Microorganisms — Open Access Journal

Many efforts have focused on the adsorption of metals from contaminated water by microbes. Synechococcus PCC7002, a major marine cyanobacteria, is widely applied to remove metals from the ocean’s photic zone. However, its ability to adsorb cesium (Cs) nuclides has received little attention. In this study, the biosorption behavior of Cs(I) from ultrapure distilled water by living Synechococcus PCC7002 was investigated based on kinetic and isotherm studies, and the biosorption mechanism was characterized by Fourier-transform infrared spectroscopy, Raman spectroscopy, scanning electron microscopy, transmission electron microscopy, energy-dispersive X-ray spectrometry, and three-dimensional excitation emission matrix fluorescence spectroscopy. Synechococcus PCC7002 showed extremely high tolerance to Cs ions and its minimal inhibitory concentration was 8.6 g/L. Extracellular polymeric substances (EPS) in Synechococcus PCC7002 played a vital role in this tolerance. The biosorption of Cs by Synechococcus PCC7002 conformed to a Freundlich-type isotherm model and pseudo-second-order kinetics. The binding of Cs(I) was primarily attributed to the extracellular proteins in EPS, with the amino, hydroxyl, and phosphate groups on the cell walls contributing to Cs adsorption. The biosorption of Cs involved two mechanisms: Passive adsorption on the cell surface at low Cs concentrations and active intracellular adsorption at high Cs concentrations. The results demonstrate that the behavior and mechanism of Cs adsorption by Synechococcus PCC7002 differ based on the Cs ions concentration. Full article

It has been well established that a vegetarian and polyphenol-rich diet, including fruits, vegetables, teas, juices, wine, indigestible fiber and whole grains, provide health-promoting phytochemicals and phytonutrients that are beneficial for the heart and brain. What is not well-characterized is the affect these foods have when co-metabolized within our dynamic gut and its colonizing flora. The concept of a heart shunt within the microbiota-gut-brain axis underscores the close association between brain and heart health and the so-called “French paradox” offers clues for understanding neurodegenerative and cerebrovascular diseases. Moreover, oxidation-redox reactions and redox properties of so-called brain and heart-protective foods are underappreciated as to their enhanced or deleterious mechanisms of action. Focusing on prodromal stages, and common mechanisms underlying heart, cerebrovascular and neurodegenerative diseases, we may unmask and understanding the means to better treat these related diseases. Full article

While advances in genomic sequencing have highlighted significant strain variability between and within Salmonella serovars, only a few protein variants have been directly related to evolutionary adaptation for survival, such as host specificity or differential virulence. The current study investigated whether allelic variation of the Salmonella adhesin/invasin PagN influences bacterial interaction with their receptors. The Salmonella enterica, subspecies enterica serovar Typhi (S. Typhi) allelic variant of PagN was found to bind significantly better to different enterocytes as well as to the extracellular matrix protein laminin than did the major Salmonella enterica, subspecies enterica serovar Typhimurium (S. Typhimurium) allele. The two alleles differed at amino acid residues 49 and 109 in two of the four predicted PagN surface loops, and residue substitution analysis revealed that a glutamic acid at residue 49 increased the adhesive and invasive properties of S. Typhi PagN. PagN sequence comparisons from 542 Salmonella strains for six representative S. enterica serovars and S. diarizonae further supported the role of glutamic acid at residues 49 and 109 in optimizing adhesion to cells and laminin, as well as for cell invasion. In summary, this study characterized unique residues in allelic variants of a virulence factor that participates in the colonization and invasive properties of different Salmonella stains, subspecies and serovars. Full article

This study aimed to evaluate the effects of the four kinds of additives on the silage quality and the relevant bacterial community diversity by Illumina HiSeq 16S rRNA sequencing. The four kinds of additives were Lactobacillus plantarum (LP), organic acids including gallic acid (GA) and phenyllactic acid (PA), pectin (PEC), and enzymes including pectinase (PEE) and cellulase (CE). After 30 d of fermentation, the pH value was shown to have the lowest value in the PEE and PEC groups, followed by the PA group, and then in CE and GA groups; the highest value of pH was found in both LP and control groups. The ammonia nitrogen concentration was lower in the PEE group compared to the other groups except for the PA group. In the comparisons among the seven groups, Lactobacillus was higher in the LP group, Paracoccus was higher in the GA group, Weissella was higher in the PA group, Leuconostoc was higher in the PEC group, Bacillus, Aeromonas, and Curvibacter were higher in the PEE group, and Coriobacteriaceae_UCG_002 was higher in the CE group compared to the other groups. This study proposed that the addition of PEC and PEE improved the fermentation quality of alfalfa silage compared to other additives by improving the bacterial community of Leuconostoc, and Bacillus and Aeromonas, respectively. Moreover, the enhanced fermentation quality of alfalfa silage by the supplementation of PEC and PEE might be attributed to other unclassified genera. This study provides an implication that pectin degradation is an important determinant for alfalfa silage fermentation through the rescheduling of bacterial community diversity. Full article

