Microorganisms

27 pages, 3264 KiB

Open AccessArticle

The Antimicrobial Effect of Various Single-Strain and Multi-Strain Probiotics, Dietary Supplements or Other Beneficial Microbes against Common Clinical Wound Pathogens

by Sabina Fijan, Primož Kocbek, Andrej Steyer, Polona Maver Vodičar and Maja Strauss

Microorganisms 2022, 10(12), 2518; https://doi.org/10.3390/microorganisms10122518 - 19 Dec 2022

Cited by 7 | Viewed by 2343

Abstract

The skin is the largest organ in the human body and is colonized by a diverse microbiota that works in harmony to protect the skin. However, when skin damage occurs, the skin microbiota is also disrupted, and pathogens can invade the wound and [...] Read more.

The skin is the largest organ in the human body and is colonized by a diverse microbiota that works in harmony to protect the skin. However, when skin damage occurs, the skin microbiota is also disrupted, and pathogens can invade the wound and cause infection. Probiotics or other beneficial microbes and their metabolites are one possible alternative treatment for combating skin pathogens via their antimicrobial effectiveness. The objective of our study was to evaluate the antimicrobial effect of seven multi-strain dietary supplements and eleven single-strain microbes that contain probiotics against 15 clinical wound pathogens using the agar spot assay, co-culturing assay, and agar well diffusion assay. We also conducted genera-specific and species-specific molecular methods to detect the DNA in the dietary supplements and single-strain beneficial microbes. We found that the multi-strain dietary supplements exhibited a statistically significant higher antagonistic effect against the challenge wound pathogens than the single-strain microbes and that lactobacilli-containing dietary supplements and single-strain microbes were significantly more efficient than the selected propionibacteria and bacilli. Differences in results between methods were also observed, possibly due to different mechanisms of action. Individual pathogens were susceptible to different dietary supplements or single-strain microbes. Perhaps an individual approach such as a ‘probiogram’ could be a possibility in the future as a method to find the most efficient targeted probiotic strains, cell-free supernatants, or neutralized cell-free supernatants that have the highest antagonistic effect against individual clinical wound pathogens. Full article

(This article belongs to the Special Issue Probiotics and Antimicrobial Effect)

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33 pages, 4141 KiB

Open AccessReview

Gastro-Intestinal Microbiota in Equines and Its Role in Health and Disease: The Black Box Opens

by Frédérique Chaucheyras-Durand, Audrey Sacy, Kip Karges and Emmanuelle Apper

Microorganisms 2022, 10(12), 2517; https://doi.org/10.3390/microorganisms10122517 - 19 Dec 2022

Cited by 8 | Viewed by 3648

Abstract

Horses are large non-ruminant herbivores and rely on microbial fermentation for energy, with more than half of their maintenance energy requirement coming from microbial fermentation occurring in their enlarged caecum and colon. To achieve that, the gastro-intestinal tract (GIT) of horses harbors a [...] Read more.

Horses are large non-ruminant herbivores and rely on microbial fermentation for energy, with more than half of their maintenance energy requirement coming from microbial fermentation occurring in their enlarged caecum and colon. To achieve that, the gastro-intestinal tract (GIT) of horses harbors a broad range of various microorganisms, differing in each GIT segment, which are essential for efficient utilization of feed, especially to use nutrients that are not or little degraded by endogenous enzymes. In addition, like in other animal species, the GIT microbiota is in permanent interplay with the host’s cells and is involved in a lot of functions among which inflammation, immune homeostasis, and energy metabolism. As for other animals and humans, the horse gut microbiome is sensitive to diet, especially consumption of starch, fiber, and fat. Age, breeds, stress during competitions, transportation, and exercise may also impact the microbiome. Because of its size and its complexity, the equine GIT microbiota is prone to perturbations caused by external or internal stressors that may result in digestive diseases like gastric ulcer, diarrhea, colic, or colitis, and that are thought to be linked with systemic diseases like laminitis, equine metabolic syndrome or obesity. Thus, in this review we aim at understanding the common core microbiome -in terms of structure and function- in each segment of the GIT, as well as identifying potential microbial biomarkers of health or disease which are crucial to anticipate putative perturbations, optimize global practices and develop adapted nutritional strategies and personalized nutrition. Full article

(This article belongs to the Special Issue Gut Microbiota and the Impact on Animal Models of Disease)

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17 pages, 3365 KiB

Open AccessArticle

Disalicylic Acid Provides Effective Control of Pectobacterium brasiliense

by Sapir Tuizer, Manoj Pun, Iris Yedidia and Zohar Kerem

Microorganisms 2022, 10(12), 2516; https://doi.org/10.3390/microorganisms10122516 - 19 Dec 2022

Viewed by 1375

Abstract

Bis(2-carboxyphenyl) succinate (disalicylic acid; DSA) is composed of two salicylic acids connected by a succinyl linker. Here, we propose its use as a new, synthetic plant-protection agent. DSA was shown to control Pectobacterium brasiliense, an emerging soft-rot pathogen of potato and ornamental [...] Read more.

Bis(2-carboxyphenyl) succinate (disalicylic acid; DSA) is composed of two salicylic acids connected by a succinyl linker. Here, we propose its use as a new, synthetic plant-protection agent. DSA was shown to control Pectobacterium brasiliense, an emerging soft-rot pathogen of potato and ornamental crops, at minimal inhibitory concentrations (MIC) lower than those of salicylic acid. Our computational-docking analysis predicted that DSA would inhibit the quorum-sensing (QS) synthase of P. brasiliense ExpI more strongly than SA would. In fact, applying DSA to P. brasiliense inhibited its biofilm formation, secretion of plant cell wall-degrading enzymes, motility and production of acyl–homoserine lactones (AHL) and, subsequently, impaired its virulence. DSA also inhibited the production of AHL by a QS-negative Escherichia coli strain (DH5α) that had been transformed with P. brasiliense AHL synthase, as demonstrated by the biosensors Chromobacterium violaceaum CV026 and E. coli pSB401. Inhibition of the QS machinery appears to be one of the mechanisms by which DSA inhibits specific virulence determinants. A new route is proposed for the synthesis of DSA, which holds greater potential for use as an anti-virulence agent than its precursor SA. Based on these findings, DSA is an excellent candidate for repurposing for new applications. Full article

(This article belongs to the Special Issue Dickeya and Pectobacterium: Ecology, Pathology and Plant Protection 2.0)

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13 pages, 2632 KiB

Open AccessArticle

Probiotic Properties of Chicken-Derived Highly Adherent Lactic Acid Bacteria and Inhibition of Enteropathogenic Bacteria in Caco-2 Cells

by Pudi Wang, Songbiao Chen, Chengshui Liao, Yanyan Jia, Jing Li, Ke Shang, Jian Chen, Pinghua Cao, Wang Li, Yuanxiao Li, Zuhua Yu and Ke Ding

Microorganisms 2022, 10(12), 2515; https://doi.org/10.3390/microorganisms10122515 - 19 Dec 2022

Cited by 3 | Viewed by 1944

Abstract

Lactic acid bacteria (LAB) as probiotic candidates have various beneficial functions, such as regulating gut microbiota, inhibiting intestinal pathogens, and improving gut immunity. The colonization of the intestine is a prerequisite for probiotic function. Therefore, it is necessary to screen the highly adherent [...] Read more.

