Microbiology Research

4 pages, 225 KiB

Open AccessArticle

Bartonella alsatica in Wild and Domestic Rabbits (Oryctolagus cuniculus) in The Netherlands

by Marja J. L. Kik, Ryanne I. Jaarsma, Jooske IJzer, Hein Sprong, Andrea Gröne and Jolianne M. Rijks

Microbiol. Res. 2021, 12(2), 524-527; https://doi.org/10.3390/microbiolres12020036 - 16 Jun 2021

Cited by 1 | Viewed by 2638

Abstract

Members of the genus Bartonella are Gram-negative facultative intracellular bacteria that are transmitted by arthropod vectors. Bartonella alsatica was detected in the spleens and livers of 7 out of 56 wild rabbits (Oryctolagus cuniculus) and in the liver of 1 out [...] Read more.

Members of the genus Bartonella are Gram-negative facultative intracellular bacteria that are transmitted by arthropod vectors. Bartonella alsatica was detected in the spleens and livers of 7 out of 56 wild rabbits (Oryctolagus cuniculus) and in the liver of 1 out of 87 domestic rabbits in the Netherlands. The molecular evidence of B. alsatica infection in wild as well as domestic rabbits indicates the possibility of exposure to humans when these come in close contact with rabbits and possibly their fleas with subsequent risk of Bartonella infection and disease. Full article

11 pages, 1725 KiB

Open AccessArticle

Isolation, Description and Genome Analysis of a Putative Novel Methylobacter Species (‘Ca. Methylobacter coli’) Isolated from the Faeces of a Blackbuck (Indian Antelope)

by Kumal Khatri, Jyoti Mohite, Pranitha Pandit, Rahul A. Bahulikar and Monali C. Rahalkar

Microbiol. Res. 2021, 12(2), 513-523; https://doi.org/10.3390/microbiolres12020035 - 15 Jun 2021

Cited by 9 | Viewed by 3369

Abstract

Enteric fermentation of methane by ruminant animals represents a major source of anthropogenic methane. Significantly less information is available on the existence of methanotrophs in the gut of ruminants. Therefore, detailed strain descriptions of methanotrophs isolated from ruminant faeces or gut are rare. [...] Read more.

Enteric fermentation of methane by ruminant animals represents a major source of anthropogenic methane. Significantly less information is available on the existence of methanotrophs in the gut of ruminants. Therefore, detailed strain descriptions of methanotrophs isolated from ruminant faeces or gut are rare. We present a first report on the enrichment and isolation of a methanotroph, strain BlB1, from the faeces of an Indian antelope (blackbuck). The 16S rRNA gene sequence of strain BlB1 showed the highest identity (98.40% identity) to Methylobacter marinus A45^T and Methylobacter luteus NCIMB 11914^T. Strain BlB1 showed coccoidal cells (1.5–2 µm in diameter), which formed chains or aggregates of 3–4 cells of light yellow-coloured colonies on agarose when incubated with methane in the gas phase. The draft genome of BlB1 (JADMKV01) is 4.87 Mbp in size, with a G + C content of 51.3%. The draft genome showed 27.4% digital DNA-DNA hybridization (DDH) and 83.07% average nucleotide identity (ANIb) values with that of its closest phylogenetic neighbour, Methylobacter marinus A45^T. Due to the lower values of DDH and ANIb with the nearest species, and <98.7% 16S rRNA gene sequence identity, we propose that strain BlB1 belongs to a novel species of Methylobacter. However, as the culture has to be maintained live and resisted cryopreservation, deposition in culture collections was not possible and hence we propose a Candidatus species name, ‘Ca. Methylobacter coli’ BlB1. ‘Ca. Methylobacter coli’ BlB1 would be the first described methanotroph from ruminants worldwide, with a sequenced draft genome. This strain could be used as a model for studies concerning methane mitigation from ruminants. Full article