During the last few decades there has been a staggering rise in human consumption of soybean-oil (SO). The microbiome and specific taxa composing it are dramatically affected by diet; specifically, by high-fat diets. Increasing evidence indicates the association between dysbiosis and health or disease state, including cardiovascular diseases (CVD) and atherosclerosis pathogenesis in human and animal models. To investigate the effects of high SO intake, C57BL/6 mice were orally supplemented with SO-based emulsion (SOE) for one month, followed by analyses of atherosclerosis-related biomarkers and microbiota profiling by 16S rRNA gene sequencing of fecal DNA. SOE-supplementation caused compositional changes to 64 taxa, including enrichment in Bacteroidetes, Mucispirillum, Prevotella and Ruminococcus, and decreased Firmicutes. These changes were previously associated with atherosclerosis in numerous studies. Among the shifted taxa, 40 significantly correlated with at least one atherosclerosis-related biomarker (FDR < 0.05), while 13 taxa positively correlated with the average of all biomarkers. These microbial alterations also caused a microbial-derived metabolic-pathways shift, including enrichment in different amino-acid metabolic-pathways known to be implicated in CVD. In conclusion, our results demonstrate dysbiosis following SOE supplementation associated with atherosclerosis-related biomarkers. These findings point to the microbiome as a possible mediator to CVD, and it may be implemented into non-invasive diagnostic tools or as potential therapeutic strategies. Full article

The gut microbiota may have an impact on obesity. To date, the majority of studies in obese patients reported microbiota composition in stool samples. The aim of this study was to investigate the duodenal mucosa dysbiosis in adult obese individuals from Campania, a region in Italy with a very high percentage of obese people, to highlight microbial taxa likely associated with obesity. Duodenum biopsies were taken during upper gastrointestinal endoscopy in 19 obese (OB) and 16 lean control subjects (CO) and microbiome studied by 16S rRNA gene sequencing. Duodenal microbiome in our groups consisted of six phyla: Proteobacteria, Firmicutes, Actinobacteria, Fusobacteria, Bacteroidetes and Acidobacteria. Proteobacteria (51.1% vs. 40.1%) and Firmicutes (33.6% vs. 44.9%) were significantly (p < 0.05) more and less abundant in OB compared with CO, respectively. Oribacterium asaccharolyticum, Atopobium parvulum and Fusobacterium nucleatum were reduced (p < 0.01) and Pseudomonadales were increased (p < 0.05) in OB compared with CO. Receiver operating characteristic curve analysis showed Atopobium and Oribacterium genera able to discriminate with accuracy (power = 75% and 78%, respectively) OB from CO. In conclusion, increased Proteobacteria and decreased Firmicutes (Lachnospiraceae) characterized the duodenal microbiome of obese subjects. These data direct to further studies to evaluate the functional role of the dysbiotic-obese-associated signature. Full article

Large areas in Northern Russia are covered by extensive mires, which represent a complex mosaic of ombrotrophic raised bogs, minerotrophic and eutrophic fens, all in a close proximity to each other. In this paper, we compared microbial diversity patterns in the surface peat layers of the neighbouring raised bogs and eutrophic fens that are located within two geographically remote mire sites in Vologda region using 16S rRNA gene sequencing. Regardless of location, the microbial communities in raised bogs were highly similar to each other but were clearly distinct from those in eutrophic fens. Bogs were dominated by the Acidobacteria (30%–40% of total 16S rRNA gene reads), which belong to the orders Acidobacteriales and Bryobacterales. Other bog-specific bacteria included the Phycisphaera-like group WD2101 and the families Isosphaeraceae and Gemmataceae of the Planctomycetes, orders Opitutales and Pedosphaerales of the Verrucomicrobia and a particular group of alphaproteobacteria within the Rhizobiales. In contrast, fens hosted Anaerolineae-affiliated Chloroflexi, Vicinamibacteria- and Blastocatellia-affiliated Acidobacteria, Rokubacteria, uncultivated group OM190 of the Planctomycetes and several groups of betaproteobacteria. The Patescibacteria were detected in both types of wetlands but their relative abundance was higher in fens. A number of key parameters that define the distribution of particular bacterial groups in mires were identified. Full article

