase in yield and disease resistance under field conditions. Transplants were planted into plots treated by NPK (nitrogen, phosphorus and potassium), fungicides, soil solarization, MeBr fumigation, PGPR and untreated soil. Treatments were assessed for incidence of soil-borne phytopathogens viz. Phytophthora capsici and Colletotrichum sp. Highly significant increases in bell pepper transplant growth occurred in response to formulations of PGPR isolates. Transplant vigor and survival in the field were also improved by PGPR treatments. Consortium of Bacillus subtilis and Bacillus pumilus reduced disease incidence of damping off by 1.81% and anthracnose by 1.75%. Numbers of colony forming units of Phytophthora capsici and Colletotrichum sp. were significantly higher in all plots than those treated with PGPR consortium. Incidence of seed rot and seedling blight on bell pepper was significantly lower in PGPR-treated plots and highest in untreated plots. Total fruit yield of bell pepper increased by 379.36% with PGPR consortium (Bacillus subtilis and Bacillus pumilus). Full article

Forty-two Rhizoctonia isolates were collected from rice, mung bean, and grasses from Laguna, Philippines. Sixteen isolates were binucleate Rhizoctonia (BNR), while 26 were multinucleate Rhizoctonia (MNR). BNR isolates produced white to brown, small sclerotia (<1.0 mm) except for mung bean isolates. Twenty MNR isolates produced big (>1.0 mm), light to dark brown sclerotia, three produced salmon-colored masses in the medium, and three did not produce sclerotia. Twenty-three MNR isolates were identified as R. solani AG1-IA using specific primers. Deduced Internal Transcribed Spacer (ITS) sequences of BNR isolates D1FL, NVL, and ScNL shared 100, 97, and 100% identity with R. oryzae-sativae, respectively, while MNR isolates BMgL, IbMgL, and MaSL that produced salmon-colored masses shared 100, 90, and 100% identity with R. oryzae, respectively. Preliminary analysis of the DNA fingerprint patterns generated by repetitive-element PCR (rep-PCR) clustered the 42 isolates into three: R. solani, R. oryzae-sativae, and R. oryzae, together with Ceratobasidium sp. R. solani isolates were pathogenic on rice (TN1), barnyard grass, mungbean (Pagasa 3), and tomato (Athena), while R. oryzae and R. oryzae-sativae isolates were only pathogenic on rice, Echinochloa crus-galli, and tomato. R. solani and R. oryzae were found to be more virulent than R. oryzae-sativae. Full article

Zika virus has been declared as a public health emergency of international concern. The Center for Disease Control and Prevention has issued guidelines reminding healthcare workers about the importance of taking steps to prevent the spread of Zika virus, how to test and isolate patients suspected of carrying the Zika virus, and how to protect themselves from infection. Therefore, it is of utmost importance for healthcare professionals to be fully aware of Zika virus preparedness, and response measures should an outbreak occur in Malaysia in order to quickly and efficiently contain the outbreak, ensure the safety of individual or healthcare personnel safety, as well as to prevent further spreading of the disease. This research aims to show how prepared Malaysian healthcare professionals are against Zika virus and how well can they respond during an outbreak. In total, 504 healthcare professionals (128 general practitioners, 215 community pharmacists, 161 nurses) from private health clinics were the target population of the four states of Malaysia where Zika cases suspected. The sample size of each category was calculated by using a formula for estimating the population proportion. An additional 10% of the calculated sample size was added to compensate the non-response rate. The Center For Disease Control and Prevention and World Health Organisation provided a checklist to assess how prepared healthcare professionals are for an Zika outbreak. This checklist was modified to a questionnaire in order to assess health care professionals’ preparedness and response to the Zika outbreak. Community pharmacists are still lacking in their preparedness and perceived response to the Zika outbreak compared to the general practitioners in the private sector. Hence community pharmacists should attend training given by the Ministry of Health Malaysia as a continuing education, which may help them to respond during a Zika outbreak. Full article

