Microorganisms

Phase variation (PV) is a well-known phenomenon of high-frequency reversible gene-expression switching. PV arises from genetic and epigenetic mechanisms and confers a range of benefits to bacteria, constituting both an innate immune strategy to infection from bacteriophages as well as an adaptation strategy within an infected host. PV has been well-characterized in numerous bacterial species; however, there is limited direct evidence of PV in the human opportunistic pathogen Staphylococcus aureus. This review provides an overview of the mechanisms that generate PV and focuses on earlier and recent findings of PV in S. aureus, with a brief look at the future of the field. Full article

In the present study, we isolated and characterized Lactococcus lactis (L. lactis) subsp. lactis from a female Cuvier’s beaked whale (Ziphius cavirostris) stranded in Shizuoka, Japan. Only five isolates (CBW1-5), grown on Lactobacilli de Man Rogosa Sharpe (MRS) agar plates prepared using 50% artificial seawater, were positive in L. lactis species-specific primer PCR. Their 16S rRNA sequences were highly similar to those of L. lactis subsp. lactis JCM 5805^T. The Gram reaction, motility, gas production from glucose, catalase production, and growth conditions were consistent with those of the type strain. Additionally, carbohydrate utilization of the strains was consistent with previously reported marine organism-derived strains. The pH-neutralized cell-free culture supernatant of strain CBW2 inhibited the growth of Bacillus subtilis subsp. subtilis ATCC 6051 and Vibrio alginolyticus ATCC 17749, whereas protease treatment eliminated or diminished its inhibitory activity. The strain possesses a precursor of the nisin structural gene (nisA), which showed 100% homology with nisin Z, and nisin biosynthesis-related genes (nisB, nisC, nisT, nisP, nisF, nisI, and nisRK), suggesting that the strain produces a nisin-like substance. This study provides fundamental information on whale-derived L. lactis subsp. lactis which may be useful for reducing the carriage of B. subtilis subsp. subtilis and V. alginolyticus. Full article

Carbapenem-resistant Acinetobacter pittii (CRAP) is a causative agent of nosocomial infections. This study aimed to characterize clinical isolates of CRAP from a tertiary hospital in Northeast Thailand. Six isolates were confirmed as extensively drug-resistant Acinetobacter pittii (XDRAP). The bla_NDM-1 gene was detected in three isolates, whereas bla_IMP-14 and bla_IMP-1 were detected in the others. Multilocus sequence typing with the Pasteur scheme revealed ST220 in two isolates, ST744 in two isolates, and ST63 and ST396 for the remaining two isolates, respectively. Genomic characterization revealed that six XDRAP genes contained antimicrobial resistance genes: ST63 (A436) and ST396 (A1) contained 10 antimicrobial resistance genes, ST220 (A984 and A864) and ST744 (A56 and A273) contained 9 and 8 antimicrobial resistance genes, respectively. The single nucleotide polymorphism (SNP) phylogenetic tree revealed that the isolates A984 and A864 were closely related to A. pittii YB-45 (ST220) from China, while A436 was related to A. pittii WCHAP100020, also from China. A273 and A56 isolates (ST744) were clustered together; these isolates were closely related to strains 2014S07-126, AP43, and WCHAP005069, which were isolated from Taiwan and China. Strict implementation of infection control based upon the framework of epidemiological analyses is essential to prevent outbreaks and contain the spread of the pathogen. Continued surveillance and close monitoring with molecular epidemiological tools are needed. Full article

The continuous characterization of genome-wide diversity in population and case–cohort samples, allied to the development of new algorithms, are shedding light on host ancestry impact and selection events on various infectious diseases. Especially interesting are the long-standing associations between humans and certain bacteria, such as the case of Helicobacter pylori, which could have been strong drivers of adaptation leading to coevolution. Some evidence on admixed gastric cancer cohorts have been suggested as supporting Homo-Helicobacter coevolution, but reliable experimental data that control both the bacterium and the host ancestries are lacking. Here, we conducted the first in vitro coinfection assays with dual human- and bacterium-matched and -mismatched ancestries, in African and European backgrounds, to evaluate the genome wide gene expression host response to H. pylori. Our results showed that: (1) the host response to H. pylori infection was greatly shaped by the human ancestry, with variability on innate immune system and metabolism; (2) African human ancestry showed signs of coevolution with H. pylori while European ancestry appeared to be maladapted; and (3) mismatched ancestry did not seem to be an important differentiator of gene expression at the initial stages of infection as assayed here. Full article