Gut microbiota refers to a complex network of microbes, which exerts a marked influence on the host’s health. It is composed of bacteria, fungi, viruses, and helminths. Bacteria, or collectively, the bacteriome, comprises a significant proportion of the well-characterized microbiome. However, the other communities referred to as ‘dark matter’ of microbiomes such as viruses (virome), fungi (mycobiome), archaea (archaeome), and helminths have not been completely elucidated. Development of new and improved metagenomics methods has allowed the identification of complete genomes from the genetic material in the human gut, opening new perspectives on the understanding of the gut microbiome composition, their importance, and potential clinical applications. Here, we review the recent evidence on the viruses, fungi, archaea, and helminths found in the mammalian gut, detailing their interactions with the resident bacterial microbiota and the host, to explore the potential impact of the microbiome on host’s health. The role of fecal virome transplantations, pre-, pro-, and syn-biotic interventions in modulating the microbiome and their related concerns are also discussed. Full article

: Human Campylobacter jejuni infections inducing campylobacteriosis including post-infectious sequelae such as Guillain-Barré syndrome and reactive arthritis are rising worldwide and progress into a global burden of high socioeconomic impact. Intestinal immunopathology underlying campylobacteriosis is a classical response of the innate immune system characterized by the accumulation of neutrophils and macrophages which cause tissue destruction, barrier defects and malabsorption leading to bloody diarrhea. Clinical studies revealed that enteritis and post-infectious morbidities of human C. jejuni infections are strongly dependent on the structure of pathogenic lipooligosaccharides (LOS) triggering the innate immune system via Toll-like-receptor (TLR)-4 signaling. Compared to humans, mice display an approximately 10,000 times weaker TLR-4 response and a pronounced colonization resistance (CR) against C. jejuni maintained by the murine gut microbiota. In consequence, investigations of campylobacteriosis have been hampered by the lack of experimental animal models. We here summarize recent progress made in the development of murine C. jejuni infection models that are based on the abolishment of CR by modulating the murine gut microbiota and by sensitization of mice to LOS. These advances support the major role of LOS driven innate immunity in pathogenesis of campylobacteriosis including post-infectious autoimmune diseases and promote the preclinical evaluation of novel pharmaceutical strategies for prophylaxis and treatment. Full article

Certain species of the genus Bifidobacterium represent human symbionts. Many studies have shown that the establishment of symbiosis with such bifidobacterial species confers various beneficial effects on human health. Among the more than ten (sub)species of human gut-associated Bifidobacterium that have significantly varied genetic characteristics at the species level, Bifidobacterium bifidum is unique in that it is found in the intestines of a wide age group, ranging from infants to adults. This species is likely to have adapted to efficiently degrade host-derived carbohydrate chains, such as human milk oligosaccharides (HMOs) and mucin O-glycans, which enabled the longitudinal colonization of intestines. The ability of this species to assimilate various host glycans can be attributed to the possession of an adequate set of extracellular glycoside hydrolases (GHs). Importantly, the polypeptides of those glycosidases frequently contain carbohydrate-binding modules (CBMs) with deduced affinities to the target glycans, which is also a distinct characteristic of this species among members of human gut-associated bifidobacteria. This review firstly describes the prevalence and distribution of B. bifidum in the human gut and then explains the enzymatic machinery that B. bifidum has developed for host glycan degradation by referring to the functions of GHs and CBMs. Finally, we show the data of co-culture experiments using host-derived glycans as carbon sources, which underpin the interesting altruistic behavior of this species as a cross-feeder. Full article

Bacterial biofilm provides bacteria with resistance and protection against conventional antimicrobial agents and the host immune system. Bacteriophages are known to move across the biofilm to make it permeable to antimicrobials. Mineral hydroxyapatite (HA) can improve the lytic activity of bacteriophages, and, together with eicosanoic acid (C20:0), can destroy the biofilm structure. Here, we demonstrate the efficacy of the combined use of phage, HA and C20:0 against Xanthomonas campestris pv campestris (Xcc) biofilm. We used nuclear magnetic resonance (NMR)-based metabolomics to investigate the molecular determinants related to the lytic action, aiming at identifying the metabolic pathways dysregulated by phage treatment. Furthermore, we identified specific markers (amino acids, lactate and galactomannan) which are involved in the control of biofilm stability. Our data show that Xccφ1, alone or in combination with HA and C20:0, interferes with the metabolic pathways involved in biofilm formation. The approach described here might be extended to other biofilm-producing bacteria. Full article

