Culture-independent detection of low-abundant Clostridioides difficile in environmental DNA via PCR

Clostridioides difficile represents a major burden to public health. As a well-known nosocomial pathogen whose occurrence is highly associated with antibiotic treatment, most examined C. difficile strains originated from clinical specimen and were isolated under selective conditions employing antibiotics. This suggests a significant bias among analyzed C. difficile strains, which impedes a holistic view on this pathogen. In order to support extensive isolation of C. difficile strains from environmental samples, we designed a detection PCR that targets the hpdBCA-operon and thereby identifies low abundances of C. difficile in environmental samples. This operon encodes the 4-hydroxyphenylacetate decarboxylase, which catalyzes the production of the antimicrobial compound para-cresol. Amplicon-based analyses of diverse environmental samples demonstrated that the designed PCR is highly specific for C. difficile and successfully detected C. difficile despite its absence in general 16S rRNA gene-based detection strategies. Further analyses revealed the potential of the hpdBCA detection PCR sequence for initial phylogenetic classification, which allows assessment of C. difficile diversity in environmental samples via amplicon sequencing. Our findings furthermore showed that C. difficile strains isolated under antibiotic treatment from environmental samples were originally dominated by other strains according to PCR amplicon results. This provided evidence for selective cultivation of under-represented but antibiotic-resistant isolates. Thereby, we revealed a substantial bias in C. difficile isolation and research.IMPORTANCEClostridioides difficile is a main cause of diarrheic infections after antibiotic treatment with serious morbidity and mortality worldwide. Research on this pathogen and its virulence has focused on bacterial isolation from clinical specimens under antibiotic treatment, which implies a substantial bias in isolated strains. Comprehensive studies, however, require an unbiased strain collection, which is accomplished by isolation of C. difficile from diverse environmental samples and avoidance of antibiotic-based enrichment strategies. Thus, isolation can significantly benefit from our C. difficile-specific detection PCR, which rapidly verifies C. difficile presence in environmental samples and further allows estimation of the C. difficile diversity by using next-generation sequencing.

Identification of sulfamethazine degraders in swine farm-impacted river and farmland: A comparative study of aerobic and anaerobic environments

Sulfonamides (SAs) are extensively used antibiotics in the prevention and treatment of animal diseases, leading to significant SAs pollution in surrounding environments. Microbial degradation has been proposed as a crucial mechanism for removing SAs, but the taxonomic identification of microbial functional guilds responsible for SAs degradation in nature remain largely unexplored. Here, we employed 13C-sulfamethazine (SMZ)-based DNA-stable isotope probing (SIP) and metagenomic sequencing to investigate SMZ degraders in three distinct swine farm wastewater-receiving environments within an agricultural ecosystem. These environments include the aerobic riparian wetland soil, agricultural soil, and anaerobic river sediment. SMZ mineralization activities exhibited significant variation, with the highest rate observed in aerobic riparian wetland soil. SMZ had a substantial impact on the microbial community compositions across all samples. DNA-SIP analysis demonstrated that Thiobacillus, Auicella, Sphingomonas, and Rhodobacter were dominant active SMZ degraders in the wetland soil, whereas Ellin6067, Ilumatobacter, Dongia, and Steroidobacter predominated in the agricultural soil. The genus MND1 and family Vicinamibacteraceae were identified as SMZ degrader in both soils. In contrast, anaerobic SMZ degradation in the river sediment was mainly performed by genera Microvirga, Flavobacterium, Dechlorobacter, Atopostipes, and families Nocardioidaceae, Micrococcaceae, Anaerolineaceae. Metagenomic analysis of 13C-DNA identified key SAs degradation genes (sadA and sadC), and various of dioxygenases, and aromatic hydrocarbon degradation-related functional genes, indicating their involvement in degradation of SMZ and its intermediate products. These findings highlight the variations of indigenous SAs oxidizers in complex natural habitats and emphasize the consideration of applying these naturally active degraders in future antibiotic bioremediation.