Microbiological testing is an important quality management tool in the food industry. In this study, the hygiene status of beef carcasses sampled in eight Brazilian slaughterhouses was assessed by enumeration of different hygiene indicator microorganisms, and a model to establish potential associations among these counts was proposed. The carcasses (n = 464) were surface sampled at four slaughtering steps (step 1: Hide after bleeding; step 2: Carcass after hide removal; step 3: Carcass after evisceration; step 4: Carcass after end washing) and subjected to a counting of mesophilic aerobes (MA), Enterobacteriaceae (EB), total coliforms (TC), and Escherichia coli (EC) using Petrifilm™ plates. Among the sampled beef carcasses (step 4), 32 (6.9%) and 71 (15.3%) presented counts above the microbiological criteria established by (EC) No. 1441/2007 for MA and EB, respectively. Thus, indicating that improvements in slaughter hygiene and a review of process controls are demanded in some of the studied slaughterhouses. The log count differences of EC, TC, and EB from MA were considered as response variables as a function of the slaughtering steps. Differential log counts changed consistently with the steps. The measurements, including the patterns in their inherently random variability, were fairly predictable from steps 1 and 4. The results indicated that differential log counts for TC and EC are not relevant, as their concentrations and random pattern can be inferred from counts of MA and EB. The proposed model can be used as a valuable tool for the design and adoption of feasible quality control programs in beef industries. The adoption of such a tool should have a positive contribution on consumers’ health and enhance product quality. Full article

Among non-mammalian infection model organisms, the larvae of the greater wax moth Galleria mellonella have seen increasing popularity in recent years. Unlike other invertebrate models, these larvae can be incubated at 37 °C and can be dosed relatively precisely. Despite the increasing number of publications describing the use of this model organism, there is a high variability with regard to how the model is produced in different laboratories, with respect to larva size, age, origin, storage, and rest periods, as well as dosing for infection and treatment. Here, we provide suggestions regarding how some of these factors can be approached, to facilitate the comparability of studies between different laboratories. We introduce a linear regression curve correlating the total larva weight to the liquid volume in order to estimate the in vivo concentration of pathogens and the administered drug concentration. Finally, we discuss several other aspects, including in vivo antibiotic stability in larvae, the infection doses for different pathogens and suggest guidelines for larvae selection. Full article

Vibrio alginolyticus and V. parahaemolyticus, the causative agents of Vibriosis in marine vertebrates and invertebrates, are also responsible for fatal illnesses such as gastroenteritis, septicemia, and necrotizing fasciitis in humans via the ingestion of contaminated seafood. Aquaculture farmers often rely on extensive prophylactic use of antibiotics in farmed fish to mitigate Vibrios and their biofilms. This has been postulated as being of serious concern in the escalation of antibiotic resistant Vibrios. For this reason, alternative strategies to combat aquaculture pathogens are in high demand. Bacteriophage-derived lytic enzymes and proteins are of interest to the scientific community as promising tools with which to diminish our dependency on antibiotics. Lysqdvp001 is the best-characterized endolysin with lytic activity against multiple species of Vibrios. Various homologues of Vibrio phage endolysins have also been studied for their antibacterial potential. These novel endolysins are the major focus of this mini review. Full article

To successfully deliver probiotic benefits to the consumer, several criteria must be met. Here, we discuss the often-forgotten challenges in manufacturing the strains and incorporating them in consumer products that provide the required dose at the end of shelf life. For manufacturing, an intricate production process is required that ensures both high yield and stability and must also be able to meet requirements such as the absence of specific allergens, which precludes some obvious culture media ingredients. Reproducibility is important to ensure constant high performance and quality. To ensure this, quality control throughout the whole production process, from raw materials to the final product, is essential, as is the documentation of this quality control. Consumer product formulation requires extensive skill and experience. Traditionally, probiotic lactic acid bacteria and bifidobacteria have been incorporated in fermented dairy products, with limited shelf life and refrigerated storage. Currently, probiotics may be incorporated in dietary supplements and other “dry” food matrices which are expected to have up to 24 months of stability at ambient temperature and humidity. With the right choice of production process, product formulation, and strains, high-quality probiotics can be successfully included in a wide variety of delivery formats to suit consumer requirements. Full article

