Appl. Microbiol., Volume 3, Issue 1 (March 2023) – 21 articles

Cutaway peatlands in the midlands of the Republic of Ireland are rarely the focus of scientific studies. The soil quality and related microenvironment have been severely impacted by peat extraction. Returning them to a ‘near-natural state’ would require greater insights into this ecological niche. The current research took the initiative to study the microbiology of vast cutaway sites in the midlands of Ireland. Peat was collected over two seasons in January, February and April. Homogenised peat was aseptically cultured on a range of specific and non-specific culture media. Microbial enumeration, Gram staining and other microscopic observations of morphologically distinct microorganisms were performed. The total viable bacterial and fungal numbers were highest in February (1.33 × 10⁵ CFU ml⁻¹ and 5.93 × 10⁶ CFU ml⁻¹, respectively) and were lowest in April (1.14 × 10³ CFU ml⁻¹ and 5.57 × 10⁶ CFU ml⁻¹). Penicillium spp. and Trichoderma spp. were common in all the sites. The highest values of phosphate solubilisation index were recorded in peat collected in April (SI = 3.167 & 3.000). Overall, there is a statistically significant difference (p ≤ 0.0001) among the microbial numbers across the three months. This variation could be due to the temperature and pH differences across peat soil. Full article

A phenomenological model of planktonic microbial cultures, reported in previous papers, suggests that the whole growth progress seems planned by the microbial population since a pre-growth latency phase, during which the population level remains at its starting level. This model is in line with recent suggestions about the behavior of complex systems, as long as it allows for the gathering of the growth trends of a number of real batch cultures in a single master plot of reduced variables, in spite of their metabolic and physiological differences. One important issue of the model concerns the origin of the time scale for the microbes that can differ from that for the observer. The present paper reports some consequences of the model in view of its potential use in predictive microbiology and proposes an extension to the steady and decay phases of the culture evolution suggesting that, consistent with the assumptions about the growth phase, the decay occurs by a scan of the cell generation steps. This view leads to the conclusion that the steady phase between growth and decay trends actually corresponds to the loss of the oldest cell generations, which represents minor fractions of the microbial population. Such early decay is almost undetectable in a log scale, looking like a steady phase. To account for cases that show a broad maximum instead of an intermediate steady trend, a single continuous function, still related to the model, can describe the whole growth and decay trend of the microbial culture. Full article

The fish gut microbiome plays an essential role in the host’s development and survival. Environmental factors can shape the gut microbiome and potentially mediate physiological performance. Seasonal environments that experience regular abiotic and biotic transitions likely drive variability in the gut microbiome. However, we know very little about how seasonal transitions interact with the gut microbiome, especially at northern latitudes where seasonality is exaggerated. Therefore, in this study, we analyzed the native gut microbiome of a flexible top predator fish species, the lake trout, across seasons in a boreal lake using 16S rRNA sequencing. Seasonal changes explained one third of the bacterial variance. The relative abundance of several bacterial taxa influenced the observed seasonal differences in the community; pathogenic Pseudomonas and Stenotrophomonas were most abundant in the spring and winter seasons, and chemoheterotrophic Macrococcus and Lelliottia were most abundant in the summer. The fall season was dominated by unclassified Clostridiaceae, potentially linked to a shift in lake trout foraging. Therefore, we present novel evidence that suggests seasonality is likely to shape the native gut microbiome of lake trout; however, the mechanistic links between the environment and the microbial diversity of the gut remain to be uncovered. Full article

The development of alternative (and free-of-antibiotics) antibacterial and antibiofilm agents is an important strategy to circumvent the resistance of bacteria to antibiotics. Herein, we explore the production of mixed oxides by incorporating silver nanoparticles in titanium dioxide as a silver concentration-dependent antibacterial agent that is further incorporated in Tilapia fish skin (a promising prototype of xenograft), integrating the antibacterial activity of mixed oxide into the intrinsic properties of Tilapia skin. The antibiofilm activity of samples prepared with high concentrations of silver (10 wt% of precursor AgNO₃) has been considered a good antibiofilm response. The influence of silver content is also observed with respect to the minimum bactericidal concentration, which is reduced to 3.13 mg/mL with a characteristic kill time in the order of 30 min that is associated with antibiofilm activity in biofilm-forming strains of Staphylococcus aureus. These results indicate that modified Tilapia fish skin acquires antibacterial behavior and can be explored for xenografts with prospective applications in the light-dependent actuation of TiO₂-based compounds. Full article