Impact of Different Drying Methods on the Microbiota, Volatilome, Color, and Sensory Traits of Sea Fennel (Crithmum maritimum L.) Leaves

Sea fennel (Crithmum maritimum L.) is a strongly aromatic herb of the Apiaceae family, whose full exploitation by the modern food industry is of growing interest. This study aimed at investigating the microbiological quality, volatile profile, and sensory traits of sea fennel spices produced using room-temperature drying, oven drying, microwave drying, and freeze drying. All the assayed methods were able to remove moisture up until water activity values below 0.6 were reached; however, except for microwave drying, none of the assayed methods were effective in reducing the loads of contaminating microorganisms. The metataxonomic analysis highlighted the presence of phytopathogens and even human pathogens, including members of the genera Bacillus, Pseudomonas, Alternaria, and Cryptococcus. When compared to fresh leaves, dried leaves showed increased L* (lightness) and c* (chroma, saturation) values and reduced hue angle. Dried leaves were also characterized by decreased levels of terpene hydrocarbons and increased levels of aldehydes, alcohols, and esters. For the sensory test, the microwave-dried samples obtained the highest appreciation by the trained panel. Overall, the collected data indicated microwave drying as the best option for producing sea fennel spices with low microbial loads, brilliant green color, and high-quality sensory traits.

Evaluation of the Deterioration of Untreated Commercial Polystyrene by Psychrotrophic Antarctic Bacterium

Polystyrene (PS) and microplastic production pose persistent threats to the ecosystem. Even the pristine Antarctic, which is widely believed to be pollution-free, was also affected by the presence of microplastics. Therefore, it is important to comprehend the extent to which biological agents such as bacteria utilise PS microplastics as a carbon source. In this study, four soil bacteria from Greenwich Island, Antarctica, were isolated. A preliminary screening of the isolates for PS microplastics utilisation in the Bushnell Haas broth was conducted with the shake-flask method. The isolate AYDL1 identified as Brevundimonas sp. was found to be the most efficient in utilising PS microplastics. An assay on PS microplastics utilisation showed that the strain AYDL1 tolerated PS microplastics well under prolonged exposure with a weight loss percentage of 19.3% after the first interval (10 days of incubation). Infrared spectroscopy showed that the bacteria altered the chemical structure of PS while a deformation of the surface morphology of PS microplastics was observed via scanning electron microscopy after being incubated for 40 days. The obtained results may essentially indicate the utilisation of liable polymer additives or "leachates" and thus, validate the mechanistic approach for a typical initiation process of PS microplastics biodeterioration by the bacteria (AYDL1)-the biotic process.

Luteibacter flocculans sp. nov., Isolated from a Eutrophic Pond and Isolation and Characterization of Luteibacter Phage vB_LflM-Pluto

Luteibacter is a genus of the Rhodanobacteraceae family. The present study describes a novel species within the genus Luteibacter (EIF3^T). The strain was analyzed genomically, morphologically and physiologically. Average nucleotide identity analysis revealed that it is a new species of Luteibacter. In silico analysis indicated two putative prophages (one incomplete, one intact). EIF3^T cells form an elliptical morphotype with an average length of 2.0 µm and width of 0.7 µm and multiple flagella at one end. The bacterial strain is an aerobic Gram-negative with optimal growth at 30 °C. EIF3^T is resistant towards erythromycin, tetracycline and vancomycin. We propose the name Luteibacter flocculans sp. nov. with EIF3^T (=DSM 112537^T = LMG 32416^T) as type strain. Further, we describe the first known Luteibacter-associated bacteriophage called vB_LflM-Pluto.

In silico prediction of potential indigenous microbial biomarkers in Penaeus vannamei identified through meta-analysis and genome-scale metabolic modelling

BACKGROUND

Understanding the microbiome is crucial as it contributes to the metabolic health of the host and, upon dysbiosis, may influence disease development. With the recent surge in high-throughput sequencing technology, the availability of microbial genomic data has increased dramatically. Amplicon sequence-based analyses majorly profile microbial abundance and determine taxonomic markers. Furthermore, the availability of genome sequences for various microbial organisms has prompted the integration of genome-scale metabolic modelling that provides insights into the metabolic interactions influencing host health. However, the analysis from a single study may not be consistent, necessitating a meta-analysis.