Utilization of plant growth-promoting bacteria colonizing roots is environmentally friendly technology instead of using chemicals in agriculture, and understanding of the effects of their colonization modes in promoting plant growth is important for sustainable agriculture. We herein screened the six potential plant growth-promoting bacteria isolated from Beta vulgaris L. (Rhizobium sp. HRRK 005, Polaromonas sp. HRRK 103, Variovorax sp. HRRK 170, Mesorhizobium sp. HRRK 190, Streptomyces sp. HRTK 192, and Novosphingobium sp. HRRK 193) using a series of biochemical tests. Among all strains screened, HRRK 170 had the highest potential for plant growth promotion, given its ability to produce plant growth substances and enzymes such as siderophores and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, respectively, concomitantly with active growth in a wider range of temperatures (10–30 °C) and pH (5.0–10.0). HRRK 170 colonized either as spots or widely on the root surface of all vegetable seedlings tested, but significant growth promotion occurred only in two vegetables (Chinese cabbage and green pepper) within a certain cell density range localized in the plant roots. The results indicate that HRRK 170 could function as a plant growth promoter, but has an optimum cell density for efficient use. Full article

Prokaryotes have an essential gene—gyrase—that catalyzes negative supercoiling of plasmid and chromosomal DNA. Negative supercoils influence DNA replication, transcription, homologous recombination, site-specific recombination, genetic transposition and sister chromosome segregation. Although E. coli and Salmonella Typhimurium are close relatives with a conserved set of essential genes, E. coli DNA has a supercoil density 15% higher than Salmonella, and E. coli cannot grow at the supercoil density maintained by wild type (WT) Salmonella. E. coli is addicted to high supercoiling levels for efficient chromosomal folding. In vitro experiments were performed with four gyrase isoforms of the tetrameric enzyme (GyrA₂:GyrB₂). E. coli gyrase was more processive and faster than the Salmonella enzyme, but Salmonella strains with chromosomal swaps of E. coli GyrA lost 40% of the chromosomal supercoil density. Reciprocal experiments in E. coli showed chromosomal dysfunction for strains harboring Salmonella GyrA. One GyrA segment responsible for dis-regulation was uncovered by constructing and testing GyrA chimeras in vivo. The six pinwheel elements and the C-terminal 35–38 acidic residues of GyrA controlled WT chromosome-wide supercoiling density in both species. A model of enzyme processivity modulated by competition between DNA and the GyrA acidic tail for access to β-pinwheel elements is presented. Full article

Two bacteria capable of efficiently degrading atrazine were isolated from soil, and named ATLJ-5 and ATLJ-11. ATLJ-5 and ATLJ-11 were identified as Bacillus licheniformis and Bacillus megaterium, respectively. The degradation efficiency of atrazine (50 mg/L) by strain ATLJ-5 can reach about 98.6% after 7 days, and strain ATLJ-11 can reach 99.6% under the same conditions. The degradation of atrazine is faster when two strains are used in combination. Adding the proper amount of fresh soil during the degradation of atrazine by these two strains can also increase the degradation efficiency. The strains ATLJ-5 and ATLJ-11 have high tolerance to atrazine, and can tolerate at least 1000 mg/L of atrazine. In addition, the strains ATLJ-5 and ATLJ-11 have been successfully made into a microbial agent that can be used to treat atrazine residues in soil. The degradation efficiency of atrazine (50 mg/kg) could reach 99.0% by this microbial agent after 7 days. These results suggest that the strains ATLJ-5 and ATLJ-11 can be used for the treatment of atrazine pollution. Full article