Lactobacillus fermentum UCO-979C (Lf979C) beneficially modulates the cytokine response of gastric epithelial cells and macrophages after Helicobacter pylori infection in vitro. Nevertheless, no in vivo studies were performed with this strain to confirm its beneficial immunomodulatory effects. This work evaluated whether Lf979C improves protection against H. pylori infection in mice by modulating the innate immune response. In addition, we evaluated whether its exopolysaccharide (EPS) was involved in its beneficial effects. Lf979C significantly reduced TNF-α, IL-8, and MCP-1 and augmented IFN-γ and IL-10 in the gastric mucosa of H. pylori-infected mice. The differential cytokine profile induced by Lf979C in H. pylori-infected mice correlated with an improved reduction in the pathogen gastric colonization and protection against inflammatory damage. The purified EPS of Lf979C reduced IL-8 and enhanced IL-10 levels in the gastric mucosa of infected mice, while no effect was observed for IFN-γ. This work demonstrates for the first time the in vivo ability of Lf979C to increase resistance against H. pylori infection by modulating the gastric innate immune response. In addition, we advanced knowledge of the mechanisms involved in the beneficial effects of Lf979C by demonstrating that its EPS is partially responsible for its immunomodulatory effect. Full article

In a survey of microfungi from plant debris collected in Vietnam, two new hyphomycetous species were found, which belong to the genera Heliocephala and Pseudopenidiella and the family Microthyriaceae (Microthyriales, Dothideomycetes). Maximum Likelihood and Bayesian Inference sequence analyses of the internal transcribed spacers (ITS) and large subunit (LSU) of the ribosomal DNA barcodes allowed assessing the phylogenetic relationships of the new species with other species of the respective genera. Heliocephala variabilis sp. nov. was closely related to Heliocephala elegans, Heliocephala gracilis, and Heliocephala zimbabweensis, from which it was morphologically distinguished by its smaller conidiophores and non-rostrate conidia of up to four septa on the natural substratum. Pseudopenidiella vietnamensis sp. nov. was related to Pseudopenidiella piceae and Pseudopenidiella podocarpi and differed from the former principally by its lack of microcondiophores and from P. podocarpi by having larger macroconidiophores and smooth conidia. Key morphological features to distinguish the accepted species in Heliocephala and Pseudopenidiella are also provided. In addition, Pseudopenidiella pini was excluded from the genus on the basis of its morphological features. Full article

Microorganisms are the driving force behind the circulation and transformation of the soil substance. The development of soil bacterial communities is critical for ecosystem restoration and evolution. In the Loess Plateau, coal mining activities have aggravated the deterioration of the fragile local ecological environment. The adaptive development of soil bacterial communities in response to different ecological processes caused by coal mining activities was explored through high-throughput sequencing technology and an ecological network analysis of the mining subsidence area of the Daliuta Coal Mine and vegetation rehabilitation area of the Heidaigou Coal Mine in the Loess Plateau. The results showed that while mining subsidence was inhibited, vegetation rehabilitation promoted the soil physicochemical properties. Soil organic matter, available phosphorus and available potassium in the subsidence area decreased significantly (P < 0.05), while soil organic matter, soil water, pH and EC in the vegetation rehabilitation area increased significantly (P < 0.05). The diversity index in the subsidence area decreased by about 20%, while that in the vegetation rehabilitation area increased by 63%. Mining subsidence and vegetation rehabilitation had a distinct influence on the molecular ecological networks of the soil bacteria, which tended to be more complex after the mining subsidence, and the number of connections in the network increased otherwise significantly enhanced interactive relationships. After the vegetation rehabilitation, the number of modules in the ecological network increased, but the contents of modules tended to be simpler. Soil bacterial communities adapted to the changes by changing the relationships between bacteria in response to different ecological processes. This study provides new insights into the monitoring and abatement of the damaged ecological environment in mines. Full article

Spinal infection poses a demanding diagnostic and treatment problem for which a multidisciplinary approach with spine surgeons, radiologists, and infectious disease specialists is required. Infections are usually caused by bacterial microorganisms, although fungal infections can also occur. The most common route for spinal infection is through hematogenous spread of the microorganism from a distant infected area. Most patients with spinal infections diagnosed in early stages can be successfully managed conservatively with antibiotics, bed rest, and spinal braces. In cases of gross or pending instability, progressive neurological deficits, failure of conservative treatment, spinal abscess formation, severe symptoms indicating sepsis, and failure of previous conservative treatment, surgical treatment is required. In either case, close monitoring of the patients with spinal infection with serial neurological examinations and imaging studies is necessary. Full article