Novel benzoxazines were synthesized by microwave irradiation and tested for their potential binding affinity towards receptors of advanced glycation end products (RAGE). We found that the compound (2-(2-bromophenyl)-6-methyl-2,4-dihydro-1H-benzo[d][1,3]oxazine) (3i) is a lead inhibitor of RAGE. Further, our in silico prediction that benzoxazines dock towards the AGE binding region of RAGE suggests that these ligands could bind effectively at the hydrophobic pocket of the receptor and additionally form key interactions with Arg48 and Arg104, revealing its diversity in developing anti-RAGE drugs to treat AGE–RAGE-dominant disease conditions. Functionally, we herein report the anti-tuberculosis activity of small molecules which could be bioactive in the culture of mycobacterium tuberculosis. Full article

The commercial onshore aquaculture of the spiny lobster Panulirus ornatus, while in its infancy, has progressed rapidly from the enabling research that continues at the University of Tasmania. The development of lobster feeds, both fresh and manufactured, has been critical to the success of this emerging aquaculture sector. Fresh feeds derived from mussel represent the gold standard in terms of the growth performance of juvenile lobsters. Nonetheless, concerns regarding availability, sustainability, and potential biosecurity issues of fresh feeds highlight the importance of developing manufactured feeds for lobster aquaculture. Wild lobsters are assumed to have a balanced natural diet that allows for standard growth and development, and as such natural diets are often used as a reference for feed development. Similarly, the gut microbiota associated with a natural diet is assumed to reflect a healthy microbial assemblage. The aim of this study was to compare the microbiota of the hindgut and hepatopancreas of cultured P. ornatus fed with a commercial prawn pellet or mussel to that of wild spiny lobster juveniles. Gut samples were analysed using Oxford Nanopore 16S rRNA gene sequencing. Based on principal coordinate analysis, the gut bacteria of cultured lobsters were different from the wild juveniles. The core microbiota of the hindgut and hepatopancreas libraries were phyla Proteobacteria (Gamma, Alpha) and Bacteroidetes. Vibrio was the most dominant genus in both organs. The differences in bacterial relative abundance were mainly between cultured (pellet-, mussel-fed) and wild lobsters. In conclusion, bacteria in the cultured lobsters had significantly different profiles to that of the wild juveniles, indicating that current onshore aquaculture practices alter the gut microbiota. A number of different feeding and culture practices may be required if the aim of closed culture practices is to attain a gut microbiota in cultured animals that is representative of that found in wild spiny lobsters. Full article

Gut microbes are immunologically tolerated in the gastrointestinal tract but trigger aggressive immune responses upon translocation across the gut barrier. Although oral tolerance, a physiological process that dampens immune responses to food proteins and commensal microbiota, remains poorly defined, significant progress was made during and after the Human Immunodeficiency Virus epidemic in the 1980s and the discovery of regulatory T cells in 1995. Additional insight was gained after the discoveries of innate lymphoid cells in 2008 and the functional elucidation of mucosal mast cells. Prior to the historical discovery of human pathogens, the etiologies of most human diseases were considered unknown. The same was true about many genetic disorders prior to the Human Genome Project. Here, we hypothesize that many of the remaining idiopathic conditions, including autoimmune, fibroproliferative, and neuropsychiatric diseases as well as some cancers, can be considered microbial translocation disorders triggered by the host immune responses to extraintestinal gut microbes and/or their constituent parts. In addition to microbial translocation, we also discuss potential interventions for intestinal barrier rehabilitation, including antibodies against tumor necrosis factor-like ligand 1A and membrane lipid replacement supplements. Full article

Endophytic yeast species were studied in the internal tissues of ripe cultivated vegetables and fruits. A total of 19 yeast species, 11 ascomycete species, and 8 basidiomycete species were observed in the internal tissues of all fruits examined. The opportunistic yeast Candida parapsilosis was present in all plants studied. Several virulence factors (production of hydrolytic enzymes and sensitivity to antifungal agents) were examined in all 107 isolates of C. parapsilosis from the internal tissues of fruits. The most virulent isolates were found in vegetables. C. parapsilosis is widespread in nature and is often isolated from a variety of non-human sources. It is frequently involved in invasive infections that seriously affect human health. This species poses a high risk to immunocompromised individuals, such as HIV patients and surgical patients or children whose immune systems are not sufficiently mature. Since virulent isolates of Candida parapsilosis have been found in vegetables and fruits; their raw consumption may not be safe. Finally, we emphasize the importance of ongoing phenotypic and genetic studies of endophytic isolates of Candida parapsilosis and their comparison with clinical isolates. Full article