Lactic acid bacteria (LAB) as probiotic candidates have various beneficial functions, such as regulating gut microbiota, inhibiting intestinal pathogens, and improving gut immunity. The colonization of the intestine is a prerequisite for probiotic function. Therefore, it is necessary to screen the highly adherent LAB. In this study, the cell surface properties, such as hydrophobicity, auto-aggregation, co-aggregation, and adhesion abilities of the six chicken-derived LAB to Caco-2 cells were investigated. All six strains showed different hydrophobicity (21.18–95.27%), auto-aggregation (13.61–30.17%), co-aggregation with Escherichia coli ATCC 25922 (10.23–36.23%), and Salmonella enterica subsp. enterica serovar Typhimurium ATCC 13311 (11.71–39.35%), and adhesion to Caco-2 cells (8.57–26.37%). Pediococcus pentosaceus 2–5 and Lactobacillus reuteri L-3 were identified as the strains with strong adhesion abilities (26.37% and 21.57%, respectively). Moreover, these strains could survive in a gastric acid environment at pH 2, 3, and 4 for 3 h and in a bile salt environment at 0.1%, 0.2%, and 0.3% (w/v) concentration for 6 h. Furthermore, the cell-free supernatant of P. pentosaceus 2–5 and L. reuteri L-3 inhibited the growth of enteropathogenic bacteria and the strains inhibited the adhesion of these pathogens to Caco-2 cells. In this study, these results suggested that P. pentosaceus 2–5 and L. reuteri L-3, isolated from chicken intestines might be good probiotic candidates to be used as feed additives or delivery vehicles of biologically active substances. Full article

(This article belongs to the Special Issue Bacteria and Fungi Probiotics)

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13 pages, 5051 KiB

Open AccessArticle

Enzymatic Characterization of Unused Biomass Degradation Using the Clostridium cellulovorans Cellulosome

by Mohamed Yahia Eljonaid, Hisao Tomita, Fumiyoshi Okazaki and Yutaka Tamaru

Microorganisms 2022, 10(12), 2514; https://doi.org/10.3390/microorganisms10122514 - 19 Dec 2022

Viewed by 1383

Abstract

The cellulolytic system of Clostridium cellulovorans mainly consisting of a cellulosome that synergistically collaborates with non-complexed enzymes was investigated using cellulosic biomass. The cellulosomes were isolated from the culture supernatants with shredded paper, rice straw and sugarcane bagasse using crystalline cellulose. Enzyme solutions, [...] Read more.

The cellulolytic system of Clostridium cellulovorans mainly consisting of a cellulosome that synergistically collaborates with non-complexed enzymes was investigated using cellulosic biomass. The cellulosomes were isolated from the culture supernatants with shredded paper, rice straw and sugarcane bagasse using crystalline cellulose. Enzyme solutions, including the cellulosome fractions, were analyzed by SDS-PAGE and Western blot using an anti-CbpA antibody. As a result, C. cellulovorans was able to completely degrade shredded paper for 9 days and to be continuously cultivated by the addition of new culture medium containing shredded paper, indicating, through TLC analysis, that its degradative products were glucose and cellobiose. Regarding the rice straw and sugarcane bagasse, while the degradative activity of rice straw was most active using the cellulosome in the culture supernatant of rice straw medium, that of sugarcane bagasse was most active using the cellulosome from the supernatant of cellobiose medium. Based on these results, no alcohols were found when C. acetobutylicum was cultivated in the absence of C. cellulovorans as it cannot degrade the cellulose. While 1.5 mM of ethanol was produced with C. cellulovorans cultivation, both n-butanol (1.67 mM) and ethanol (1.89 mM) were detected with the cocultivation of C. cellulovorans and C. acetobutylicum. Regarding the enzymatic activity evaluation against rice straw and sugarcane bagasse, the rice straw cellulosome fraction was the most active when compared against rice straw. Furthermore, since we attempted to choose reaction conditions more efficiently for the degradation of sugarcane bagasse, a wet jet milling device together with L-cysteine as a reducing agent was used. As a result, we found that the degradation activity was almost twice as high with 10 mM L-cysteine compared with without it. These results will provide new insights for biomass utilization. Full article

(This article belongs to the Section Microbial Biotechnology)

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19 pages, 5636 KiB

Open AccessArticle

Exploring Diversity and Polymer Degrading Potential of Epiphytic Bacteria Isolated from Marine Macroalgae

by Pravin Kumar, Ashish Verma, Shiva S. Sundharam, Anup Kumar Ojha and Srinivasan Krishnamurthi

Microorganisms 2022, 10(12), 2513; https://doi.org/10.3390/microorganisms10122513 - 19 Dec 2022

Cited by 5 | Viewed by 2511

Abstract

The macroalgae surface allows specific bacterial communities to colonize, resulting in complex biological interactions. In recent years, several researchers have studied the diversity and function of the epiphytic bacteria associated with algal host, but largely these interactions remain underexplored. In the present study [...] Read more.

The macroalgae surface allows specific bacterial communities to colonize, resulting in complex biological interactions. In recent years, several researchers have studied the diversity and function of the epiphytic bacteria associated with algal host, but largely these interactions remain underexplored. In the present study we analysed the cultivable diversity and polymer degradation potential of epiphytic bacteria associated with five different marine macroalgae (Sargassum, Ulva, Padina, Dictyota and Pterocladia sp.) sampled from the central west coast of India. Out of the total 360 strains isolated, purified and preserved, about 238 strains were identified through 16S rRNA gene sequence analysis and processed for polymer (cellulose, pectin, xylan and starch) degrading activities. Phylogeny placed the strains within the classes Actinobacteria, Bacilli, Alpha-proteobacteria, and Gamma-proteobacteria and clustered them into 45 genera, wherein Vibrio, Bacillus, Pseudoalteromonas, Alteromonas, Staphylococcus and Kocuria spp. were the most abundant with 20 strains identified as potentially novel taxa within the genera Bacillus, Cellulosimicrobium, Gordonia, Marinomonas, Vibrio, Luteimonas and Pseudoalteromonas. In terms of polymer hydrolysis potential, 61.3% had xylanase activity, while 59.7%, 58.8%, and 52.2% had amylase, cellulase, and pectinase activity, respectively. Overall, 75.6% of the strains degraded more than one polysaccharide, 24% degraded all polymers, while nine strains (3.8%) degraded raw sugarcane bagasse. This study showed great potential for seaweed-associated bacteria in the bio-remediation of agro-waste based raw materials, which can be employed in the form of green technology. Full article

(This article belongs to the Special Issue Microbial Communities on the Surface of Algae)

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Graphical abstract

14 pages, 1236 KiB

Open AccessReview

Ciliate Morpho-Taxonomy and Practical Considerations before Deploying Metabarcoding to Ciliate Community Diversity Surveys in Urban Receiving Waters

by Yan Zhao and Gaytha A. Langlois

Microorganisms 2022, 10(12), 2512; https://doi.org/10.3390/microorganisms10122512 - 19 Dec 2022

Cited by 1 | Viewed by 1888

Abstract

Disentangling biodiversity and community assembly effects on ecosystem function has always been an important topic in ecological research. The development and application of a DNA metabarcoding method has fundamentally changed the way we describe prokaryotic communities and estimate biodiversity. Compared to prokaryotes (bacteria [...] Read more.

Disentangling biodiversity and community assembly effects on ecosystem function has always been an important topic in ecological research. The development and application of a DNA metabarcoding method has fundamentally changed the way we describe prokaryotic communities and estimate biodiversity. Compared to prokaryotes (bacteria and archaea), the eukaryotic microbes (unicellular eukaryotes) also fulfill extremely important ecological functions in different ecosystems regarding their intermediate trophic positions. For instance, ciliated microbes (accounting for a substantial portion of the diversity of unicellular eukaryotes) perform pivotal roles in microbial loops and are essential components in different ecosystems, especially in water purification processes. Therefore, the community composition of ciliated species has been widely utilized as a proxy for water quality and biological assessment in urban river ecosystems and WWTPs (wastewater treatment plants). Unfortunately, investigating the dynamic changes and compositions in ciliate communities relies heavily on existing morpho-taxonomical descriptions, which is limited by traditional microscopic approaches. To deal with this dilemma, we discuss the DNA-based taxonomy of ciliates, the relative merits and challenges of deploying its application using DNA metabarcoding for surveys of ciliate community diversity in urban waterbodies, and provide suggestions for minimizing relevant sources of biases in its implementation. We expect that DNA metabarcoding could untangle relationships between community assembly and environmental changes affecting ciliate communities. These analyses and discussions could offer a replicable method in support of the application of evaluating communities of ciliated protozoa as indicators of urban freshwater ecosystems. Full article

(This article belongs to the Special Issue Ciliates as Model Organisms: From ‘omics’ to Genetics, Ecology and Signaling)

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9 pages, 1597 KiB

Open AccessCommunication

Aggregatibacter actinomycetemcomitans and Filifactor alocis as Associated with Periodontal Attachment Loss in a Cohort of Ghanaian Adolescents

by Zeinab Razooqi, Carola Höglund Åberg, Francis Kwamin, Rolf Claesson, Dorte Haubek, Jan Oscarsson and Anders Johansson

Microorganisms 2022, 10(12), 2511; https://doi.org/10.3390/microorganisms10122511 - 19 Dec 2022

Cited by 5 | Viewed by 1431

Abstract

The aims of the present study were to document the presence of Aggregatibacter actinomyctemcomitans and the emerging oral pathogen Filifactor alocis, as well as to identify genotypes of these bacterial species with enhanced virulence. In addition, these data were analyzed in relation [...] Read more.