► Show Figures

Figure 1

Figure 1
Morphology of strain BlB1: (A) live cells were observed under a phase-contrast microscope (Nikon 80i, Japan microscope with a camera) under 100X magnification with oil emulsion; (B) fixed and processed culture was observed under Scanning Electron Microscopy (SEM) (Zeiss model EVO-MA-15 SEM); (C) Gram-staining under light microscopy; (D) colony morphology on solid NMS medium plate; (E) BlB1 forms a turbid suspension with a yellow tinge in liquid dilute NMS medium. Full article ">Figure 2
Maximum likelihood bootstrap tree of the 16S rRNA gene sequence of strain BlB1 in comparison with the 16S rRNA genes of closest valid species. The evolutionary history was inferred by using the maximum likelihood method and Tamura-Nei model and 1000 bootstraps (values >50 shown). The bar represents 2% divergence. The phylogenetic tree was constructed using MEGA X. Full article ">Figure 3
Maximum likelihood bootstrap tree of the pMMO B subunit protein sequences of strain BlB1 in comparison with the protein from type strains of valid species. The evolutionary history was completed using the maximum likelihood method based on the Poisson correction model and 1000 bootstraps. The bar represents 2% divergence. The phylogenetic tree was constructed using MEGA X. Full article ">Figure 4
Phylogenomic tree constructed using the PATRIC database showing the relationship of ‘Ca. Methylobacter coli’ strain BlB1 with other species of Methylobacter with an outgroup. Full article ">

10 pages, 1241 KiB

Open AccessArticle

Hygienic Characteristics and Detection of Antibiotic Resistance Genes in Crickets (Acheta domesticus) Breed for Flour Production

by Luca Grispoldi, Musafiri Karama, Saeed El-Ashram, Cristina Maria Saraiva, Juan García-Díez, Athanasios Chalias, Salvatore Barbera and Beniamino T. Cenci-Goga

Microbiol. Res. 2021, 12(2), 503-512; https://doi.org/10.3390/microbiolres12020034 - 15 Jun 2021

Cited by 4 | Viewed by 2826

Abstract

During the last ten years, the worldwide interest in using insects as food and feed has surged. Edible insects fall within the category of novel foods, i.e., the category of food not consumed in significant amounts in the European Union before 15 May [...] Read more.

During the last ten years, the worldwide interest in using insects as food and feed has surged. Edible insects fall within the category of novel foods, i.e., the category of food not consumed in significant amounts in the European Union before 15 May 1997 (the date of entry into force of Regulation (EC) No. 258/1997, later repealed by Regulation (EU) No. 2283/2015). One of the most promising insect species to be raised for food is the house cricket (Acheta domesticus). In this study, the rearing of a stock of house crickets was studied over a period of four months. The microbiological quality of the farm was studied using swabs on the surface of the rearing boxes to analyze the trend over time of different populations of microorganisms (total aerobic mesophilic microbiota, Lactobacillus spp., enterococci, Staphylococcus spp., Enterobacteriaceae, total coliforms, Pseudomonas spp. and molds). The presence of four antimicrobial resistance genes (aph, blaZ, sul1, and tetM) was investigated by polymerase chain reaction. A production scheme was also developed in order to obtain a cricket-based flour, which was analyzed for its microbiological and chemical-centesimal profile. The results obtained in this study demonstrate that the contamination increases with time and that a proper management of the farming system for insects is of the utmost importance, as it is for conventional farm animals such as ungulates, poultry, and rabbits. The old-fashioned adage “all full, all empty” for the farming system summarizes the need for proper cleaning and disinfection of the structures at the end of each production cycle. Full article

(This article belongs to the Special Issue Microbiology of Edible Insects)

► Show Figures

Figure 1

12 pages, 1049 KiB

Open AccessReview

Oral Iron Supplementation—Gastrointestinal Side Effects and the Impact on the Gut Microbiota

by Sarah R. Bloor, Rudolph Schutte and Anthony R. Hobson

Microbiol. Res. 2021, 12(2), 491-502; https://doi.org/10.3390/microbiolres12020033 - 12 Jun 2021

Cited by 38 | Viewed by 30060

Abstract

Iron deficiency anaemia (IDA) is a worldwide healthcare problem affecting approximately 25% of the global population. The most common IDA treatment is oral iron supplementation, which has been associated with gastrointestinal (GI) side effects such as constipation and bloating. These can result in [...] Read more.

Iron deficiency anaemia (IDA) is a worldwide healthcare problem affecting approximately 25% of the global population. The most common IDA treatment is oral iron supplementation, which has been associated with gastrointestinal (GI) side effects such as constipation and bloating. These can result in treatment non-adherence and the persistence of IDA. Intravenous iron does not cause GI side effects, which may be due to the lack of exposure to the intestinal lumen. Luminal iron can cause changes to the gut microbiota, aiding the promotion of pathogenic species and decreasing beneficial protective species. Iron is vital for methanogenic archaea, which rely on iron for growth and metabolism. Increased intestinal methane has been associated with slowing of intestinal transit, constipation, and bloating. Here we explore the literature to understand a potential link between iron and methanogenesis as a novel way to understand the mechanism of oral iron supplementation induced GI side effects. Full article