Modern biotechnology benefits from the introduction of novel chassis organisms in remedying the limitations of already-established strains. For this, Paracoccus pantotrophus was chosen for in-depth assessment. Its unique broad metabolism and robustness against abiotic stressors make this strain a well-suited chassis candidate. This study set out to comprehensively overview abiotic influences on the growth performance of five P. pantotrophus strains. These data can aid in assessing the suitability of this genus for chassis development by using the type strain as a preliminary model organism. The five P. pantotrophus strains DSM 2944^T, DSM 11072, DSM 11073, DSM 11104, and DSM 65 were investigated regarding their growth on various carbon sources and other nutrients. Our data show a high tolerance against osmotic pressure for the type strain with both salts and organic osmolytes. It was further observed that P. pantotrophus prefers organic acids over sugars. All of the tested strains were able to grow on short-chain alkanes, which would make P. pantotrophus a candidate for bioremediation and the upcycling of plastics. In conclusion, we were able to gain insights into several P. pantotrophus strains, which will aid in further introducing this species, or even another species from this genus, as a candidate for future biotechnological processes. Full article

Many publications report coatings that exhibit antimicrobial potency applicable to high-touch surfaces and desirable for healthcare settings to contribute to reductions in the occurrence of Hospital Acquired Infections (HAI). In this review, the importance of surface contamination and the transmission of microbes is addressed. The standard strategy to tackle fomites is to implement proper disinfection and cleaning practices and periodically monitor the environment’s cleanliness. However, the probability of recontamination of cleaned surfaces is high. Therefore, an additional first line of defense against pathogen transmission and subsequent infection is the antimicrobial surface that can eliminate or at least repel pathogens, introducing a barrier to the spread of infection. It is a simple concept, but formulating a durable, antimicrobial coating with broad-spectrum antimicrobial and antifouling activities has proven challenging. The challenges and progress made in developing such material are reviewed. Full article

Lactobacillus plantarum is a catalase-negative species and distributes in human intestinal tracts. However, the cytoprotective effects of the catalase-activated L. plantarum strain have yet to be exploited against reactive oxygen species (ROS). Here, a catalase-activated L. plantarum CGMCC 6888 (CatA⁺) was obtained using exogenous added heme. The scavenging free radical abilities of this strain were obviously increased. Moreover, the activated catalase A in L. plantarum CGMCC 6888 endowed the intestinal epithelium NCM460 with lower ROS content after degrading H₂O₂. In addition, the transcription levels of Nrf2 and Nrf2-related antioxidant enzyme genes (HO-1, GCLC, NQO-1 and TXNRD1) and tight junction protein genes (ZO-1, OCLN, and JAM-1) were upregulated significantly when co-incubated with CGMCC 6888/CatA⁺. This work confirmed that the catalase A conferred L. plantarum with the strong protection effects in the intestinal epithelial cells against ROS. Full article

The bacterial foodborne enteropathogen Escherichia albertii, despite enjoying increased attention paid to its pathogenesis, global dissemination, and antimicrobial resistance capacity, remains difficult to identify from human foods. The primary objective of this study was to develop and test a selective and differential plating medium for the isolation of E. albertii from enteric pathogens commonly transmitted via fresh poultry meat, namely E. coli and Salmonella enterica. MacConkey agar supplemented with α-D-+-melibiose and the lactose analogue X-gal was prepared and used to differentially enumerate E. albertii, Salmonella, and E. coli from inoculated ground chicken meat. The medium, MXgMac agar, differentiated the inoculated pathogens with a greater degree of efficiency than did the previously developed E. albertii-selective medium xylose–rhamnose–melibiose (XRM) MacConkey agar, based on differential usage of the lactose analogue and melibiose. Chicken-derived feces and litter samples were subsequently tested using the medium and found not to contain E. albertii by 16S rRNA gene amplification. MXgMac agar facilitates improved differential recovery of E. albertii and other enteric pathogens from poultry meat versus other E. albertii selective/differential media. Full article