The aims of the present study were to document the presence of Aggregatibacter actinomyctemcomitans and the emerging oral pathogen Filifactor alocis, as well as to identify genotypes of these bacterial species with enhanced virulence. In addition, these data were analyzed in relation to periodontal pocket depth (PPD) and the progression of PPD from the sampled periodontal sites during a two-year period. Subgingival plaque samples were collected from 172 periodontal pockets of 68 Ghanaian adolescents. PPD at sampling varied from 3–14 mm and the progression from baseline, i.e., two years earlier up to 8 mm. The levels of A. actinomycetemcomitans and F. alocis were determined with quantitative PCR. The highly leukotoxic JP2-genotype of A. actinomycetemcomitans and the ftxA a gene of F. alocis, encoding a putative Repeats-in-Toxin (RTX) protein, were detected with conventional PCR. The prevalence of A. actinomycetemcomitans was 57%, and 14% of the samples contained the JP2 genotype. F. alocis was detected in 92% of the samples and the ftxA gene in 52%. The levels of these bacterial species were significantly associated with enhanced PPD and progression, with a more pronounced impact in sites positive for the JP2 genotype or the ftxA gene. Taken together, the results indicate that the presence of both A. actinomycetemcomitans and F. alocis with their RTX proteins are linked to increased PPD and progression of disease. Full article

(This article belongs to the Special Issue Interaction between Oral Microbiota and Immunity in Health and Diseases)

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14 pages, 2990 KiB

Open AccessArticle

Improvement of Zn (II) and Cd (II) Biosorption by Priestia megaterium PRJNA526404 Isolated from Agricultural Waste Water

by Othman M. Alzahrani, Aly E. Abo-Amer and Rehab M. Mohamed

Microorganisms 2022, 10(12), 2510; https://doi.org/10.3390/microorganisms10122510 - 19 Dec 2022

Cited by 3 | Viewed by 1538

Abstract

Heavy metals are considered as dangerous pollutants even in relatively low concentrations. Biosorption is an ecofriendly technology that uses microbial biomasses for adsorbing heavy metals from wastewater on their surfaces based on physicochemical pathways. Ten agricultural wastewater samples were collected from different sites [...] Read more.

Heavy metals are considered as dangerous pollutants even in relatively low concentrations. Biosorption is an ecofriendly technology that uses microbial biomasses for adsorbing heavy metals from wastewater on their surfaces based on physicochemical pathways. Ten agricultural wastewater samples were collected from different sites in Sohag Governorate, Egypt. One hundred and nineteen zinc and cadmium-resistant bacterial isolates were recovered from the water samples. Interestingly, the isolate R1 was selected as the most resistant to Zn²⁺ and Cd²⁺. This isolate was morphologically and biochemically characterized and identified by sequencing of 16S rRNA gene as Priestia megaterium, and then deposited in the GenBank database under the accession number PRJNA526404. Studying the effects of pH and contact time on the biosorption process revealed that the maximum biosorption was achieved within 50 min at pH 7 and 8 for Zn²⁺ and Cd²⁺, respectively, by the living and lyophelized biomass of Priestia megaterium PRJNA526404. The preliminary characterization of the main chemical groups present on the cell wall, which are responsible for heavy metal biosorption, was performed by Infrared analysis (IR). Kinetics studies revealed that data were fitted towards the models hypothesized by Langmuir and Freundlich isotherm equations. The maximum capacity values (q_max) for biosorption of zinc and cadmium reached by using living and lyophelized biomass were 196.08; 227.27 and 178.57; 212.777 mg/g, respectively, and it was indicated that lyophilization improved efficiency of the biomass to heavy metals compared to living cells. The results indicated that Priestia megaterium PRJNA526404 had good application prospect in cadmium and zinc water remediation. Full article

(This article belongs to the Section Environmental Microbiology)

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11 pages, 1526 KiB

Open AccessCommunication

Allelic Variants of P66 Gene in Borrelia bavariensis Isolates from Patients with Ixodid Tick-Borne Borreliosis

by Kristina Golidonova, Eduard Korenberg, Ekaterina Krupinskaya, Vera Matrosova and Alexander Gintsburg

Microorganisms 2022, 10(12), 2509; https://doi.org/10.3390/microorganisms10122509 - 19 Dec 2022

Viewed by 1587

Abstract

Protein P66 is one of the crucial virulence factors of Borrelia, inducing the production of specific antibodies in patients with ixodid tick-borne borreliosis (ITBB). Various species of Borrelia are characterized by genetic variability of the surface-exposed loop of P66. However, little is [...] Read more.

Protein P66 is one of the crucial virulence factors of Borrelia, inducing the production of specific antibodies in patients with ixodid tick-borne borreliosis (ITBB). Various species of Borrelia are characterized by genetic variability of the surface-exposed loop of P66. However, little is known about this variability in Borrelia bavariensis. Here we describe the variability of the nucleotide sequences of P66 gene locus in isolates of B. bavariensis. Analysis of nucleotide sequences of P66 in 27 isolates of B. bavariensis from ITBB patients revealed three allelic variants of this gene. The alignment score of amino acid sequences in the isolates showed amino acid replacements in various positions confirming the presence of three allelic variants. Two of them are characteristic only for some isolates of B. bavariensis of the Eurasian gene pool from various parts of the geographic ranges of B. bavariensis from various samples. At least three allelic variants of P66 B. bavariensis have been identified, which have different amino acid expression, occur with different frequency in ITBB patients and, presumably, can have different effects on the course of the infection. Full article

(This article belongs to the Special Issue Advanced Research on Ticks and Tick-Borne Diseases)

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22 pages, 3938 KiB

Open AccessArticle

Genome-Based Analysis of Virulence Factors and Biofilm Formation in Novel P. aeruginosa Strains Isolated from Household Appliances

by Annika Kiel, Ines Creutz, Christian Rückert, Bernhard Peter Kaltschmidt, Andreas Hütten, Karsten Niehaus, Tobias Busche, Barbara Kaltschmidt and Christian Kaltschmidt

Microorganisms 2022, 10(12), 2508; https://doi.org/10.3390/microorganisms10122508 - 19 Dec 2022

Cited by 1 | Viewed by 2653

Abstract

In household washing machines, opportunistic pathogens such as Pseudomonas aeruginosa are present, which represent the household as a possible reservoir for clinical pathogens. Here, four novel P. aeruginosa strains, isolated from different sites of household appliances, were investigated regarding their biofilm formation. Only [...] Read more.

In household washing machines, opportunistic pathogens such as Pseudomonas aeruginosa are present, which represent the household as a possible reservoir for clinical pathogens. Here, four novel P. aeruginosa strains, isolated from different sites of household appliances, were investigated regarding their biofilm formation. Only two isolates showed strong surface-adhered biofilm formation. In consequence of these phenotypic differences, we performed whole genome sequencing using Oxford Nanopore Technology together with Illumina MiSeq. Whole genome data were screened for the prevalence of 285 virulence- and biofilm-associated genes as well as for prophages. Linking biofilm phenotypes and parallelly appearing gene compositions, we assume a relevancy of the las quorum sensing system and the phage-encoded bacteriophage control infection gene bci, which was found on integrated phi297 DNA in all biofilm-forming isolates. Additionally, only the isolates revealing strong biofilm formation harbored the ϕCTX-like prophage Dobby, implicating a role of this prophage on biofilm formation. Investigations on clinically relevant pathogens within household appliances emphasize their adaptability to harsh environments, with high concentrations of detergents, providing greater insights into pathogenicity and underlying mechanisms. This in turn opens the possibility to map and characterize potentially relevant strains even before they appear as pathogens in society. Full article

(This article belongs to the Section Biofilm)

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18 pages, 1389 KiB

Open AccessReview

Dietary Fiber Intake and Gut Microbiota in Human Health

by Jiongxing Fu, Yan Zheng, Ying Gao and Wanghong Xu

Microorganisms 2022, 10(12), 2507; https://doi.org/10.3390/microorganisms10122507 - 18 Dec 2022

Cited by 25 | Viewed by 9003

Abstract

Dietary fiber is fermented by the human gut microbiota, producing beneficial microbial metabolites, such as short-chain fatty acids. Over the last few centuries, dietary fiber intake has decreased tremendously, leading to detrimental alternations in the gut microbiota. Such changes in dietary fiber consumption [...] Read more.