Quorum sensing is a type of chemical communication by which bacterial populations control expression of their genes in a coordinated manner. This regulatory mechanism is commonly used by pathogens to control the expression of genes encoding virulence factors and that of genes involved in the bacterial adaptation to variations in environmental conditions. In phytopathogenic bacteria, several mechanisms of quorum sensing have been characterized. In this review, we describe the different quorum sensing systems present in phytopathogenic bacteria, such as those using the signal molecules named N-acyl-homoserine lactone (AHL), diffusible signal factor (DSF), and the unknown signal molecule of the virulence factor modulating (VFM) system. We focus on studies performed on phytopathogenic bacteria of major importance, including Pseudomonas, Ralstonia, Agrobacterium, Xanthomonas, Erwinia, Xylella,Dickeya, and Pectobacterium spp. For each system, we present the mechanism of regulation, the functions targeted by the quorum sensing system, and the mechanisms by which quorum sensing is regulated. Full article

Kale (Brassica oleracea var. acephala) is a vegetable common in most cultures but is less studied as a functional food compared to other cruciferous vegetables, such as broccoli. We investigated the effect of supplementing a high-fat diet (HFD) with kale (HFKV) in C57BL/6J mice. We particularly explored its role in metabolic parameters, gut bacterial composition and diversity using 16S rRNA sequencing, systematically compared changes under each phylum and predicted the functional potential of the altered bacterial community using PICRUSt2. Like other cruciferous vegetables, kale attenuated HFD-induced inflammation. In addition, kale modulated HFD-induced changes in cecal microbiota composition. The HFD lowered bacterial diversity, increased the Firmicutes: Bacteroidetes (F/B) ratio and altered composition. Specifically, it lowered Actinobacteria and Bacteroidetes (Bacteroidia, Rikenellaceae and Prevotellaceae) but increased Firmicutes (mainly class Bacilli). Kale supplementation lowered the F/B ratio, increased both alpha and beta diversity and reduced class Bacilli and Erysipelotrichi but had no effect on Clostridia. Within Actinobacteria, HFKV particularly increased Coriobacteriales/Coriobacteriaceae about four-fold compared to the HFD (p < 0.05). Among Bacteroidia, HFKV increased the species Bacteroides thetaiotaomicron by over two-fold (p = 0.05) compared to the HFD. This species produces plant polysaccharide digesting enzymes. Compared to the HFD, kale supplementation enhanced several bacterial metabolic functions, including glycan degradation, thiamine metabolism and xenobiotic metabolism. Our findings provide evidence that kale is a functional food that modulates the microbiota and changes in inflammation phenotype. Full article

An important prerequisite for the effective control, timely diagnosis, and successful treatment of mycobacterial infections in both humans and animals is a rapid, specific, and sensitive detection technique. Culture is still considered the gold standard in the detection of viable mycobacteria; however, mycobacteria are extremely fastidious and slow-growing microorganisms, and therefore cultivation requires a very long incubation period to obtain results. Polymerase Chain Reaction (PCR) methods are also frequently used in the diagnosis of mycobacterial infections, providing faster and more accurate results, but are unable to distinguish between a viable and non-viable microorganism, which results in an inability to determine the success of tuberculosis patient treatment or to differentiate between an active and passive infection of animals. One suitable technique that overcomes these shortcomings mentioned is the phage amplification assay (PA). PA specifically detects viable mycobacteria present in a sample within 48 h using a lytic bacteriophage isolated from the environment. Nowadays, an alternative approach to PA, a commercial kit called Actiphage™, is also employed, providing the result within 6–8 h. In this approach, the bacteriophage is used to lyse mycobacterial cells present in the sample, and the released DNA is subsequently detected by PCR. The objective of this review is to summarize information based on the PA used for detection of mycobacteria significant in both human and veterinary medicine from various kinds of matrices. Full article

