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Frontiers in Microbiology 2021Coastal zones are exposed to various anthropogenic impacts, such as different types of wastewater pollution, e.g., treated wastewater discharges, leakage from sewage...
Coastal zones are exposed to various anthropogenic impacts, such as different types of wastewater pollution, e.g., treated wastewater discharges, leakage from sewage systems, and agricultural and urban runoff. These various inputs can introduce allochthonous organic matter and microbes, including pathogens, into the coastal marine environment. The presence of fecal bacterial indicators in the coastal environment is usually monitored using traditional culture-based methods that, however, fail to detect their uncultured representatives. We have conducted a year-around survey of the pelagic microbiome of the dynamic coastal ecosystem, subjected to different anthropogenic pressures to depict the seasonal and spatial dynamics of traditional and alternative fecal bacterial indicators. To provide an insight into the environmental conditions under which bacterial indicators thrive, a suite of environmental factors and bacterial community dynamics were analyzed concurrently. Analyses of 16S rRNA amplicon sequences revealed that the coastal microbiome was primarily structured by seasonal changes regardless of the distance from the wastewater pollution sources. On the other hand, fecal bacterial indicators were not affected by seasons and accounted for up to 34% of the sequence proportion for a given sample. Even more so, traditional fecal indicator bacteria () and alternative wastewater-associated bacteria (, , and ) were part of the core coastal microbiome, i.e., present at all sampling stations. Microbial source tracking and Lagrangian particle tracking, which we employed to assess the potential pollution source, revealed the importance of riverine water as a vector for transmission of allochthonous microbes into the marine system. Further phylogenetic analysis showed that the in our data set was affiliated with the pathogenic , suggesting that a potential exposure risk for bacterial pathogens in anthropogenically impacted coastal zones remains. We emphasize that molecular analyses combined with statistical and oceanographic models may provide new insights for environmental health assessment and reveal the potential source and presence of microbial indicators, which are otherwise overlooked by a cultivation approach.
PubMed: 35111137
DOI: 10.3389/fmicb.2021.765091 -
MBio Aug 2023the deep-sea annelid found at sunken whalefalls, is known to host Oceanospirillales bacterial endosymbionts intracellularly in specialized roots, which help it feed...
the deep-sea annelid found at sunken whalefalls, is known to host Oceanospirillales bacterial endosymbionts intracellularly in specialized roots, which help it feed exclusively on vertebrate bones. Past studies, however, have also made mention of external bacteria on their trunks. During a 14-yr study, we reveal a dynamic, yet persistent, shift of Campylobacterales integrated into the epidermis of , which change over time as the whale carcass degrades on the sea floor. The Campylobacterales associated with seven species of , which comprise 67% of the bacterial community on the trunk, appear initially dominated by the genus (at early time points <24 mo), the at intermediate stages (~50 mo), and the at later stages (>140 mo) of whale carcass decomposition. Metagenome analysis of the epibiont metabolic capabilities suggests potential for a transition from heterotrophy to autotrophy and differences in their capacity to metabolize oxygen, carbon, nitrogen, and sulfur. Compared to free-living relatives, the epibiont genomes were enriched in transposable elements, implicating genetic exchange on the host surface, and contained numerous secretions systems with eukaryotic-like protein (ELP) domains, suggesting a long evolutionary history with these enigmatic, yet widely distributed deep-sea worms. IMPORTANCE Symbiotic associations are widespread in nature and we can expect to find them in every type of ecological niche. In the last twenty years, the myriad of functions, interactions and species comprising microbe-host associations has fueled a surge of interest and appreciation for symbiosis. During this 14-year study, we reveal a dynamic population of bacterial epibionts, integrated into the epidermis of 7 species of a deep-sea worm group that feeds exclusively on the remains of marine mammals. The bacterial genomes provide clues of a long evolutionary history with these enigmatic worms. On the host surface, they exchange genes and appear to undergo ecological succession, as the whale carcass habitat degrades over time, similar to what is observed for some free-living communities. These, and other annelid worms are important keystone species for diverse deep-sea environments, yet the role of attached external bacteria in supporting host health has received relatively little attention.