One-day-old chicks were assigned one of four dietary treatments in a 2 × 2 factorial design in which the main effects were diet (adequate vs. low protein) and the addition of protease (0 vs. 200 g/1000 kg of feed). Chick performance (days 0–14) was recorded and their excreta were analyzed for short chain fatty acids, ammonia, and composition of the microbiota using 16S rRNA gene sequencing. Birds fed the low protein diet had lower body weight gain and poorer overall feed conversion ratio (FCR) (p 0.04); however, these parameters were not affected by the inclusion of protease (p 0.27). Protease inclusion did not affect any particular bacterial genus in the excreta, but it increased the total number of observed OTUs (p = 0.04) and Faith’s phylogenetic diversity (p = 0.05). Abundance of Proteus and Acinetobacter were lower in the excreta of chicks fed the low protein diet (p = 0.01). Abundance of Bacteroides was associated with poorer FCR, while Proteus was associated with improved FCR (p 0.009). Although diet had a stronger impact than protease on chick performance, both diet and protease yielded some changes in the intestinal microbiotas of the birds. Full article

Marine yeasts can occur in a wide range of habitats, including in marine invertebrates, in which they may play important roles; however, investigation of marine yeasts in marine invertebrates is scarce. Therefore, this study aims to explore the diversity of yeasts associated with corals and zoanthids in the Gulf of Thailand. Thirty-three coral and seven zoanthid samples were collected at two sampling sites near Mu and Khram islands. Fifty yeast strains were able to be isolated from 25 of the 40 samples collected. Identification based on sequence analyses of the D1/D2 domain of the large subunit rRNA gene revealed a higher number of strains in the phylum Basidiomycota (68%) than in the phylum Ascomycota. The ascomycetous yeasts comprised nine known species from four genera (Candida, Meyerozyma, Kodamaea, and Wickerhamomyces), whereas the basidiomycetous yeasts comprised 10 known species from eight genera (Vishniacozyma, Filobasidium, Naganishia, Papiliotrema, Sterigmatomyces, Cystobasidium, Rhodotorula, and Rhodosporidiobolus) and one potentially new species. The species with the highest occurrence was Rhodotorula mucilaginosa. Using principal coordinate analysis (PCoA) ordination, no marked differences were found in the yeast communities from the two sampling sites. The estimation of the expected richness of species was higher than the actual richness of species observed. Full article

Persistent use of the insecticide D-cyphenothrin has resulted in heavy environmental contamination and public concern. However, microbial degradation of D-cyphenothrin has never been investigated and the mechanism remains unknown. During this study, for the first time, an efficient D-cyphenothrin-degrading bacterial strain Staphylococcus succinus HLJ-10 was identified. Response surface methodology was successfully employed by using Box-Behnken design to optimize the culture conditions. At optimized conditions, over 90% degradation of D-cyphenothrin (50 mg·L⁻¹) was achieved in a mineral salt medium within 7 d. Kinetics analysis revealed that its half-life was reduced by 61.2 d, in comparison with the uninoculated control. Eight intermediate metabolites were detected in the biodegradation pathway of D-cyphenothrin including cis-D-cyphenothrin, trans-D-cyphenothrin, 3-phenoxybenzaldehyde, α-hydroxy-3-phenoxy-benzeneacetonitrile, trans-2,2-dimethyl-3-propenyl-cyclopropanol, 2,2-dimethyl-3-propenyl-cyclopropionic acid, trans-2,2-dimethyl-3-propenyl-cyclopropionaldehyde, and 1,2-benzenedicarboxylic acid, dipropyl ester. This is the first report about the degradation of D-cyphenothrin through cleavage of carboxylester linkage and diaryl bond. In addition to degradation of D-cyphenothrin, strain HLJ-10 effectively degraded a wide range of synthetic pyrethroids including permethrin, tetramethrin, bifenthrin, allethrin, and chlorempenthrin, which are also widely used insecticides with environmental contamination problems. Bioaugmentation of D-cyphenothrin-contaminated soils with strain HLJ-10 substantially enhanced its degradation and over 72% of D-phenothrin was removed from soils within 40 d. These findings unveil the biochemical basis of a highly efficient D-cyphenothrin-degrading bacterial isolate and provide potent agents for eliminating environmental residues of pyrethroids. Full article