Saccharomyces yeasts are widely distributed in the environment and microbiota of higher organisms. The killer phenotype of yeast, encoded by double-stranded RNA (dsRNA) virus systems, is a valuable trait for host survival. The mutual relationship between the different yet clearly defined LA and M virus pairs suggests complex fitting context. To define the basis of this compatibility, we established a system devoted to challenging inherent yeast viruses using viral proteins expressed in trans. Virus exclusion by abridged capsid proteins was found to be complete and nonspecific, indicating the presence of generic mechanisms of Totiviridae maintenance in yeast cells. Indications of specificity in both the exclusion of LA viruses and the maintenance of M viruses by viral capsid proteins expressed in trans were observed. This precise specificity was further established by demonstrating the importance of the satellite virus in the maintenance of LA virus, suggesting the selfish behavior of M dsRNA. Full article

Dryland xeric conditions exert a deterministic effect on microbial communities, forcing life into refuge niches. Deposited rocks can form a lithic niche for microorganisms in desert regions. Mineral weathering is a key process in soil formation and the importance of microbial-driven mineral weathering for nutrient extraction is increasingly accepted. Advances in geobiology provide insight into the interactions between microorganisms and minerals that play an important role in weathering processes. In this study, we present the examination of the microbial diversity in dryland rocks from the Tsauchab River banks in Namibia. We paired culture-independent 16S rRNA gene amplicon sequencing with culture-dependent (isolation of bacteria) techniques to assess the community structure and diversity patterns. Bacteria isolated from dryland rocks are typical of xeric environments and are described as being involved in rock weathering processes. For the first time, we extracted extra- and intracellular DNA from rocks to enhance our understanding of potentially rock-weathering microorganisms. We compared the microbial community structure in different rock types (limestone, quartz-rich sandstone and quartz-rich shale) with adjacent soils below the rocks. Our results indicate differences in the living lithic and sublithic microbial communities. Full article

An evaluation was conducted of the colonization of Pseudomonas protegens MP12, a plant-growth promoting and antagonistic strain, inoculated in vine plants during a standard process of grapevine nursery propagation. Three in vivo inoculation protocols (endophytic, rhizospheric, and epiphytic) were implemented and monitored by means of both culture-dependent and independent techniques. Endophytic treatment resulted in the colonization of the bacterium inside the vine cuttings, which spread to young leaves during the forcing period. Microscopy analysis performed on transformed dsRed-tagged P. protegens MP12 cells confirmed the bacterium’s ability to penetrate the inner part of the roots. However, endophytic MP12 strain was no longer detected once the plant materials had been placed in the vine nursery field. The bacterium also displayed an ability to colonize the rhizosphere and, when the plants were uprooted at the end of the vegetative season, its persistence was confirmed. Epiphytic inoculation, performed by foliar spraying of cell suspension, was effective in controlling artificially-induced Botrytis cinerea infection in detached leaves. The success of rhizospheric and leaf colonization in vine plants suggests potential for the future exploitation of P. protegens MP12 as biofertilizer and biopesticide. Further investigation is required into the stability of the bacterium’s colonization of vine plants under real-world conditions in vineyards. Full article

We previously constructed a Saccharomyces cerevisiae carotenoid producer BL03-D-4 which produced much more carotenoid in YPM (modified YPD) media than YPD media. In this study, the impacts of nutritional components on carotenoid accumulation of BL03-D-4 were investigated. When using YPM media, the carotenoid yield was increased 10-fold compared to using the YPD media. To elucidate the hidden mechanism, a transcriptome analysis was performed and showed that 464 genes changed significantly in YPM media. Furthermore, inspired by the differential gene expression analysis which indicated that ADY2, HES1, and CUP1 showed the most remarkable changes, we found that the improvement of carotenoid accumulation in YPM media was mainly due to the copper ions, since supplementation of 0.08 mM CuSO₄ in YPD media could increase carotenoid yield 9.2-fold. Reverse engineering of target genes was performed and carotenoid yield could be increased 6.4-fold in YPD media through overexpression of ACE1. The present study revealed for the first time the prominent promotion of carotenoid yield by copper ions in engineered S. cerevisiae and provided a new target ACE1 for genetic engineering of S. cerevisiae for the bioproduction of carotenoids. Full article