Microsomes are commonly used to perform in vitro drug metabolism, predominantly to form phase I drug metabolites. Pooled microsomes from multiple donors can contain microorganisms from underlying microbial diseases. Exposure to microbes can also occur during extraction if aseptic processing is compromised. Although microbial presence does not affect the metabolic activity of microsomes, presence of unwanted microorganisms can cause interference if the downstream application of microsomal drug metabolites is screening for antibacterial activity. In this work, traditional biochemical tests and advanced proteomics-based identification techniques were used to identify two gram-negative bacteria in pooled human liver microsomes. Several decontamination procedures were assessed to eradicate these two bacteria from the microsomes without affecting its metabolic capacity, and organic extraction was found to be the most convenient and efficient approach to decontaminate microsomes and screen drug metabolites for antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA). Full article

Prebiotics beneficially affect the gut microbiome. Bimuno^®, a prebiotic supplement containing galactooligosaccharides (GOS), has multiple demonstrated prebiotic effects. Using short-term colonic incubations, the influence of GOS on the colonic microbiota of three healthy human adults was evaluated. Colonic reactors inoculated with fecal samples were untreated (blank) or supplemented with GOS. pH, gas pressure, short-chain fatty acids (SCFAs), lactic acid, branched SCFAs, ammonium, and microbial community composition were evaluated at 0 h, 6 h, 24 h, and 48 h. pH decreased and gas pressure increased (+29.01 kPa) with GOS treatment versus blank. Total SCFA (+22.4 mM), acetate (+14.1 mM), propionate (+5.5 mM), and butyrate (+5.8 mM) were higher for GOS than blank. Acetate and propionate production were highest earlier in the experiment, while butyrate production was highest between 24 h and 48 h. With GOS, lactic acid production increased between 0 h and 6 h (+14.4 mM) followed by apparent consumption. Levels of branched SCFAs and ammonium were low with GOS and reduced versus blank (respectively, −2.1 mM and −256.0 mg/L). GOS significantly increased the relative abundance of Bifidobacterium longum (LDA = 4; p = 0.006), and significantly increased the absolute abundance of Bifidobacteriaceae (p < 0.001), Lactobacillaceae (p < 0.05), Bifidobacterium adolescentis (LDA = 4.5; p < 0.001), and Bifidobacterium ruminantium (LDA= 3.2; p = 0.01). This in vitro model demonstrated the prebiotic potential of GOS as supplementation resulted in increased beneficial bacteria, SCFA, and lactic acid and decreased branched SCFA, pH, and ammonium. Full article

Understanding the impacts of herbicides on soil microbial communities is important, as these organisms mediate a wide range of ecosystem services. Here, we investigated whether the diversity and function of soil microbial communities were significantly influenced by one-off applications of atrazine, diuron, fluazifop-P-butyl, haloxyfop-P-methyl and pendimethalin as pure compounds at their recommended doses over multiple time points (1, 3, 7, 14, 30 and 60 days). Phylogenetic marker gene sequencing revealed that none of the herbicides influenced the numbers of bacterial and archaeal taxa or the evenness of their abundances. Similarly, none of the herbicides influenced the composition of bacterial and archaeal communities, except for diuron, fluazifop-P-methyl and pendimethalin, which were associated with larger relative abundances of a small number of OTUs on day 30 only. Functionally, none of the herbicides significantly influenced fluorescein diacetate hydrolysis (FDA) and beta-glucosidase activities or the induced respiratory responses of soil microbial communities to a range of substrates. These data indicate that the active herbicide ingredients tested may have minimal non-target effects when applied once at their recommended dose. Given their frequent use, it is important to next consider whether these herbicides have more pronounced effects at higher doses and application frequencies. Full article

An increasing prevalence and spread of Clostridioides difficile infection (CDI) caused by DH/NAP11/106/ST-42 has been observed worldwide, probably fostered by its great capacity to produce spores or by the higher resistance rates observed for some strains. Based on the results of our previous study where RT106 showed higher recurrence rates than other relevant ribotypes, a genetic analysis by whole-genome sequencing (WGS) of primary and recurrent RT106 isolates from ten patients was performed to determine whether the higher rate of recurrence associated with RT106 is due to relapses, caused by the same strain, or reinfections, caused by different strains. MLST profiles, resistance mutations, and phylogenetic relatedness were determined by comparative single nucleotide variant (SNV) analysis. All isolates were classified as ST42, and those belonging to the same patient were isogenic, with one exception; strains belonging to different patients were not with two exceptions, pointing to putative transmission events. Phylogenetic analysis also suggested the presence of similar local epidemic lineages associated with moxifloxacin resistance, except for one patient whose isolates clustered with different nonresistant US strains. Our results show that recurrent CDIs caused by RT06/ST42 are mainly due to relapses caused by the primary strains, showing the higher capacity of RT106/ST42 to persist and cause recurrences as compared to other ribotypes. Full article