Dietary fiber is fermented by the human gut microbiota, producing beneficial microbial metabolites, such as short-chain fatty acids. Over the last few centuries, dietary fiber intake has decreased tremendously, leading to detrimental alternations in the gut microbiota. Such changes in dietary fiber consumption have contributed to the global epidemic of obesity, type 2 diabetes, and other metabolic disorders. The responses of the gut microbiota to the dietary changes are specific to the type, amount, and duration of dietary fiber intake. The intricate interplay between dietary fiber and the gut microbiota may provide clues for optimal intervention strategies for patients with type 2 diabetes and other noncommunicable diseases. In this review, we summarize current evidence regarding dietary fiber intake, gut microbiota modulation, and modification in human health, highlighting the type-specific cutoff thresholds of dietary fiber for gut microbiota and metabolic outcomes. Full article

(This article belongs to the Special Issue Feature Reviews in Gut Microbiota)

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10 pages, 597 KiB

Open AccessArticle

Stenotrophomonas maltophilia Epidemiology, Resistance Characteristics, and Clinical Outcomes: Understanding of the Recent Three Years’ Trends

by Taghreed A. Hafiz, Esraa Aldawood, Alaa Albloshi, Shahad S. Alghamdi, Murad A. Mubaraki, Ahmed S. Alyami and Marwh G. Aldriwesh

Microorganisms 2022, 10(12), 2506; https://doi.org/10.3390/microorganisms10122506 - 18 Dec 2022

Cited by 15 | Viewed by 2624

Abstract

Background. Stenotrophomonas maltophilia is an emerging pathogen classified as a public health concern, that infects critically ill patients and has expressed resistance against antimicrobial therapy. The aim of this study was to examine the epidemiological pattern, resistance characteristics and clinical outcomes of S. [...] Read more.

Background. Stenotrophomonas maltophilia is an emerging pathogen classified as a public health concern, that infects critically ill patients and has expressed resistance against antimicrobial therapy. The aim of this study was to examine the epidemiological pattern, resistance characteristics and clinical outcomes of S. maltophilia infections in hospitalized patients. Methods. The study included 393 S. maltophilia isolates from different clinical specimens as well as the clinical data of 209 Intensive Care Unit (ICU) patients. The patients’ data were obtained from medical and laboratory files. Descriptive statistics and a univariate analysis were used to report and compare the demographics, clinical data, and outcomes. Results. The S. maltophilia was mostly isolated from the respiratory specimens of ICU patients. The adult patients were more likely to develop serious infections and worse outcomes than were pediatric patients. The most common co-infecting pathogens were SARS-CoV2 and Pseudomonas aeruginosa. The death rate was 44.5% and increased to 47.1% in the case of a respiratory infection. Septic shock was the most significant predictor of mortality. Older age and mechanical ventilation were independent and significant risk factors that worsened the outcomes in patients with respiratory infections. Conclusions. The identification of S. maltophilia as a threat highlights the importance of surveillance studies in this region. Full article

(This article belongs to the Section Public Health Microbiology)

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13 pages, 5414 KiB

Open AccessArticle

Grinding Beads Influence Microbial DNA Extraction from Organic-Rich Sub-Seafloor Sediment

by Jingjing Niu, Hong Chen, Lanlan Cai, Maoqiu He, Rui Zhang and Long Wang

Microorganisms 2022, 10(12), 2505; https://doi.org/10.3390/microorganisms10122505 - 18 Dec 2022

Cited by 1 | Viewed by 1647

Abstract

Sub-seafloor sediment is the largest microbial habitat on Earth. The study of microbes in sub-seafloor sediment is largely limited by the technical challenge of acquiring ambient microbial DNA because of sediment heterogeneity. Changes in the extraction method, even just by one step, can [...] Read more.

Sub-seafloor sediment is the largest microbial habitat on Earth. The study of microbes in sub-seafloor sediment is largely limited by the technical challenge of acquiring ambient microbial DNA because of sediment heterogeneity. Changes in the extraction method, even just by one step, can affect the extraction yields for complicated sediment samples. In this work, sub-seafloor sediment samples from the Baltic Sea with high organic carbon content were used to evaluate the influence of different grinding beads on DNA extraction. We found that the grinding beads can affect the DNA extraction from the organic-matter- and biosiliceous-clay-rich samples. A mixture of 0.5-mm and 0.1-mm grinding beads exhibited higher DNA yields and recovered more unique taxa than other bead combinations, such as Stenotrophomonas from Gammaproteobacteria and Leptotrichia from Fusobacteria; therefore, these beads are more suitable than the others for DNA extraction from the samples used in this study. This advantage might be magnified in samples with high biomass. On the contrary, the use of only small beads might lead to underestimation for certain Gram-positive strains. Overall, the discovery of abundant widespread deep biosphere clades in our samples indicated that our optimized DNA extraction method successfully recovered the in situ microbial community. Full article

(This article belongs to the Section Environmental Microbiology)

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17 pages, 1520 KiB

Open AccessArticle

Natural Infections of Potato Plants Grown from Minitubers with Blackleg-Causing Soft Rot Pectobacteriaceae

by Jan van der Wolf, Marjon Krijger, Odette Mendes, Viola Kurm and Jack Gros

Microorganisms 2022, 10(12), 2504; https://doi.org/10.3390/microorganisms10122504 - 17 Dec 2022

Cited by 3 | Viewed by 1778

Abstract

Information on the infection incidence of blackleg-causing soft rot Pectobacteriaceae (BL-SRP) in potato crops grown from minitubers (PB1-crop) and the distribution of BL-SRP in individual plants was collected during a two-year survey conducted at five potato growers located in the Netherlands. In the [...] Read more.

Information on the infection incidence of blackleg-causing soft rot Pectobacteriaceae (BL-SRP) in potato crops grown from minitubers (PB1-crop) and the distribution of BL-SRP in individual plants was collected during a two-year survey conducted at five potato growers located in the Netherlands. In the last weeks before haulm destruction, leaves, stems, and tubers of 100 or 200 plants were analyzed separately for the presence of Pectobacterium parmentieri, P. brasiliense, P. atrosepticum, and Dickeya spp. Extracted plant parts enriched for BL-SRP were analyzed with TaqMan assays specific for the detection of blackleg-causing BL-SRP. In 2019, low incidences of P. parmentieri (1–6%) in leaves were found at four growing sites. At one farm, reactions were detected in TaqMan assays for D. zeae and D. chrysanthemi in leaves. In 2020, the crops of two growers were largely free from BL-SRP. At one farm, a high infection incidence (21%) was found for D. fangzhongdai in tubers. The isolated pathogen was able to cause potato blackleg. At two other farms, high infection incidences in tubers were found with P. brasiliense (35–39%) and P. parmentieri (12–19%), whereas the incidence of P. brasiliense in leaves was also high (8%). In conclusion, high infection incidences with BL-SRP in potatoes can be found in a PB1 crop at the end of the growing season. Infections in individual plants were found either in tubers or in leaves. The potential sources of initial infection are discussed. Full article

(This article belongs to the Special Issue Dickeya and Pectobacterium: Ecology, Pathology and Plant Protection 2.0)

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17 pages, 2602 KiB

Open AccessArticle

Ralstonia solanacearum Facing Spread-Determining Climatic Temperatures, Sustained Starvation, and Naturally Induced Resuscitation of Viable but Non-Culturable Cells in Environmental Water

by Belén Álvarez, María M. López and Elena G. Biosca

Microorganisms 2022, 10(12), 2503; https://doi.org/10.3390/microorganisms10122503 - 16 Dec 2022

Cited by 6 | Viewed by 2089

Abstract

Ralstonia solanacearum is a bacterial phytopathogen affecting staple crops, originally from tropical and subtropical areas, whose ability to survive in temperate environments is of concern under global warming. In this study, two R. solanacearum strains from either cold or warm habitats were stressed [...] Read more.