Recently, the outbreak of the coronavirus disease 2019 (COVID-19), caused by the SARS-CoV-2 virus, in China and its subsequent spread across the world has caused numerous infections and deaths and disrupted normal social activity. Presently, various techniques are used for the diagnosis of SARS-CoV-2 infection, with various advantages and weaknesses to each. In this paper, we summarize promising methods, such as reverse transcription-polymerase chain reaction (RT-PCR), serological testing, point-of-care testing, smartphone surveillance of infectious diseases, nanotechnology-based approaches, biosensors, amplicon-based metagenomic sequencing, smartphone, and wastewater-based epidemiology (WBE) that can also be utilized for the detection of SARS-CoV-2. In addition, we discuss principles, advantages, and disadvantages of these detection methods, and highlight the potential methods for the development of additional techniques and products for early and fast detection of SARS-CoV-2. Full article

Several haloarchaea are reported to be pleomorphic, while others exhibit remarkable shapes, such as squares. Recently, Haloferax volcanii was found to alter its morphology during growth. Cells are motile rods in early exponential phase, and immotile plates in stationary phase. It is unknown if this growth phase dependent cell shape alteration is a specific feature of Hfx. volcanii, or conserved amongst haloarchaea. Here, we studied the cell shape and motility of two haloarchaea species Haloarcula hispanica and Haloarcula californiae. With a combination of light and electron microscopy, we observed that both strains undergo a growth phase dependent morphological development, albeit in a slightly different fashion as Hfx. volcanii. For both Haloarcula strains, the cell size is changing throughout growth. Cell shape seems to be related with motility, as highly motile cells on semi-solid agar plates are predominantly rod-shaped. We conclude that the growth phase dependent cell morphology alteration might be a common feature amongst haloarchaea, and that cell shape is generally linked with a motile life style. The conservation of this phenomenon underscores the importance of studies of the molecular mechanisms regulating cell shape in archaea. Full article

Malaria is responsible for major diseases of humans, while associated haemosporidians are important factors in regulating wildlife populations. Polychromophilus, a haemosporidian parasite of bats, is phylogenetically close to human-pathogenic Plasmodium species, and their study may provide further clues for understanding the evolutionary relationships between vertebrates and malarial parasites. Our aim was to investigate the distribution of Polychromophilus spp. in Eastern Europe and test the importance of host ecology and roost site on haemosporidian parasite infection of bats. We sampled bats and their ectoparasites at eight locations in Romania and Bulgaria. DNA was extracted from blood samples and ectoparasites and tested individually for the presence of DNA of Polychromophilus spp. using a nested PCR targeting a 705 bp fragment of cytB. Two species of Polychromophilus were identified: Po. melanipherus in Miniopterus schreibersii and associated ectoparasites and Po. murinus in rhinolophid and vespertilionid bats (6 species) and their ticks and nycteribiid flies. Only cave-dwelling bat species (and their ectoparasites) showed infections, and we found a strong correlation between infections with Polychromophilus parasites and Nycteribiidae prevalence. We report the high genetic diversity of Polychromophilus spp. in Eastern Europe, suggesting that the simultaneous presence of varied host and vector assemblages enhances bat haemosporidian parasite diversity. Full article

Deserts cover a significant proportion of the Earth’s surface and continue to expand as a consequence of climate change. Mutualistic arbuscular mycorrhizal (AM) fungi are functionally important plant root symbionts, and may be particularly important in drought stressed systems such as deserts. Here we provide a first molecular characterization of the AM fungi occurring in several desert ecosystems worldwide. We sequenced AM fungal DNA from soil samples collected from deserts in six different regions of the globe using the primer pair WANDA-AML2 with Illumina MiSeq. We recorded altogether 50 AM fungal phylotypes. Glomeraceae was the most common family, while Claroideoglomeraceae, Diversisporaceae and Acaulosporaceae were represented with lower frequency and abundance. The most diverse site, with 35 virtual taxa (VT), was in the Israeli Negev desert. Sites representing harsh conditions yielded relatively few reads and low richness estimates, for example, a Saudi Arabian desert site where only three Diversispora VT were recorded. The AM fungal taxa recorded in the desert soils are mostly geographically and ecologically widespread. However, in four sites out of six, communities comprised more desert-affiliated taxa (according to the MaarjAM database) than expected at random. AM fungal VT present in samples were phylogenetically clustered compared with the global taxon pool, suggesting that nonrandom assembly processes, notably habitat filtering, may have shaped desert fungal assemblages. Full article