Vaccination is an effective prevention of influenza infection. However, certain individuals develop a lower antibody response after vaccination, which may lead to susceptibility to subsequent infection. An important challenge in human health is to find baseline gene signatures to help identify individuals who are at higher risk for infection despite influenza vaccination. We developed a multi-level machine learning strategy to build a predictive model of vaccine response using pre−vaccination antibody titers and network interactions between pre−vaccination gene expression levels. The first-level baseline−antibody model explains a significant amount of variation in post-vaccination response, especially for subjects with large pre−existing antibody titers. In the second level, we clustered individuals based on pre−vaccination antibody titers to focus gene−based modeling on individuals with lower baseline HAI where additional response variation may be predicted by baseline gene expression levels. In the third level, we used a gene−association interaction network (GAIN) feature selection algorithm to find the best pairs of genes that interact to influence antibody response within each baseline titer cluster. We used ratios of the top interacting genes as predictors to stabilize machine learning model generalizability. We trained and tested the multi-level approach on data with young and older individuals immunized against influenza vaccine in multiple cohorts. Our results indicate that the GAIN feature selection approach improves model generalizability and identifies genes enriched for immunologically relevant pathways, including B Cell Receptor signaling and antigen processing. Using a multi-level approach, starting with a baseline HAI model and stratifying on baseline HAI, allows for more targeted gene−based modeling. We provide an interactive tool that may be extended to other vaccine studies. Full article

Butyrate-producing bacteria can biosynthesize butyrate and alleviate inflammatory diseases. However, few studies have reported that the genus Collinsella has the ability to produce butyric acid. Here, our study depicts a Collinsella strain, which is a rod-shaped obligate anaerobe that is able to produce butyric acid. This microorganism was isolated from a human gut, and the optimal growth conditions were found to be 37 °C on PYG medium with pH 6.5. The 16S rRNA gene sequence demonstrated that this microorganism shared 99.93% similarity with C. aerofaciens ATCC 25986^T, which was higher than the threshold (98.65%) for differentiating two species. Digital DNA–DNA hybridization and average nucleotide identity values also supported that this microorganism belonged to the species C. aerofaciens. Distinct phenotypic characteristics between TF06-26 and the type strain of C. aerofaciens, such as the fermentation of D-lactose, D-fructose and D-maltose, positive growth under pH 5 and 0.2% (w/v) cholate, suggested this strain was a novel subspecies. Comparative genome analysis revealed that butyric acid kinase and phosphate butyryltransferase enzymes were coded exclusively by this strain, indicating a specific butyric acid-producing function of this C. aerofaciens subspecies within the genus Collinsella. Thus, Collinsella aerofaciens subsp. shenzhenensis subsp. nov. was proposed, with set strain TF06-26^T (=CGMCC 1.5216^T = DSM 105138^T) as the type strain. Full article

Previously known as Enterobacter sakazakii from 1980 to 2007, Cronobacter sakazakii is an opportunistic bacterium that survives and persists in dry and low-moisture environments, such as powdered infant formula. Although C. sakazakii causes disease in all age groups, infections caused by this pathogen are particularly fatal in infants born premature and those younger than two months. The pathogen has been isolated from various environments such as powdered infant formula manufacturing facilities, healthcare settings, and domestic environments, increasing the chance of infection through cross-contamination. The current study discusses the outbreak history of C. sakazakii and the ability of the microorganism to produce biofilms on biotic and abiotic surfaces. The study further discusses the fate of the pathogen in low-moisture environments, articulates preventive measures for healthcare providers and nursing parents, and delineates interventions that could be utilized in infant formula manufacturing to minimize the risk of contamination with Cronobacter sakazakii. Full article