Abandoned and flooded ore mines are examples of hostile environments (cold, dark, oligotrophic, trace metal) with a potential vast diversity of microbial communities rarely characterized. This study aimed to understand the effects of depth, the source of water (surface or groundwater), and abiotic factors on the communities present in the old Forsyth iron mine in Quebec (Canada). Water and biofilm samples from the mine were sampled by a team of technical divers who followed a depth gradient (0 to 183 m deep) to study the planktonic and sessile communities’ diversity and structure. We used 16S/18S rRNA amplicon to characterize the taxonomic diversity of Bacteria, Archaea, and Eukaryotes. Our results show that depth was not a significant factor explaining the difference in community composition observed, but lifestyle (planktonic/sessile) was. We discovered a vast diversity of microbial taxa, with taxa involved in carbon- and sulfur-cycling. Sessile communities seem to be centered on C₁-cycling with fungi and heterotrophs likely adapted to heavy-metal stress. Planktonic communities were dominated by ultra-small archaeal and bacterial taxa, highlighting harsh conditions in the mine waters. Microbial source tracking indicated sources of communities from surface to deeper layers and vice versa, suggesting the dispersion of organisms in the mine, although water connectivity remains unknown. Full article

The recent description and characterization of several novel and unique lumpy skin disease virus (LSDV) strains have revealed the inadequacy of current techniques for differentiating between vaccine- and wild-type viruses. The lack of reliable sequencing targets for promptly distinguishing circulating recombinant vaccine-like strains (RVLSs) highlights the need to develop a single and simple differentiation tool. In this study, we analyzed the available LSDV whole-genome sequences and identified a 705-bp region in open reading frame (ORF) LW134. Based on a single run of nucleotide sequencing and phylogenetic analysis, the region with 13 informative single nucleotide polymorphisms (SNPs) was capable of accurately segregating the novel RVLSs into the same five clusters previously confirmed by whole-genome sequencing. In addition, archived RVLSs from Russia were analyzed for further characterization using the newly described single PCR and sequencing assay. The ORF LW134 assay identified one archived RVLS as a novel cluster distinct from the previously described five clusters, while clustering the remaining samples into previously designated lineages, demonstrating the reliability of the assay. The novel PCR and sequencing assays described in this study have great potential for accurately delineating the molecular and evolutionary affiliation of circulating RVLSs. Full article

According to current knowledge, a properly colonized human microbiota contributes to the proper functioning of the body. The composition of the natural flora changes depending on age, health, living conditions, and the use of antimicrobial agents: antibiotics, disinfectants, and some cosmetics. The human body is diversely populated with microorganisms and undergoes constant changes under the influence of various factors, and its proper composition is extremely important for the proper functioning of the body. Given the above, it was decided that we would review current scientific research that explains the cause–effect relationship between the composition of microorganisms populating the human body and health, focusing on women’s health. As a result, an overview paper was prepared based on 109 scientific sources from 2009–2022. Special attention was paid to the most recent scientific studies of the last five years, which account for more than 75% of the cited sources. Full article

The oyster industry is a significant component of United States aquaculture and is vulnerable to various food frauds. In addition to species substitution, mislabeling of oyster geographical origin is performed for economic gains. The geographical origin misrepresentations are performed to claim a famed region of origin known for its unique flavor profile. DNA barcoding is the gold standard method for identifying seafood species but has limited resolution to the species level. This pilot study was conducted to characterize and compare the oyster gill microbiome as an alternative approach for tracking oysters’ origin. Commercially available raw east coast oysters (Crassostrea virginica) from two distinct geographical locations were purchased. Genomic DNA isolated from the gills was processed for microbiome analysis. The data revealed distinct microbiome signatures among the two sample sets. Oysters from Louisiana showed the presence of eighteen unique bacterial genera, whereas Maryland oysters showed a higher abundance of twelve genera. Findings from this study demonstrate the applicability of microbiome analysis as an emerging alternative approach for identifying geographical origin misrepresentations. Full article