Ralstonia solanacearum is a bacterial phytopathogen affecting staple crops, originally from tropical and subtropical areas, whose ability to survive in temperate environments is of concern under global warming. In this study, two R. solanacearum strains from either cold or warm habitats were stressed by simultaneous exposure to natural oligotrophy at low (4 °C), temperate (14 °C), or warm (24 °C) temperatures in environmental water. At 4 °C, the effect of temperature was higher than that of oligotrophy, since R. solanacearum went into a viable but non-culturable (VBNC) state, which proved to be dependent on water nutrient contents. Resuscitation was demonstrated in vitro and in planta. At 14 °C and 24 °C, the effect of oligotrophy was higher than that of temperature on R. solanacearum populations, displaying starvation-survival responses and morphological changes which were stronger at 24 °C. In tomato plants, starved, cold-induced VBNC, and/or resuscitated cells maintained virulence. The strains behaved similarly regardless of their cold or warm areas of origin. This work firstly describes the natural nutrient availability of environmental water favoring R. solanacearum survival, adaptations, and resuscitation in conditions that can be found in natural settings. These findings will contribute to anticipate the ability of R. solanacearum to spread, establish, and induce disease in new geographical and climatic areas. Full article

(This article belongs to the Special Issue Plant Pathogenic Microorganisms: State-of-the-Art Research in Spain)

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15 pages, 2325 KiB

Open AccessArticle

Rhizobium pusense-Mediated Selenium Nanoparticles–Antibiotics Combinations against Acanthamoeba sp.

by Pradnya B. Nikam, Jitendra D. Salunkhe, Kiran R. Marathe, Mousa A. Alghuthaymi, Kamel A. Abd-Elsalam and Satish V. Patil

Microorganisms 2022, 10(12), 2502; https://doi.org/10.3390/microorganisms10122502 - 16 Dec 2022

Cited by 2 | Viewed by 1625

Abstract

Severe ocular infections by Acanthamoeba sp. lead to keratitis, resulting in irreversible vision loss in immune-compromised individuals. When a protozoal infection spreads to neural tissues, it causes granulomatous encephalitis, which can be fatal. Treatment often takes longer due to the transition of amoeba [...] Read more.

Severe ocular infections by Acanthamoeba sp. lead to keratitis, resulting in irreversible vision loss in immune-compromised individuals. When a protozoal infection spreads to neural tissues, it causes granulomatous encephalitis, which can be fatal. Treatment often takes longer due to the transition of amoeba from trophozoites to cyst stages, cyst being the dormant form of Acanthamoeba. A prolonged use of therapeutic agents, such as ciprofloxacin (Cipro), results in severe side effects; thus, it is critical to improve the therapeutic efficacy of these widely used antibiotics, possibly by limiting the drug-sensitive protozoal-phase transition to cyst formation. Owing to the biomedical potential of selenium nanoparticles (SeNPs), we evaluated the synergistic effects of ciprofloxacin and Rhizobium pusense–biogenic SeNPs combination. SeNPs synthesized using Rhizobium pusense isolated from root nodules were characterized using UV–Visible spectrophotometer, FT-IR, SEM with EDX, particle size analysis, and Zeta potential. The combination was observed to reduce the sub-lethal dose of Cipro, which may help reduce its side effects. The selenium and ciprofloxacin (SeNPs–Cipro) combination reduced the LC₅₀ by 33.43%. The anti-protozoal efficacy of SeNPs–Cipro was found to transduce through decreased protozoal-cyst formations and the inhibition of the galactosidase and protease enzymes of trophozoites. Furthermore, high leakage of sugar, proteins, and amino acids during the SeNPs–Cipro treatment was one primary reason for killing the trophozoites. These experimental results may be helpful in the further pre-clinical evaluation of SeNPs–Cipro to combat protozoal infections. Future studies for combinations of SeNPs with other antibiotics need to be conducted to know the potential of SeNPs against antibiotic resistance in Acanthamoeba. Full article

(This article belongs to the Special Issue Microbial Nanotechnology)

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15 pages, 2420 KiB

Open AccessArticle

Living and Regenerative Material Encapsulating Self-Assembled Shewanella oneidensis-CdS Hybrids for Photocatalytic Biodegradation of Organic Dyes

by Mingyue Tao, Chenyang Jin, Hongfei Lu, Kai Jin, Lin Yu, Jinliang Liu, Jing Zhang, Xiaohui Zhu and Yihan Wu

Microorganisms 2022, 10(12), 2501; https://doi.org/10.3390/microorganisms10122501 - 16 Dec 2022

Cited by 2 | Viewed by 1933

Abstract

Reductive biodegradation by microorganisms has been widely explored for detoxifying recalcitrant contaminants; however, the biodegradation capacity of microbes is limited by the energy level of the released electrons. Here, we developed a method to self-assemble Shewanella oneidensis-CdS nanoparticle hybrids with significantly improved [...] Read more.

Reductive biodegradation by microorganisms has been widely explored for detoxifying recalcitrant contaminants; however, the biodegradation capacity of microbes is limited by the energy level of the released electrons. Here, we developed a method to self-assemble Shewanella oneidensis-CdS nanoparticle hybrids with significantly improved reductive biodegradation capacity and constructed a living material by encapsulating the hybrids in hydrogels. The material confines the nano-bacteria hybrids and protects them from environmental stress, thus improving their recyclability and long-term stability (degradation capacity unhindered after 4 weeks). The developed living materials exhibited efficient photocatalytic biodegradation of various organic dyes including azo and nitroso dyes. This study highlights the feasibility and benefits of constructing self-assembled nano-bacteria hybrids for bioremediation and sets the stage for the development of novel living materials from nano-bacteria hybrids. Full article

(This article belongs to the Special Issue Microbial Nanotechnology)

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10 pages, 1123 KiB

Open AccessArticle

Attenuation of Pseudomonas aeruginosa Virulence by Pomegranate Peel Extract

by Samuele Peppoloni, Bruna Colombari, Davide Tagliazucchi, Alessandra Odorici, Cristiano Ventrucci, Aida Meto and Elisabetta Blasi

Microorganisms 2022, 10(12), 2500; https://doi.org/10.3390/microorganisms10122500 - 16 Dec 2022

Cited by 3 | Viewed by 1474

Abstract

Pseudomonas aeruginosa is an opportunistic pathogen often responsible for biofilm-associated infections. The high adhesion of bacterial cells onto biotic/abiotic surfaces is followed by production of an extracellular polysaccharidic matrix and formation of a sessile community (the biofilm) by the release of specific quorum-sensing [...] Read more.