The consumption of various meats prevalent throughout the world affects host health probably by associating with compositional shifts of gut microbiota. However, the responses of gut microbiota to different types of meat are not well understood. In this study, we explored the effects of cooked fish (white meat), and pork and beef (red meat) on gut microbiota and blood lipid metabolism in male C57BL/6 mice by comparing to those fed laboratory chow. Significant differences in microbial communities were observed among meat- and chow-fed mice. Compared with the chow group, the red and white meat groups obviously increased in abundance of Clostridium, and decreased in Prevotella abundance. The richness and diversity of gut microbiota were markedly decreased in the two red meat groups, with lower abundance of Oscillospira and higher abundance of Escherichia. Meanwhile, there were significant meat-related differences in blood lipid metabolites, with lower levels of high-density lipoprotein, low-density lipoprotein, cholesterol, and in mice fed white, compared with red, meat. Lipopolysaccharide-binding protein was significantly lower in fish-fed mice. Our results indicate that different types of meat potentially influence gut microbial compositions and blood metabolic profiles, suggesting a need to focus on clinically relevant bacteria in gut microbiota associated with increasing meat consumption. Full article

Listeria monocytogenes is a Gram positive foodborne pathogen that can colonize the gastrointestinal tract of a number of hosts, including humans. These environments contain numerous stressors such as bile, low oxygen and acidic pH, which may impact the level of colonization and persistence of this organism within the GI tract. The ability of L. monocytogenes to establish infections and colonize the gastrointestinal tract is directly related to its ability to overcome these stressors, which is mediated by the efficient expression of several stress response mechanisms during its passage. This review will focus upon how and when this occurs and how this impacts the outcome of foodborne disease. Full article

To explore proteolytic activity of endophytic fungi inhabiting date palm roots, a Penicillium bilaiae isolate, displaying the highest level of protease production, has been recovered. Response surface methodology (RSM) was applied to optimize culture conditions for protease production by the fungus. Plackett-Burman design allowed for screening of variables effective in protease production. Results indicated that temperature, initial pH and glucose concentration dramatically affect protease yield. These factors were further optimized using a Box-Behnken design and RSM. A combination of initial pH (6.26), temperature (24.5 °C), glucose (13.75 g/L), NaNO₃ (1.5 g/L), MgSO₄ (0.2 g/L), KH₂PO₄ (0.5 g/L) and KCl (0.5 g/L) were optimum for maximum production of protease. A 1086-fold enhancement of protease production was gained after optimization. Biochemical properties of fungal protease including the effect of pH and temperature on the activity and the stability of proteolytic enzyme were determined. Moreover, the influence of carbon and nitrogen sources, metal ions, detergents as well as enzyme inhibitors was investigated. Our results highlighted that protease of Penicillium bilaiae isolate TDPEF30 could be considered as a promising candidate for industrial applications. Full article

Microbes growing onto solid surfaces form complex 3-D biofilm structures characterized by the production of extracellular polymeric compounds and an increased resistance to drugs. The quantification of biofilm relays currently on a number of different approaches and techniques, often leading to different evaluations of the ability to form biofilms of the studied microbial strains. Measures of biofilm biomass were carried out with crystal violet (CV) and a direct reading at 405 nm, whereas the activity was assessed with the XTT ((2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide) method. The strains of four pathogenic species of the genus Candida (C. albicans, C. glabrata, C. parapsilosis and C. tropicalis) and of Staphylococcus aureus were employed to determine the effective relatedness among techniques and the specific activity of the biofilm, as a ratio between the XTT and the CV outcomes. Since the ability to form biomass and to be metabolically active are not highly related, their simultaneous use allowed for a categorization of the strains. This classification is putatively amenable of further study by comparing the biofilm type and the medical behavior of the strains. Full article