RESULTS

We conducted a meta-analysis and integrated with constraint-based metabolic modelling approach, focusing on the microbiome of pacific white shrimp Penaeus vannamei, an extensively cultured marine candidate species. Meta-analysis revealed that Acinetobacter and Alteromonas are significant indicators of "health" and "disease" specific taxonomic biomarkers, respectively. Further, we enumerated metabolic interactions among the taxonomic biomarkers by applying a constraint-based approach to the community metabolic models (4416 pairs). Under different nutrient environments, a constraint-based flux simulation identified five beneficial species: Acinetobacter spWCHA55, Acinetobacter tandoii SE63, Bifidobacterium pseudolongum 49 D6, Brevundimonas pondensis LVF1, and Lutibacter profundi LP1 mediating parasitic interactions majorly under sucrose environment in the pairwise community. The study also reports the healthy biomarkers that can co-exist and have functionally dependent relationships to maintain a healthy state in the host.

CONCLUSIONS

Toward this, we collected and re-analysed the amplicon sequence data of P. vannamei (encompassing 117 healthy and 142 disease datasets). By capturing the taxonomic biomarkers and modelling the metabolic interaction between them, our study provides a valuable resource, a first-of-its-kind analysis in aquaculture scenario toward a sustainable shrimp farming.

Isolation of a Host-Confined Phage Metagenome Allows the Detection of Phages Both Capable and Incapable of Plaque Formation

Bacteriophages, also called phages, are viruses of bacteria. They are the most common and diverse biological entities on this planet. For metagenomic investigation, their diversity is also their biggest obstacle. The direct metagenomic sequence of environmental phage communities often leads to short genomic fragments limiting the investigation to a few individual aspects of phage biology and diversity.The presented protocol for generating a host-associated metagenome reduces the phage diversity to a concise and accessible size. Metagenome sequencing often leads to complete genomes, and the availability of a suitable host system ensures further experimental investigation.

Brevundimonas and Serratia as host systems for assessing associated environmental viromes and phage diversity by complementary approaches

Focusing on visible plaques for phage isolation leaves the question if we miss the diversity of non-plaque forming phages. We addressed this question through direct plaque-based isolation by employing the new hosts Brevundimonas pondensis LVF1 and Serratia marcescens LVF3 dsDNA, ssDNA, dsRNA, and ssRNA host-associated metavirome analysis. Of the 25 distinctive dsDNA phage isolates, 14 were associated with Brevundimonas and 11 with Serratia. TEM analysis revealed that 6 were myoviruses, 18 siphoviruses and 1 podovirus, while phages infecting Brevundimonas belonged all to siphoviruses. The associated viromes suggested a higher phage diversity in summer than in winter, and dsDNA phages were the dominant group. Isolation of vB_SmaP-Kaonashi was possible after investigating the viromes associated with Serratia, demonstrating the great potential of accompanying host-associated metavirome analysis. The ssDNA virome analysis showed that the B. pondensis LVF1 host is associated with Microviridae and Inoviridae phages, although none of them were isolated. The results demonstrated that the classical isolation technique is not exhausted, leading to the isolation of new dsDNA phages. It can be further improved by combination with metavirome techniques, which revealed further diversity.

Down in the pond: Isolation and characterization of a new Serratia marcescens strain (LVF3) from the surface water near frog's lettuce (Groenlandia densa)

Serratia marcescens is a species that belongs to the family of Yersiniaceae. This family comprises taxa representing opportunistic human- and phytopathogens but also plant growth-promoting rhizobacteria (PGPR). This study describes a novel Gram-negative strain (LVF3R) of the species Serratia marcescens. The strain was characterized genomically, morphologically, and physiologically. In addition, the potential of the isolate to act as a host strain to assess the diversity of Serratia associated phages in environmental samples was explored. Average nucleotide identity analysis revealed that LVF3R belongs to the species Serratia marcescens. In silico analysis and ProphageSeq data resulted in the identification of one prophage, which is capable of viral particle formation. Electron microscopy showed cells of a rod-shaped, flagellated morphotype. The cells revealed a length and width of 1-1.6 μm and 0.8 μm, respectively. LVF3R showed optimal growth at 30 C and in the presence of up to 2% (w/v) NaCl. It exhibited resistances to ampicillin, erythromycin, oxacillin, oxytetracycline, rifampicin, tetracycline, and vancomycin. Genome data indicate that strain S. marcescens LVF3R is a potential PGPR strain. It harbors genes coding for indole acetic acid (IAA) biosynthesis, siderophore production, plant polymer degradation enzymes, acetoin synthesis, flagellar proteins, type IV secretion system, chemotaxis, phosphorous solubilization, and biofilm formation.