► Show Figures

Figure 1

11 pages, 2844 KiB

Open AccessArticle

Effect of Co-Inoculation of Bacillus sp. Strain with Bacterial Endophytes on Plant Growth and Colonization in Tomato Plant (Solanum lycopersicum)

by Ahsanul Salehin, Ramesh Raj Puri, Md Hafizur Rahman Hafiz and Kazuhito Itoh

Microbiol. Res. 2021, 12(2), 480-490; https://doi.org/10.3390/microbiolres12020032 - 6 May 2021

Cited by 7 | Viewed by 3086

Abstract

Colonization of a biofertilizer Bacillus sp. OYK strain, which was isolated from a soil, was compared with three rhizospheric and endophytic Bacillus sp. strains to evaluate the colonization potential of the Bacillus sp. strains with a different origin. Surface-sterilized seeds of tomato ( [...] Read more.

Colonization of a biofertilizer Bacillus sp. OYK strain, which was isolated from a soil, was compared with three rhizospheric and endophytic Bacillus sp. strains to evaluate the colonization potential of the Bacillus sp. strains with a different origin. Surface-sterilized seeds of tomato (Solanum lycopersicum L. cv. Chika) were sown in the sterilized vermiculite, and four Bacillus sp. strains were each inoculated onto the seed zone. After cultivation in a phytotron, plant growth parameters and populations of the inoculants in the root, shoot, and rhizosphere were determined. In addition, effects of co-inoculation and time interval inoculation of Bacillus sp. F-33 with the other endophytes were examined. All Bacillus sp. strains promoted plant growth except for Bacillus sp. RF-37, and populations of the rhizospheric and endophytic Bacillus sp. strains were 1.4–2.8 orders higher in the tomato plant than that of Bacillus sp. OYK. The plant growth promotion by Bacillus sp. F-33 was reduced by co-inoculation with the other endophytic strains: Klebsiella sp. Sal 1, Enterobacter sp. Sal 3, and Herbaspirillum sp. Sal 6., though the population of Bacillus sp. F-33 maintained or slightly decreased. When Klebsiella sp. Sal 1 was inoculated after Bacillus sp. F-33, the plant growth-promoting effects by Bacillus sp. F-33 were reduced without a reduction of its population, while when Bacillus sp. F-33 was inoculated after Klebsiella sp. Sal 1, the effects were increased in spite of the reduction of its population. Klebsiella sp. Sal 1 colonized dominantly under both conditions. The higher population of rhizospheric and endophytic Bacillus sp. in the plant suggests the importance of the origin of the strains for their colonization. The plant growth promotion and colonization potentials were independently affected by the co-existing microorganisms. Full article

► Show Figures

Figure 1

Figure 1
The effects of inoculation of Bacillus sp. strains on the growth of the tomato plant. The tomato plant was cultivated using sterilized vermiculite, and the parameters were measured at 24 days after seed inoculation. CTL represents the control samples inoculated with autoclaved cultures. The bars represent the standard deviation (n = 6), and different letters indicate significant differences at p < 0.05 by Tukey’s test. Full article ">Figure 2
Colonization of seed-inoculated Bacillus sp. strains in the rhizosphere (a), root (b), and shoot (c) of the tomato plant. The tomato plant was cultivated using sterilized vermiculite, and colonization was examined at 24 days after seed inoculation. No colony appeared in the control samples. The bars represent the standard deviation (n = 4), and different letters indicate significant differences at p < 0.05 by Tukey’s test. Full article ">Figure 3
The effects of co-inoculation of Bacillus sp. F-33 with the other endophytic strains, Klebsiella sp. Sal 1, Enterobacter sp. Sal 3, and Herbaspirillum sp. Sal 6, on the growth of the tomato plant. The tomato plant was cultivated using sterilized vermiculite, and the parameters were measured at 14 days after seed inoculation. CTL represents the control samples inoculated with autoclaved cultures. The bars represent the standard deviation (n = 6), and different letters indicate significant differences at p < 0.05 by Tukey’s test. Full article ">Figure 4
The effect of the seed-co-inoculated Bacillus sp. F-33 with the other endophytic strains, Klebsiella sp. Sal 1, Enterobacter sp. Sal 3, and Herbaspirillum sp. Sal 6, on colonization in the rhizosphere (a), root (b), and shoot (c) of the tomato plant. The tomato plant was cultivated using sterilized vermiculite, and colonization was examined at 14 days after seed-co-inoculation. The bracket on the x-axis indicates each population in co-inoculation, and no bracket indicates single inoculation. No colony appeared in the control samples. The bars represent the standard deviation (n = 4), and different letters indicate significant differences at p < 0.05 by Tukey’s test. Full article ">Figure 5
The effects of the time interval of inoculation on plant growth promotion and colonization of Bacillus sp. F-33 and Klebsiella sp. Sal 1 in the tomato plant. The tomato plant was cultivated using sterilized vermiculite, and the parameters were measured at 14 days after seed inoculation. In the time interval of inoculation, F-33 + Sal 1 and Sal 1 + F-33, the second inoculation was conducted 7 days after the first inoculation and analyzed 7 days after the second inoculation. CTL represents the control samples inoculated with autoclaved cultures. The bars represent the standard deviation (n = 5), and different letters indicate significant differences at p < 0.05 by Tukey’s test. Full article ">Figure 6
The effect of the time interval of inoculation of Bacillus sp. F-33 and Klebsiella sp. Sal 1 on colonization in the rhizosphere (a), root (b), and shoot (c) of the tomato plant. The tomato plant was cultivated using sterilized vermiculite, and colonization was examined at 14 days after seed inoculation. In the time interval of inoculation, F-33 + Sal 1 and Sal 1 + F-33, the second inoculation was conducted 7 days after the first inoculation and analyzed 7 days after the second inoculation. The bracket on the x-axis indicates each population in the time interval of inoculation, and the arrows on the bracket indicate the order of inoculation. No bracket indicates a single inoculation. No colony appeared in the control samples. The bars represent the standard deviation (n = 3), and different letters indicate significant differences at p < 0.05 by Tukey’s test. Full article ">