Urban expansion causes coastal wetland loss, and environmental stressors associated with development can lead to wetland degradation and loss of ecosystem services. This study investigated the effect of urbanization on prokaryotic community composition in tidal freshwater wetlands. Sites in an urban, suburban, and rural setting were located near Buenos Aires, Argentina, and Washington D.C., USA. We sampled soil associated with two pairs of functionally similar plant species, and used Illumina sequencing of the 16S rRNA gene to examine changes in prokaryotic communities. Urban stressors included raw sewage inputs, nutrient pollution, and polycyclic aromatic hydrocarbons. Prokaryotic communities changed along the gradient (nested PerMANOVA, Buenos Aires: p = 0.005; Washington D.C.: p = 0.001), but did not differ between plant species within sites. Indicator taxa included Methanobacteria in rural sites, and nitrifying bacteria in urban sites, and we observed a decrease in methanogens and an increase in ammonia-oxidizers from rural to urban sites. Functional profiles in the Buenos Aires communities showed higher abundance of pathways related to nitrification and xenobiotic degradation in the urban site. These results suggest that changes in prokaryotic taxa across the gradient were due to surrounding stressors, and communities in urban and rural wetlands are likely carrying out different functions. Full article

The objective of this study was to evaluate the effects of the dietary supplementation of Bacillus subtilis DSM 32315 (probiotic) on the performance and intestinal microbiota of broiler chickens infected with Clostridium perfringens (CP). One-day-old broiler chickens were assigned to 3 treatments with 8 replicate pens (50 birds/pen). The treatments were: non-infected control; infected control; and infected supplemented with probiotic (1 × 10⁶ CFU/g of feed). On day of hatch, all birds were sprayed with a coccidia vaccine based on the manufacturer recommended dosage. On d 18–20 the infected birds were inoculated with CP via feed. Necrotic enteritis (NE) lesion score was performed on d 21. Digestive tract of 2 birds/pen was collected on d 21 to analyze the ileal and cecal microbiota by 16S rRNA sequencing. Performance was evaluated on d 28 and 42. On d 21, probiotic supplementation reduced (p < 0.001) the severity of NE related lesion versus infected control birds. On d 28, feed efficiency was improved (p < 0.001) in birds supplemented with probiotic versus infected control birds. On d 42, body weight gain (BW gain) and feed conversion ratio (FCR) were improved (p < 0.001) in probiotic supplemented birds versus infected control birds. The diversity, composition and predictive function of the intestinal microbial digesta changed with the infection but the supplementation of probiotic reduced these variations. Therefore, dietary supplementation of Bacillus subtilis DSM 32315 was beneficial in attenuating the negative effects of CP challenge on the performance and intestinal microbiota of broilers chickens. Full article

Mycobacterium tuberculosis (Mtb) remains an important human pathogen. The Mtb cell envelope is a critical bacterial structure that contributes to virulence and pathogenicity. Mycobacterial membrane protein large (MmpL) proteins export bulky, hydrophobic substrates that are essential for the unique structure of the cell envelope and directly support the ability of Mtb to infect and persist in the host. This review summarizes recent investigations that have enabled insight into the molecular mechanisms underlying MmpL substrate export and the role that these substrates play during Mtb infection. Full article

Multiple lines of evidence indicate that CD8 ${}^{+}$ T cells are important in the control of HIV-1 (HIV) replication. However, CD8 ${}^{+}$ T cells induced by natural infection cannot eliminate the virus or reduce viral loads to acceptably low levels in most infected individuals. Understanding the basic quantitative features of CD8 ${}^{+}$ T-cell responses induced during HIV infection may therefore inform us about the limits that HIV vaccines, which aim to induce protective CD8 ${}^{+}$ T-cell responses, must exceed. Using previously published experimental data from a cohort of HIV-infected individuals with sampling times from acute to chronic infection we defined the quantitative properties of CD8 ${}^{+}$ T-cell responses to the whole HIV proteome. In contrast with a commonly held view, we found that the relative number of HIV-specific CD8 ${}^{+}$ T-cell responses (response breadth) changed little over the course of infection (first 400 days post-infection), with moderate but statistically significant changes occurring only during the first 35 symptomatic days. This challenges the idea that a change in the T-cell response breadth over time is responsible for the slow speed of viral escape from CD8 ${}^{+}$ T cells in the chronic infection. The breadth of HIV-specific CD8 ${}^{+}$ T-cell responses was not correlated with the average viral load for our small cohort of patients. Metrics of relative immunodominance of HIV-specific CD8 ${}^{+}$ T-cell responses such as Shannon entropy or the Evenness index were also not significantly correlated with the average viral load. Our mathematical-model-driven analysis suggested extremely slow expansion kinetics for the majority of HIV-specific CD8 ${}^{+}$ T-cell responses and the presence of intra- and interclonal competition between multiple CD8 ${}^{+}$ T-cell responses; such competition may limit the magnitude of CD8 ${}^{+}$ T-cell responses, specific to different epitopes, and the overall number of T-cell responses induced by vaccination. Further understanding of mechanisms underlying interactions between the virus and virus-specific CD8 ${}^{+}$ T-cell response will be instrumental in determining which T-cell-based vaccines will induce T-cell responses providing durable protection against HIV infection. Full article