PubMed: 37382438
DOI: 10.1128/mbio.03140-22 -
Frontiers in Cellular and Infection... 2021and are two rarely detected species. In the study, we analyzed the antimicrobial susceptibility and provide detailed insights into the genotype and phylogeny of both...
and are two rarely detected species. In the study, we analyzed the antimicrobial susceptibility and provide detailed insights into the genotype and phylogeny of both species using whole-genome sequencing. Thermophilic species are the most common bacterial foodborne pathogens causing gastroenteritis in humans worldwide. The genus is part of the family and includes the species , and the rarely described , and are emergent enteropathogens and potential zoonotic agents. Here, we generated, analyzed, and characterized whole-genome sequences of and They were isolated from water poultry farms in Germany, cultured and identified by MALDI-TOF MS. With PCR the identity was verified. Antibiotic susceptibility testing was carried out with erythromycin, ciprofloxacin, doxycycline, tetracycline, gentamicin, streptomycin, ampicillin, and cefotaxime using the gradient strip method (E-test). Whole-genome sequences were generated including those of reference strains. Complete genomes for six selected strains are reported. These provide detailed insights into the genotype. With these, we predicted known AMR genes, virulence-associated genes, and plasmid replicons. Phenotypic analysis of resistance showed differences between the presence of resistance genes and the prediction of phenotypic resistance profiles. In , the nucleotide sequence of the A gene (DQ464331) can show a signature mutation resulting in an amino acid change T85>I. and showed the same gene as assessed by similarity annotation of the mutations 254C>G. Most of the isolates were found to be sensitive to ciprofloxacin. The ciprofloxacin-resistant isolate was associated with the amino acid change T85>I. But this was not predicted with antibiotic resistance databases, before. Ultimately, a phylogenetic analysis was done to facilitate in future outbreak analysis.
Topics: Anti-Bacterial Agents; Arcobacter; Drug Resistance, Bacterial; Genomics; Germany; Humans; Phylogeny
PubMed: 33816322
DOI: 10.3389/fcimb.2021.532989 -
Pathogens (Basel, Switzerland) Oct 2019This study aimed to identify the bacterial community in two wastewater treatment plants (WWTPs) and to determine the occurrence and reduction of , along with virulence...
This study aimed to identify the bacterial community in two wastewater treatment plants (WWTPs) and to determine the occurrence and reduction of , along with virulence genes ( and ). A total of 48 samples (24 influent and 24 effluent) were collected at two WWTPs in southern Arizona in the United States, monthly from August 2011 to July 2012. Bacterial DNA extract was utilized for 16S rRNA metagenomic sequencing. Quantification of 16S rRNA gene was conducted using a recently developed SYBR Green-based quantitative PCR assay Among 847 genera identified, 113 (13%) were identified as potentially pathogenic bacteria. 16S rRNA gene was detected in all influent samples and ten (83%) and nine (75%) effluent samples at each plant, respectively. Log reduction ratios of 16S rRNA gene in Plant A and Plant B were 1.7 ± 0.9 ( = 10) and 2.3 ± 1.5 ( = 9), respectively. The gene was detected by quantitative PCR in eleven (92%) and twelve (100%) of 12 influent samples from Plant A and Plant B, respectively, while the gene was detected in eight (67%) and six (50%) influent samples from Plant A and Plant B, respectively. The prevalence of potentially pathogenic bacteria in WWTP effluent indicated the need for disinfection before discharge into the environment.
PubMed: 31581714
DOI: 10.3390/pathogens8040175 -
Gut Pathogens 2020constitute emerging food- and waterborne pathogens causing gastroenteritis in humans, but the underlying mechanisms are only incompletely understood. We therefore...
BACKGROUND
constitute emerging food- and waterborne pathogens causing gastroenteritis in humans, but the underlying mechanisms are only incompletely understood. We therefore characterized isolates derived from human stool samples that had been collected during a prospective prevalence study in Germany in vitro. Thirty-six bacterial isolates belonging to the species (n = 24), (n = 10) and (n = 2) were genotyped by ERIC-PCR, the presence of 10 putative virulence genes was assessed and cytotoxic effects on the human intestinal cell line HT-29/B6 were analyzed applying the WST-assay.