25 pages, 9481 KiB

Open AccessArticle

Lysinibacillus sphaericus III(3)7 and Plasmid Vector pMK4: New Challenges in Cloning Platforms

by Diana C. León and Jenny Dussán

Microbiol. Res. 2021, 12(2), 455-479; https://doi.org/10.3390/microbiolres12020031 - 4 May 2021

Viewed by 3479

Abstract

The acquisition and especially the maintenance of a plasmid usually brings a fitness cost that reduces the reproductive rate of the bacterial host; for strains like Lysinibacillus sphaericus III(3)7, which possesses important environmental properties, this alteration along with morphological changes and reduced sporulation [...] Read more.

The acquisition and especially the maintenance of a plasmid usually brings a fitness cost that reduces the reproductive rate of the bacterial host; for strains like Lysinibacillus sphaericus III(3)7, which possesses important environmental properties, this alteration along with morphological changes and reduced sporulation rates may exert a negative effect on metabolic studies using plasmids as cloning platforms. The aim of this study is to approach the metabolic behavior of pMK4-bearing cells of L. sphaericus III(3)7 through the use of bioinformatic and in vitro analyses. An incompatibility model between the pMK4 vector and a predicted megaplasmid, pBsph, inside III(3)7 cells was constructed based on an incA region. Additionally, in vitro long-term plasmid stability was not found in plasmid-bearing cells. Alignments between replicons, mobile genetic elements and RNA-RNA interactions were assessed, pairwise alignment visualization, graphic models and morphological changes were evaluated by SEM. Metabolite analysis was done through HPLC coupled to a Q-TOF 6545, and electrospray ionization was used, finally, Aedes aegypti and Culex quinquefasciatus larvae were used for larvicidal activity assessment. Results found, a decreased growth rate, spore formation reduction and morphological changes, which supported the idea of metabolic cost exerted by pMK4. An incompatibility between pMK4 and pBsph appears to take place inside L. sphaericus III(3)7 cells, however, further in vitro studies are needed to confirm it. Full article

► Show Figures

Figure 1

15 pages, 281 KiB

Open AccessArticle

Campylobacter and Salmonella in Scavenging Indigenous Chickens in Rural Central Tanzania: Prevalence, Antimicrobial Resistance, and Genomic Features

by Elpidius Rukambile, Vitali Sintchenko, Gary Muscatello, Qinning Wang, John Kiiru, Wende Maulaga, Bishop Magidanga, Grace Banda, Richard Kock and Robyn Alders

Microbiol. Res. 2021, 12(2), 440-454; https://doi.org/10.3390/microbiolres12020030 - 3 May 2021

Cited by 5 | Viewed by 2855

Abstract

Introduction: Salmonella and Campylobacter spp. are commonly reported bacterial foodborne pathogens causing morbidity and mortality worldwide. In rural areas, where there is a high occurrence rate of human–animal interactions and poor hygiene practices, shedding animals present a high risk to humans in [...] Read more.