Human Immunodeficiency Virus type-1 (HIV-1) establishes a latent viral reservoir soon after infection, which poses a major challenge for drug treatment and curative strategies. Many efforts are therefore focused on blocking infection. To this end, both viral and host factors relevant to the onset of infection need to be considered. Given that HIV-1 is most often transmitted mucosally, strategies designed to protect against infection need to be effective at mucosal portals of entry. These strategies need to contend also with cell-free and cell-associated transmitted/founder (T/F) virus forms; both can initiate and establish infection. This review will discuss how insight from the current model of HIV-1 mucosal transmission and cell entry has highlighted challenges in developing effective strategies to prevent infection. First, we examine key viral and host factors that play a role in transmission and infection. We then discuss preventive strategies based on antibody-mediated protection, with emphasis on targeting T/F viruses and mucosal immunity. Lastly, we review treatment strategies targeting viral entry, with focus on the most clinically advanced entry inhibitors. Full article

Livestock movements create complex dynamic interactions among premises that can be represented, interpreted, and used for epidemiological purposes. These movements are a very important part of the production chain but may also contribute to the spread of infectious diseases through the transfer of infected animals over large distances. Social network analysis (SNA) can be used to characterize cattle trade patterns and to identify highly connected premises that may act as hubs in the movement network, which could be subjected to targeted control measures in order to reduce the transmission of communicable diseases such as bovine tuberculosis (TB). Here, we analyzed data on cattle movement and slaughterhouse surveillance for detection of TB-like lesions (TLL) over the 2016–2018 period in the state of Rio Grande do Sul (RS) in Brazil with the following aims: (i) to characterize cattle trade describing the static full, yearly, and monthly snapshots of the network contact trade, (ii) to identify clusters in the space and contact networks of premises from which animals with TLL originated, and (iii) to evaluate the potential of targeted control actions to decrease TB spread in the cattle population of RS using a stochastic metapopulation disease transmission model that simulated within-farm and between-farm disease spread. We found heterogeneous densities of premises and animals in the study area. The analysis of the contact network revealed a highly connected (~94%) trade network, with strong temporal trends, especially for May and November. The TLL cases were significantly clustered in space and in the contact network, suggesting the potential for both local (e.g., fence-to-fence) and movement-mediated TB transmission. According to the disease spread model, removing the top 7% connected farms based on degree and betweenness could reduce the total number of infected farms over three years by >50%. In conclusion, the characterization of the cattle network suggests that highly connected farms may play a role in TB dissemination, although being close to infected farms was also identified as a risk factor for having animals with TLL. Surveillance and control actions based on degree and betweenness could be useful to break the transmission cycle between premises in RS. Full article

Colonization by the benign tapeworm, Hymenolepis diminuta, has been associated with a reduction in intestinal inflammation and changes in bacterial microbiota. However, the role of microbiota in the tapeworm anti-inflammatory effect is not yet clear, and the aim of this study was to determine whether disruption of the microflora during worm colonization can affect the course of intestinal inflammation. We added a phase for disrupting the intestinal microbiota using antibiotics to the experimental design for which we previously demonstrated the protective effect of H. diminuta. We monitored the immunological markers, clinical parameters, bacterial microbiota, and histological changes in the colon of rats. After a combination of colonization, antibiotics, and colitis induction, we had four differently affected experimental groups. We observed a different course of the immune response in each group, but no protective effect was found. Rats treated with colonization and antibiotics showed a strong induction of the Th2 response as well as a significant change in microbial diversity. The microbial results also revealed differences in the richness and abundance of some bacterial taxa, influenced by various factors. Our data suggest that interactions between the tapeworm and bacteria may have a major impact on its protective effect. Full article