Pseudomonas aeruginosa is an opportunistic pathogen often responsible for biofilm-associated infections. The high adhesion of bacterial cells onto biotic/abiotic surfaces is followed by production of an extracellular polysaccharidic matrix and formation of a sessile community (the biofilm) by the release of specific quorum-sensing molecules, named autoinducers (AI). When the concentrations of AI reach a threshold level, they induce the expression of many virulence genes, including those involved in biofilm formation, motility, pyoverdine and pyocyanin release. P. aeruginosa embedded into biofilm becomes resistant to both conventional drugs and the host’s immune response. Accordingly, biofilm-associated infections are a major clinical problem underlining the need for new antimicrobial therapies. In this study, we evaluated the effects of pomegranate peel extract (PomeGr) in vitro on P. aeruginosa growth and biofilm formation; moreover, the release of four AI was assessed. The phenolic profile of PomeGr, exposed or not to bacteria, was determined by high-performance liquid chromatography coupled to electrospray ionization mass spectrometry (HPLC-ESI-MS) analysis. We found that bacterial growth, biofilm production and AI release were impaired upon PomeGr treatment. In addition, the PomeGr phenolic content was also markedly hampered following incubation with bacterial cells. In particular, punicalagin, punicalin, pedunculagin, granatin, di-(HHDP-galloyl-hexoside) pentoside and their isomers were highly consumed. Overall, these results provide novel insights on the ability of PomeGr to attenuate P. aeruginosa virulence; moreover, the AI impairment and the observed consumption of specific phenolic compounds may offer new tools in designing innovative therapeutic approaches against bacterial infections. Full article

(This article belongs to the Special Issue Feature Papers in Microbial Biofilms)

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13 pages, 3696 KiB

Open AccessArticle

Cefsulodin and Vancomycin: A Supplement for Chromogenic Coliform Agar for Detection of Escherichia coli and Coliform Bacteria from Different Water Sources

by Michael Schalli, Sarah Maria Inwinkl, Sabine Platzer, Rita Baumert, Franz F. Reinthaler, Petra Ofner-Kopeinig and Doris Haas

Microorganisms 2022, 10(12), 2499; https://doi.org/10.3390/microorganisms10122499 - 16 Dec 2022

Cited by 5 | Viewed by 2252

Abstract

Background microorganism growth on Chromogenic Coliform Agar (CCA) can be challenging. For this reason, a new alternative method with a Cefsulodin/Vancomycin (CV)-supplemented CCA should be developed in this study. CCA supplemented with CV was validated according to ÖNORM EN ISO 16140-4:2021 using water [...] Read more.

Background microorganism growth on Chromogenic Coliform Agar (CCA) can be challenging. For this reason, a new alternative method with a Cefsulodin/Vancomycin (CV)-supplemented CCA should be developed in this study. CCA supplemented with CV was validated according to ÖNORM EN ISO 16140-4:2021 using water from natural sources in Styria, Austria. Results show that the alternative method using the supplemented CCA has similar values in relation to sensitivity (82.2%), specificity (98.6%) and higher selectivity (59%) compared to the reference method. Repeatability and reproducibility were acceptable for the alternative method and showed similar results with the reference method. The alternative method shows a very low false positive rate and a low false negative rate paired with good performance regarding the inclusion study. The exclusion study shows the advantage of our method by suppressing background microorganisms and facilitating the process of enumeration of Escherichia coli and other coliform bacteria on CCA plates. Aeromonas hydrophila and Pseudomonas aeruginosa growth was inhibited using the supplement. To conclude, the coliform CV selective supplement combined with CCA is an appropriate tool for coliform bacteria detection in water samples. Full article

(This article belongs to the Topic Food Hygiene and Food Safety)

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17 pages, 1250 KiB

Open AccessReview

The Use of Interdisciplinary Approaches to Understand the Biology of Campylobacter jejuni

by Paulina A. Dzianach, Francisco J. Pérez-Reche, Norval J. C. Strachan, Ken J. Forbes and Gary A. Dykes

Microorganisms 2022, 10(12), 2498; https://doi.org/10.3390/microorganisms10122498 - 16 Dec 2022

Cited by 2 | Viewed by 1673

Abstract

Campylobacter jejuni is a bacterial pathogen recognised as a major cause of foodborne illness worldwide. While Campylobacter jejuni generally does not grow outside its host, it can survive outside of the host long enough to pose a health concern. This review presents an [...] Read more.

Campylobacter jejuni is a bacterial pathogen recognised as a major cause of foodborne illness worldwide. While Campylobacter jejuni generally does not grow outside its host, it can survive outside of the host long enough to pose a health concern. This review presents an up-to-date description and evaluation of biological, mathematical, and statistical approaches used to understand the behaviour of this foodborne pathogen and suggests future avenues which can be explored. Specifically, the incorporation of mathematical modelling may aid the understanding of C. jejuni biofilm formation both outside and inside the host. Predictive studies may be improved by the introduction of more standardised protocols for assessments of disinfection methods and by assessment of novel physical disinfection strategies as well as assessment of the efficiency of plant extracts on C. jejuni eradication. A full description of the metabolic pathways of C. jejuni, which is needed for the successful application of metabolic models, is yet to be achieved. Finally, a shift from animal models (except for those that are a source of human campylobacteriosis) to human-specific data may be made possible due to recent technological advancements, and this may lead to more accurate predictions of human infections. Full article

(This article belongs to the Special Issue Foodborne Pathogens: Infections and Pathogenesis)

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10 pages, 708 KiB

Open AccessArticle

The Discovery of Oropharyngeal Microbiota with Inhibitory Activity against Pathogenic Neisseria gonorrhoeae and Neisseria meningitidis: An In Vitro Study of Clinical Isolates

by Elvis Achondou Akomoneh, Jolein Gyonne Elise Laumen, Saïd Abdellati, Christophe Van Dijck, Thibau Vanbaelen, Xavier Basil Britto, Sheeba S. Manoharan-Basil and Chris Kenyon

Microorganisms 2022, 10(12), 2497; https://doi.org/10.3390/microorganisms10122497 - 16 Dec 2022

Cited by 1 | Viewed by 1699

Abstract

With increasing incidence of pathogenic Neisseria infections coupled with emerging resistance to antimicrobials, alternative approaches to limit the spread are sought. We investigated the inhibitory effect of oropharyngeal microbiota on the growth of N. gonorrhoeae and N. meningitidis and the impact of the [...] Read more.

With increasing incidence of pathogenic Neisseria infections coupled with emerging resistance to antimicrobials, alternative approaches to limit the spread are sought. We investigated the inhibitory effect of oropharyngeal microbiota on the growth of N. gonorrhoeae and N. meningitidis and the impact of the essential oil-based mouthwash Listerine Cool Mint^® (Listerine). Oropharyngeal swabs from 64 men who have sex with men (n = 118) from a previous study (PReGo study) were analysed (ClinicalTrials.gov, NCT03881007). These included 64 baseline and 54 samples following three months of daily use of Listerine. Inhibition was confirmed by agar overlay assay, and inhibitory bacteria isolated using replica plating and identified using MALDI-TOF. The number of inhibitory isolates were compared before and after Listerine use. Thirty-one pharyngeal samples (26%) showed inhibitory activity against N. gonorrhoeae and/or N. meningitidis, and 62 inhibitory isolates were characterised. Fourteen species belonging to the genera Streptococci and Rothia were identified. More inhibitory isolates were observed following Listerine use compared to baseline, although this effect was not statistically significant (p = 0.073). This study isolated and identified inhibitory bacteria against pathogenic Neisseria spp. and established that daily Listerine use did not decrease their prevalence. These findings could provide a new approach for the prevention and treatment of pharyngeal Neisseria infections. Full article

(This article belongs to the Special Issue Bacteriocins: Academic Advances and Immediate Applications)

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26 pages, 3341 KiB

Open AccessEditor’s ChoiceArticle

Cross-Feeding and Enzymatic Catabolism for Mannan-Oligosaccharide Utilization by the Butyrate-Producing Gut Bacterium Roseburia hominis A2-183

by Abhishek Bhattacharya, Lovisa Majtorp, Simon Birgersson, Mathias Wiemann, Krishnan Sreenivas, Phebe Verbrugghe, Olivier Van Aken, Ed W. J. Van Niel and Henrik Stålbrand

Microorganisms 2022, 10(12), 2496; https://doi.org/10.3390/microorganisms10122496 - 16 Dec 2022

Cited by 2 | Viewed by 2044

Abstract

β-Mannan is abundant in the human diet and in hemicellulose derived from softwood. Linear or galactose-substituted β-mannan-oligosaccharides (MOS/GMOSs) derived from β-mannan are considered emerging prebiotics that could stimulate health-associated gut microbiota. However, the underlying mechanisms are not yet resolved. Therefore, this study investigated [...] Read more.