Specific microbial profiles and changes in intestinal microbiota have been widely demonstrated to be associated with the pathogenesis of a number of extra-intestinal (obesity and metabolic syndrome) and intestinal (inflammatory bowel disease) diseases as well as other metabolic disorders, such as non-alcoholic fatty liver disease and type 2 diabetes. Thus, maintaining a healthy gut ecosystem could aid in avoiding the early onset and development of these diseases. Furthermore, it is mandatory to evaluate the alterations in the microbiota associated with pathophysiological conditions and how to counteract them to restore intestinal homeostasis. This review highlights and critically discusses recent literature focused on identifying changes in and developing gut microbiota-targeted interventions (probiotics, prebiotics, diet, and fecal microbiota transplantation, among others) for the above-mentioned pathologies. We also discuss future directions and promising approaches to counteract unhealthy alterations in the gut microbiota. Altogether, we conclude that research in this field is currently in its infancy, which may be due to the large number of factors that can elicit such alterations, the variety of related pathologies, and the heterogeneity of the population involved. Further research on the effects of probiotics, prebiotics, or fecal transplantations on the composition of the human gut microbiome is necessary. Full article

Type 1-diabetes (T1D) is an autoimmune disease characterized by immune-mediated destruction of pancreatic beta (β)-cells. Genetic and environmental interactions play an important role in immune system malfunction by priming an aggressive adaptive immune response against β-cells. The microbes inhabiting the human intestine closely interact with the enteric mucosal immune system. Gut microbiota colonization and immune system maturation occur in parallel during early years of life; hence, perturbations in the gut microbiota can impair the functions of immune cells and vice-versa. Abnormal gut microbiota perturbations (dysbiosis) are often detected in T1D subjects, particularly those diagnosed as multiple-autoantibody-positive as a result of an aggressive and adverse immunoresponse. The pathogenesis of T1D involves activation of self-reactive T-cells, resulting in the destruction of β-cells by CD8⁺ T-lymphocytes. It is also becoming clear that gut microbes interact closely with T-cells. The amelioration of gut dysbiosis using specific probiotics and prebiotics has been found to be associated with decline in the autoimmune response (with diminished inflammation) and gut integrity (through increased expression of tight-junction proteins in the intestinal epithelium). This review discusses the potential interactions between gut microbiota and immune mechanisms that are involved in the progression of T1D and contemplates the potential effects and prospects of gut microbiota modulators, including probiotic and prebiotic interventions, in the amelioration of T1D pathology, in both human and animal models. Full article

Literature has recently highlighted the enormous scientific interest on the relationship between the gut microbiota and colon cancer, and how the use of some selected probiotics can have a future impact on the adverse events which occur during this disease. Although there is no clear evidence to claim that probiotics are effective in people with cancer, recent reviews have found that probiotics can significantly reduce the incidence of diarrhea and the average frequency of daily bowel movements. However, most of this evidence needs to be more clinically convincing and further discussed. Undoubtedly, some probiotics, when properly dosed and administered, can have a strong rebalance effect on the gut microbiota and as a consequence a possible positive action on immune modulation of the gastrointestinal tract and on inflammation of the intestinal mucosa. Many recent findings indeed support the hypothesis that the daily use of some selected probiotics can be a feasible approach to effectively protect patients against the risk of some severe consequences due to radiation therapy or chemotherapy. This paper aims to review the most recent articles in order to consider a possible adjuvant approach for the use of certain well-balanced probiotics to help prevent colon cancer and the adverse effects caused by related therapies. Full article