RESULTS
Genotyping revealed high genetic diversity within the species , and . Both, and encoded for a large number of putative virulence genes, while fewer genes were detectable in isolates. Notably, the three cytolethal distending toxin (CDT) genes , and were abundant in both isolates. Furthermore, all and , but only one of the isolates exerted cytotoxic effects.
CONCLUSIONS
Our study provides evidence for the abundance of putative virulence genes in isolates and prominent cytotoxic effects of and in vitro. The presence of , , in points towards CDT secretion as potential mechanism underlying cytotoxicity as opposed to . However, the association of the virulence factors detected and human morbidity should be addressed in future studies.
PubMed: 31921357
DOI: 10.1186/s13099-019-0344-3 -
Genes Jun 2022Marine biofilms are a collective of microbes that can grow on many different surfaces immersed in marine environments. Estimating the microbial richness and specificity...
Marine biofilms are a collective of microbes that can grow on many different surfaces immersed in marine environments. Estimating the microbial richness and specificity of a marine biofilm community is a challenging task due to the high complexity in comparison with seawater. Here, we compared the resolution of full-length 16S rRNA gene sequencing technique of a PacBio platform for microbe identification in marine biofilms with the results of partial 16S rRNA gene sequencing of traditional Illumina PE250 platform. At the same time, the microbial richness, diversity, and composition of adjacent seawater communities in the same batch of samples were analyzed. Both techniques revealed higher species richness, as reflected by the Chao1 index, in the biofilms than that in the seawater communities. Moreover, compared with Illumina sequencing, PacBio sequencing detected more specific species for biofilms and less specific species for seawater. Members of , , , , and were significantly enriched in the biofilms, which is consistent with the previous understanding of species adapted to a surface-associated lifestyle and validates the taxonomic analyses in the current study. To conclude, the full-length sequencing of 16S rRNA genes has probably a stronger ability to analyze more complex microbial communities, such as marine biofilms, the species richness of which has probably been under-estimated in previous studies.
Topics: Biofilms; Genes, rRNA; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 35741812
DOI: 10.3390/genes13061050 -
PloS One 2023As a strategy for minimizing microbial infections in fish hatcheries, we have investigated how putatively probiotic bacterial populations influence biofilm formation....
As a strategy for minimizing microbial infections in fish hatcheries, we have investigated how putatively probiotic bacterial populations influence biofilm formation. All surfaces that are exposed to the aquatic milieu develop a microbial community through the selective assembly of microbial populations into a surface-adhering biofilm. In the investigations reported herein, we describe laboratory experiments designed to determine how initial colonization of a surface by nonpathogenic isolates from sturgeon eggs influence the subsequent assembly of populations from a pelagic river community, into the existing biofilm. All eight of the tested strains altered the assembly of river biofilm in a strain-specific manner. Previously formed isolate biofilm was challenged with natural river populations and after 24 hours, two strains and two-isolate combinations proved highly resistant to invasion, comprising at least 80% of the biofilm community, four isolates were intermediate in resistance, accounting for at least 45% of the biofilm community and two isolates were reduced to 4% of the biofilm community. Founding biofilms of Serratia sp, and combinations of Brevundimonas sp.-Hydrogenophaga sp. and Brevundimonas sp.-Acidovorax sp. specifically blocked populations of Aeromonas and Flavobacterium, potential fish pathogens, from colonizing the biofilm. In addition, all isolate biofilms were effective at blocking invading populations of Arcobacter. Several strains, notably Deinococcus sp., recruited specific low-abundance river populations into the top 25 most abundant populations within biofilm. The experiments suggest that relatively simple measures can be used to control the assembly of biofilm on the eggs surface and perhaps offer protection from pathogens. In addition, the methodology provides a relatively rapid way to detect potentially strong ecological interactions between bacterial populations in the formation of biofilms.