β-Mannan is abundant in the human diet and in hemicellulose derived from softwood. Linear or galactose-substituted β-mannan-oligosaccharides (MOS/GMOSs) derived from β-mannan are considered emerging prebiotics that could stimulate health-associated gut microbiota. However, the underlying mechanisms are not yet resolved. Therefore, this study investigated the cross-feeding and metabolic interactions between Bifidobacterium adolescentis ATCC 15703, an acetate producer, and Roseburia hominis A2-183 DSMZ 16839, a butyrate producer, during utilization of MOS/GMOSs. Cocultivation studies suggest that both strains coexist due to differential MOS/GMOS utilization, along with the cross-feeding of acetate from B. adolescentis E194a to R. hominis A2-183. The data suggest that R. hominis A2-183 efficiently utilizes MOS/GMOS in mono- and cocultivation. Notably, we observed the transcriptional upregulation of certain genes within a dedicated MOS/GMOS utilization locus (RhMosUL), and an exo-oligomannosidase (RhMan113A) gene located distally in the R. hominis A2-183 genome. Significantly, biochemical analysis of β-1,4 mannan-oligosaccharide phosphorylase (RhMOP130A), α-galactosidase (RhGal36A), and exo-oligomannosidase (RhMan113A) suggested their potential synergistic role in the initial utilization of MOS/GMOSs. Thus, our results enhance the understanding of MOS/GMOS utilization by potential health-promoting human gut microbiota and highlight the role of cross-feeding and metabolic interactions between two secondary mannan degraders inhabiting the same ecological niche in the gut. Full article

(This article belongs to the Special Issue Regulation and Workings of the Gastrointestinal Microbiota)

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10 pages, 1658 KiB

Open AccessArticle

Effects of Helicobacter pylori and Nitrate-Reducing Bacteria Coculture on Cells

by Hinako Ojima, Sakiko Kuraoka, Shyoutarou Okanoue, Hiroyuki Okada, Kazuyoshi Gotoh, Osamu Matsushita, Akari Watanabe and Kenji Yokota

Microorganisms 2022, 10(12), 2495; https://doi.org/10.3390/microorganisms10122495 - 16 Dec 2022

Cited by 3 | Viewed by 1525

Abstract

Helicobacter pylori infection is an important risk factor for developing gastric cancer. However, only a few H. pylori-infected people develop gastric cancer. Thus, other risk factors aside from H. pylori infection may be involved in gastric cancer development. This study aimed to [...] Read more.

Helicobacter pylori infection is an important risk factor for developing gastric cancer. However, only a few H. pylori-infected people develop gastric cancer. Thus, other risk factors aside from H. pylori infection may be involved in gastric cancer development. This study aimed to investigate whether the nitrate-reducing bacteria isolated from patients with atrophic gastritis caused by H. pylori infection are risk factors for developing atrophic gastritis and gastric neoplasia. Nitrate-reducing bacteria were isolated from patients with atrophic gastritis caused by H. pylori infection. Among the isolated bacteria, Actinomyces oris, Actinomyces odontolyticus, Rothia dentocariosa, and Rothia mucilaginosa were used in the subsequent experiments. Cytokine inducibility was evaluated in monocytic cells, and mitogen-activated protein kinase (MAPK) activity and cell cycle were assessed in the gastric epithelial cells. The cytotoxicities and neutrophil-inducing abilities of the Actinomyces and Rothia species were enhanced when cocultured with H. pylori. Th1/Th2-related cytokines were also expressed, but their expression levels differed depending on the bacterial species. Moreover, H. pylori and Actinomyces activated MAPK (ERK and p38) and affected cell cycle progression. Some nitrate-reducing bacteria cocultured with H. pylori may promote inflammation and atrophy by inducing cytokine production. In addition, the MAPK activation and cell cycle progression caused by these bacteria can contribute to gastric cancer development. Full article

(This article belongs to the Special Issue Diet, Nutrition, and Gut Microbiota)

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16 pages, 1450 KiB

Open AccessArticle

Safety Evaluation of Bacillus subtilis IDCC1101, Newly Isolated from Cheonggukjang, for Industrial Applications

by Su-Hyeon Kim, Gashaw Assefa Yehuala, Won Yeong Bang, Jungwoo Yang, Young Hoon Jung and Mi-Kyung Park

Microorganisms 2022, 10(12), 2494; https://doi.org/10.3390/microorganisms10122494 - 16 Dec 2022

Cited by 6 | Viewed by 3301

Abstract

The present study aimed to evaluate the safety of Bacillus subtilis (BS) IDCC1101, newly isolated from Cheonggukjang in Korea. Genome sequencing of BS IDCC1101 was performed to investigate the presence of secondary metabolites, virulence, antibiotic resistance, and mobile elements. Its phenotypic safety analyses [...] Read more.

The present study aimed to evaluate the safety of Bacillus subtilis (BS) IDCC1101, newly isolated from Cheonggukjang in Korea. Genome sequencing of BS IDCC1101 was performed to investigate the presence of secondary metabolites, virulence, antibiotic resistance, and mobile elements. Its phenotypic safety analyses included antibiotic susceptibility, enzyme activity, carbohydrate utilization, production of biogenic amines (BAs) and D-/L-lactate, hemolytic activity, and toxicities in HaCaT cells and rats. The genome of BS IDCC1101 consisted of 4,118,950 bp with 3077 functional genes. Among them, antimicrobial and antifungal secondary metabolites were found, such as fengycin, bacillibactin, and bacilysin. Antibiotic resistance and virulence genes did not exhibit transferability since they did not overlap with mobile elements in the genome. BS IDCC1101 was susceptible to almost all antibiotics suggested for assessment of BS’s antibiotic susceptibility by EFSA guidelines, except for streptomycin. BS IDCC1101 showed the utilization of a wide range of 27 carbohydrates, as well as enzyme activities such as alkaline phosphatase, esterase, esterase lipase, naphthol-AS-BI-phosphohydrolase, α-galactosidase, β-galactosidase, α-glucosidase, and β-glucosidase activities. Additionally, BS IDCC1101 did not exhibit the production of D-/L-lactate and hemolytic activities. Its toxicity in HaCaT cells and rats was also not detected. Thus, these genotypic and phenotypic findings indicate that BS IDCC1101 can be safely used for industrial applications. Full article

(This article belongs to the Special Issue Systems Metabolic Engineering of Industrial Microorganisms)

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15 pages, 2791 KiB

Open AccessArticle

Changes in Phylogenetic and Functional Diversity of Ciliates along the Course of a Mediterranean Karstic River

by Vesna Gulin Beljak, Antonija Kulaš, Guillaume Lentendu, Barbara Vlaičević, Marija Gligora Udovič, Mirela Sertić Perić, Fran Rebrina, Petar Žutinić, Sandi Orlić and Renata Matoničkin Kepčija

Microorganisms 2022, 10(12), 2493; https://doi.org/10.3390/microorganisms10122493 - 16 Dec 2022

Cited by 1 | Viewed by 1830

Abstract

Ciliates are a group of phagotrophic protists found in a wide variety of ecosystems. This study builds on recent studies of ciliates in the Krka river and investigates changes in the phylogenetic and functional diversity of ciliates in biofilm to predict the phylogenetic [...] Read more.

Ciliates are a group of phagotrophic protists found in a wide variety of ecosystems. This study builds on recent studies of ciliates in the Krka river and investigates changes in the phylogenetic and functional diversity of ciliates in biofilm to predict the phylogenetic and functional structure of ciliates in other karstic rivers. Biofilm samples were collected from four representative locations: upstream (Krka spring), midstream (Marasovine), and downstream (Roški slap, Skradinski buk) of the Krka river to test for differences in phylogenetic and functional diversity of ciliates in relation to location and positioning on tufa stones (light/dark-exposed side of tufa stone). Our results showed that Krka spring had higher phylogenetic species variability, lower phylogenetic diversity, and lower functional richness than Skradinski buk, suggesting phylogenetic overdispersal at Krka spring. This could be due to environmental filtering, competitive exclusion, or a combination of these factors. As the first study of its kind in the Mediterranean, our results shed light on the phylogenetic and functional diversity of ciliates in karst ecosystems and provide a basis for future ecological and conservation efforts. Full article

(This article belongs to the Special Issue Ciliates as Model Organisms: From ‘omics’ to Genetics, Ecology and Signaling)

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15 pages, 3010 KiB

Open AccessArticle

Characterization of Human Papillomavirus 16 from Kinshasa (Democratic Republic of the Congo)—Implications for Pathogenicity and Vaccine Effectiveness

by Paula Iglesias, Celine Tendobi, Silvia Carlos, Maria D. Lozano, David Barquín, Luis Chiva and Gabriel Reina

Microorganisms 2022, 10(12), 2492; https://doi.org/10.3390/microorganisms10122492 - 16 Dec 2022

Viewed by 1842

Abstract

Human Papillomavirus (HPV) type 16 is the main etiological agent of cervical cancer worldwide. Mutations within the virus genome may lead to an increased risk of cancer development and decreased vaccine response, but there is a lack of information about strains circulating in [...] Read more.