Salmonella and Campylobacter are the two leading causes of bacterial-induced foodborne illness in the US. Food production animals including cattle, swine, and chickens are transmission sources for both pathogens. The number of Salmonella outbreaks attributed to poultry has decreased. However, the same cannot be said for Campylobacter where 50–70% of human cases result from poultry products. The poultry industry selects heavily on performance traits which adversely affects immune competence. Despite increasing demand for poultry, regulations and public outcry resulted in the ban of antibiotic growth promoters, pressuring the industry to find alternatives to manage flock health. One approach is to incorporate a program that naturally enhances/modulates the bird’s immune response. Immunomodulation of the immune system can be achieved using a targeted dietary supplementation and/or feed additive to alter immune function. Science-based modulation of the immune system targets ways to reduce inflammation, boost a weakened response, manage gut health, and provide an alternative approach to prevent disease and control foodborne pathogens when conventional methods are not efficacious or not available. The role of immunomodulation is just one aspect of an integrated, coordinated approach to produce healthy birds that are also safe and wholesome products for consumers. Full article

In many countries including Japan, the status of emerging antimicrobial resistance among Serratia spp. and Citrobacter spp. in companion animals remains unknown because these genera are rarely isolated from animals. In this study, 30 Serratia spp. and 23 Citrobacter spp. isolates from companion animals underwent susceptibility testing for 10 antimicrobials. Phenotypic and genetic approaches were used to identify the mechanisms of extended-spectrum cephalosporins (ESC). Subsequently, ESC-resistant Citrobacter spp. strains underwent multilocus sequence typing and pulsed-field gel electrophoresis (PFGE). A significantly higher rate (34.8%) of ESC resistance was observed in Citrobacter spp. isolates than in Serratia spp. isolates (0%). ESC resistance was detected in five C. freundii strains, two C. portucalensis strains, and one C. koseri strain. All of the ESC-resistant Citrobacter spp. strains harbored CMY-type and/or DHA-type AmpC β-lactamases. Three C. freundii strains harbored the CTX-M-3-type extended-spectrum β-lactamases. Notably, the three blaCTX-3-producing and two blaCMY-117-bearing C. freundii strains (obtained from different patients in one hospital) had the same sequence type (ST156 and ST18, respectively) and similar PFGE profiles. We believe that ESC-resistant Citrobacter spp. are important nosocomial pathogens in veterinary medicine. Therefore, infection control in animal hospitals is essential to prevent dissemination of these resistant pathogens. Full article

Pathogenic mycobacteria are able to persist intracellularly in macrophages, whereas non-pathogenic mycobacteria are effectively combated and eliminated after their phagocytosis. It is known that TGF-β plays an important role in this context. Infection with pathogenic mycobacteria such as Mycobacterium tuberculosis or M. avium leads to production of active TGF-β, which blocks the ability of IFN-γ and TNF-α to inhibit intracellular replication. On the other hand, it is known that the long non-coding RNA (lncRNA) maternally expressed 3 (MEG3) is involved in the regulation of TGF-β. In this study, we show how the infection of THP-1-derived human macrophages with the saprophytic M. smegmatis but not with the facultatively pathogenic M. avium subsp. hominissuis leads to increased MEG3 expression. This is associated with the downregulation of DNA methyltransferases (DNMT) 1 and 3b, which are known to regulate MEG3 expression via promoter hypermethylation. Consequently, we observe a significant downregulation of TGF-β in M. smegmatis-infected macrophages but not in M. avium subsp. hominissuis pointing to lncRNAs as novel mediators of host cell response during mycobacterial infections. Full article