Topics: Animals; Rivers; Biofilms; Flavobacterium; Bacteria, Aerobic; Fishes
PubMed: 37956125
DOI: 10.1371/journal.pone.0288040 -
Microorganisms Dec 2022is an emergent gram-negative enteropathogenic bacterium widespread in different environments and hosts. During the colonization of the gastrointestinal tract, bacteria...
is an emergent gram-negative enteropathogenic bacterium widespread in different environments and hosts. During the colonization of the gastrointestinal tract, bacteria face a variety of environmental conditions to successfully establish infection in a new host. One of these challenges is the fluctuation of oxygen concentrations encountered not only throughout the host gastrointestinal tract and defences but also in the food industry. Oxygen fluctuations can lead to modulations in the virulence of the bacterium and possibly increase its pathogenic potential. In this sense, eight human isolates of were studied to evaluate the effects of microaerobic and aerobic atmospheric conditions in stressful host conditions, such as oxidative stress, acid survival, and human serum survival. In addition, the effects on the modulation of virulence traits, such as haemolytic activity, bacterial motility, biofilm formation ability, and adhesion and invasion of the Caco-2 cell line, were also investigated. Overall, aerobic conditions negatively affected the susceptibility to oxygen reactive species and biofilm formation ability but improved the isolates' haemolytic ability and motility while other traits showed an isolate-dependent response. In summary, this work demonstrates for the first time that oxygen levels can modulate the potential pathogenicity of , although the response to stressful conditions was very heterogeneous among different strains.
PubMed: 36557662
DOI: 10.3390/microorganisms10122409 -
FEBS Open Bio Oct 2020Arcobacter (A.) butzleri is an emerging zoonotic pathogen associated with gastrointestinal diseases, such as abdominal cramps and diarrhea, and is widely detected in...
Arcobacter (A.) butzleri is an emerging zoonotic pathogen associated with gastrointestinal diseases, such as abdominal cramps and diarrhea, and is widely detected in animals, showing a high prevalence in poultry and seafood. The survival and adaptation of A. butzleri to cold temperatures remains poorly studied, although it might be of interest for food safety considerations. To address this, growth patterns of eight A. butzleri isolates were determined at 8 °C for 28 days. A. butzleri isolates showed strain-dependent behavior: six isolates were unculturable after day 18, one exhibited declining but detectable cell counts until day 28 and one grew to the stationary phase level. Out of 13 A. butzleri cold shock-related genes homologous to Escherichia coli, 10 were up-regulated in response to a temperature downshift to 8 °C, as demonstrated by reverse transcription-quantitative PCR. Additionally, we compared these data with the cold-shock response in E. coli. Overall, we provide a deeper insight into the environmental adaptation capacities of A. butzleri, which we find shares similarities with the E. coli cold-shock response.
Topics: Arcobacter; Cold-Shock Response; Gene Expression; Gene Expression Profiling; Gene Expression Regulation; Temperature; Transcriptome
PubMed: 32810909
DOI: 10.1002/2211-5463.12959 -
Archives of Microbiology Nov 2023The surge in human arcobacteriosis has increased interest in determining the mechanisms involved in the pathogenesis of Arcobacter butzleri. Here, genomic analyses and...
The surge in human arcobacteriosis has increased interest in determining the mechanisms involved in the pathogenesis of Arcobacter butzleri. Here, genomic analyses and in vitro Caco-2 infection, motility, urease and antimicrobial susceptibility testing (AST) assays were used to characterise the virulence and antimicrobial resistance (AMR) determinants of strains HC-1, isolated from a patient with travellers' diarrhoea, and HC-2, isolated from another with pruritus. AMR determinants conferring resistance to tetracycline (tetO, present in both genomes) and to ampicillin and amoxicillin-clavulanic acid (bla3, present in HC-2) were identified. The same determinants associated with flagellum, chemotaxis, adhesion and invasion were detected in both, but HC-1 lacked eight flagellar genes. The urease cluster was only present in HC-1. Motility and urease tests confirmed the genetic differences between strains, but no genetic marker related to the inability of HC-2 to adhere and invade was identified. This inability could be conditioning the patient's pathology.
Topics: Humans; Virulence; Arcobacter; Caco-2 Cells; Urease; Genotype; Phenotype; Anti-Bacterial Agents
PubMed: 37923944
DOI: 10.1007/s00203-023-03709-3