Human Papillomavirus (HPV) type 16 is the main etiological agent of cervical cancer worldwide. Mutations within the virus genome may lead to an increased risk of cancer development and decreased vaccine response, but there is a lack of information about strains circulating in Sub-Saharan Africa. Endocervical cytology samples were collected from 480 women attending a voluntary cervical cancer screening program at Monkole Hospital and four outpatient centers in Kinshasa, Democratic Republic of the Congo (DRC). The prevalence of HPV infection was 18.8% and the most prevalent high-risk types were HPV16 (12.2%) followed by HPV52 (8.8%) and HPV33/HPV35 (7.8% each). HPV16 strains were characterized: 57.1% were classified as C lineage; two samples (28.6%) as A1 and one sample belonged to B1 lineage. HPV33, HPV35, HPV16, and HPV58 were the most frequent types associated with low-grade intraepithelial lesion while high-grade squamous intraepithelial lesions were predominantly associated with HPV16. Several L1 mutations (T266A, S282P, T353P, and N181T) were common in Kinshasa, and their potential effect on vaccine-induced neutralization, especially the presence of S282P, should be further investigated. Long control region (LCR) variability was high with frequent mutations like G7193T, G7521A, and G145T that could promote malignancy of these HPV16 strains. This study provides a helpful basis for understanding HPV16 variants circulating in Kinshasa and the potential association between mutations of LCR region and malignancy and of L1 and vaccine activity. Full article

(This article belongs to the Special Issue Diagnosis of Viral Infections)

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14 pages, 998 KiB

Open AccessReview

Current Data on Rickettsia felis Occurrence in Vectors, Human and Animal Hosts in Europe: A Scoping Review

by Constantina N. Tsokana, Ioanna Kapna and George Valiakos

Microorganisms 2022, 10(12), 2491; https://doi.org/10.3390/microorganisms10122491 - 16 Dec 2022

Cited by 2 | Viewed by 1449

Abstract

Rickettsia felis is an emerging pathogen with increasing reports of human cases and detection in arthropod and animal host species worldwide. In this scoping review we record the newest data reported for R. felis in Europe: the vector and host species found to be [...] Read more.

Rickettsia felis is an emerging pathogen with increasing reports of human cases and detection in arthropod and animal host species worldwide. In this scoping review we record the newest data reported for R. felis in Europe: the vector and host species found to be infected, and the geographical distribution and prevalence of R. felis infection in vectors and hosts. A total of 15 European countries reported the occurrence of R. felis in hosts and vectors during 2017–2022. The vectors found to be infected by R. felis were flea, tick and mite species; Ctenocephalides felis and Ixodes ricinus were the dominant ones. The hosts found to be infected and/or exposed to R. felis were humans, cats and small mammals. Physicians should be aware of the epidemiology and include illness caused by R. felis in the differential diagnosis of febrile disease. Veterinarians should keep training pet owners on the need for effective year-round arthropod control on their pets, especially for fleas. Full article

(This article belongs to the Special Issue Vector-Pathogen-Host Dynamics: Delineating Interactions at Every Level)

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7 pages, 478 KiB

Open AccessBrief Report

Single Center Experience Using Monoclonal COVID-19 Antibodies in the Management of Immunocompromised Patients with COVID-19

by David Klank, Bernd Claus, Raoul Bergner and Peter Paschka

Microorganisms 2022, 10(12), 2490; https://doi.org/10.3390/microorganisms10122490 - 16 Dec 2022

Cited by 1 | Viewed by 1224

Abstract

The medical care of immunocompromised patients with COVID-19 infection causes major hurdles in the management of these patients in clinical practice. However, poor responses to vaccinations in patients with oncological or autoimmune diseases require rapid action and effective care in this fragile patient [...] Read more.

The medical care of immunocompromised patients with COVID-19 infection causes major hurdles in the management of these patients in clinical practice. However, poor responses to vaccinations in patients with oncological or autoimmune diseases require rapid action and effective care in this fragile patient population. Monoclonal antibodies (mAb) offer an effective therapeutic option with a favorable toxicity profile. We have retrospectively reviewed the first 100 patients treated with mAb in our clinic and assessed the individual vaccine response, side effects of mAb, hospitalization rate and mortality. None of the outpatients treated with mAb had to be hospitalized. In particular, the third SARS-CoV-2 vaccination had a significant effect on the seroconversion (37.5% vs. 77.8% positive patients) in the entire group of patients studied. No side effects of 3°/4° were observed following mAb administration; the mortality in the entire cohort was 7%. Our data and experience show good effectiveness and a favorable tolerability profile of mAb, supporting the feasibility of this therapy in everyday clinical practice. Of note, in immunocompromised patients, both the vaccination status and success need to be recorded in a systematic manner and taken into account in terms of therapeutic intervention using mAb in case of a SARS-CoV-2 infection. Full article

(This article belongs to the Special Issue Pharmacological Interventions against Respiratory Viral Infections)

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15 pages, 2321 KiB

Open AccessArticle

TLR4/CD14/MD2 Revealed as the Limited Toll-like Receptor Complex for Chlamydia trachomatis-Induced NF-κB Signaling

by Romana Klasinc, Claire Battin, Wolfgang Paster, Michael Reiter, Philipp Schatzlmaier, Peter Rhein, Andreas Spittler, Peter Steinberger and Hannes Stockinger

Microorganisms 2022, 10(12), 2489; https://doi.org/10.3390/microorganisms10122489 - 15 Dec 2022

Cited by 2 | Viewed by 1441

Abstract

Chlamydia trachomatis (Ct) is the most common cause of genital tract infections as well as preventable blindness worldwide. Pattern recognition receptors such as toll-like receptors (TLRs) represent the initial step in recognizing pathogenic microorganisms and are crucial for the initiation of an appropriate [...] Read more.

Chlamydia trachomatis (Ct) is the most common cause of genital tract infections as well as preventable blindness worldwide. Pattern recognition receptors such as toll-like receptors (TLRs) represent the initial step in recognizing pathogenic microorganisms and are crucial for the initiation of an appropriate immune response. However, our understanding of TLR-signaling in Chlamydia-infected immune cells is incomplete. For a better comprehension of pathological inflammatory responses, robust models for interrogating TLR-signaling upon chlamydial infections are needed. To analyze the TLR response, we developed and utilized a highly sensitive and selective fluorescent transcriptional cellular reporter system to measure the activity of the transcription factor NF-κB. Upon incubation of the reporter cells with different preparations of Ct, we were able to pinpoint which components of TLRs are involved in the recognition of Ct. We identified CD14 associated with unique characteristics of different serovars as the crucial factor of the TLR4/CD14/MD2 complex for Ct-mediated activation of the NF-κB pathway. Furthermore, we found the TLR4/CD14/MD2 complex to be decisive for the uptake of Ct-derived lipopolysaccharides but not for infection and replication of Ct. Imaging flow cytometry provided information about inclusion formation in myeloid- as well as lymphocytic cells and was highest for Ct L2 with at least 25% of inclusion forming cells. Ct E inclusion formation was eminent in Jurkat cells without CD14 expression (11.1%). Thus, our model enables to determine Ct uptake and signal induction by pinpointing individual components of the recognition and signaling pathways to better understand the immune response towards infectious pathogens. Full article

(This article belongs to the Special Issue Intracellular Bacteria: From Basic Research to Clinics 2.0)

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