Introduction: Salmonella and Campylobacter spp. are commonly reported bacterial foodborne pathogens causing morbidity and mortality worldwide. In rural areas, where there is a high occurrence rate of human–animal interactions and poor hygiene practices, shedding animals present a high risk to humans in acquiring animal-associated infections. Materials and methods: Seasonal prevalence of Campylobacter jejuni, Campylobacter coli, and Salmonella spp. in scavenging indigenous chicken faeces was determined by polymerase chain reaction (PCR). Antimicrobial resistance was studied in Salmonella isolates by disc diffusion method, and whole-genome sequenced isolates were used to determine Salmonella serovars, antimicrobial resistance genes, virulence genes, and plasmid profile. Results: The overall prevalence of Campylobacter in chickens was 7.2% in the dry season and 8.0% in the rainy season (p = 0.39), and that of Salmonella was 11.1% in the dry season and 16.2% in the rainy season (p = 0.29). Salmonella serovars detected were II 35:g,m,s,t:-, Ball, Typhimurium, Haardt/Blockley, Braenderup, and Enteritidis/Gallinarum. One S. II 35:g,m,s,t:- isolate was resistant to ampicillin and the rest were either intermediate resistant or pansusceptible to the tested antimicrobials. The resistance genes observed were CatA, tetJ, and fosA7, most common in Ball than in other serovars. Seven plasmids were identified, more common in serovar Ball and less common in II 35:g,m,s,t:-. Serovar II 35:g,m,s,t:- isolates were missing some of the virulence genes important for Salmonella pathogenicity found in other serovars isolated. Conclusion: PCR detection of Campylobacter spp. and Salmonella spp. in chickens necessitate the improvement of hygiene at the household level and reducing human–chicken interaction as a strategy of preventing humans from acquiring chicken-associated bacteria, which would enter the human food chain. Infrequent use of antimicrobials in this type of poultry is most likely the reason for the low rates of antimicrobial resistance observed in this study. Full article

21 pages, 3669 KiB

Open AccessArticle

The Regulation of Non-Specific Membrane Permeability Transition in Yeast Mitochondria under Oxidative Stress

by Elena P. Isakova, Olga I. Klein and Yulia I. Deryabina

Microbiol. Res. 2021, 12(2), 419-439; https://doi.org/10.3390/microbiolres12020029 - 1 May 2021

Cited by 1 | Viewed by 2398

Abstract

In this study, the mechanism of non-specific membrane permeability (yPTP) in the Endomyces magnusii yeast mitochondria under oxidative stress due to blocking the key antioxidant enzymes has been investigated. We used monitoring the membrane potential at the cellular (potential-dependent staining) and mitochondrial levels [...] Read more.

In this study, the mechanism of non-specific membrane permeability (yPTP) in the Endomyces magnusii yeast mitochondria under oxidative stress due to blocking the key antioxidant enzymes has been investigated. We used monitoring the membrane potential at the cellular (potential-dependent staining) and mitochondrial levels and mitochondria ultra-structural images with transmission electron microscopy (TEM) to demonstrate the mitochondrial permeability transition induction due to the pore opening. Analysis of the yPTP opening upon respiring different substrates showed that NAD(P)H completely blocked the development of the yPTP. The yPTP opening was inhibited by 5–20 mM P_i, 5 mM Mg²⁺, adenine nucleotides (AN), 5 mM GSH, the inhibitor of the P_i transporter (PiC), 100 μM mersalyl, the blockers of the adenine nucleotide transporter (ANT) carboxyatractyloside (CATR), and bongkrekic acid (BA). We concluded that the non-specific membrane permeability pore opens in the E. magnusii mitochondria under oxidative stress, and the ANT and PiC are involved in its formation. The crucial role of the Ca²⁺ ions in the process has not been confirmed. We showed that the Ca²⁺ ions affected the yPTP both with and without the Ca²⁺ ionophore ETH129 application insignificantly. This phenomenon in the E. magnusii yeast unites both mitochondrial unselective channel (_ScMUC) features in the Saccharomyces cerevisiae mitochondria and the classical membrane pore in the mammalian ones (mPTP). Full article

► Show Figures

Figure 1

Figure 1
Effects of Ca2+, ATZ, and DDC on the ∆Ψ generated by the E. magnusii mitochondria respiring on a pyruvate + malate system. Additions and amounts are given in the figure by large arrows. Panel (A): Incubation medium contained 0.4 M mannitol, 0.1 M KCl, 20 mM Tris-acetate, 20 μM safranin, pH 7.4, and 0.4 mg of mitochondria protein. Trace a—control; trace b shows the effect of the addition of 500 μM Ca2+ on the ∆Ψ if the ions are taken up; trace c—the effect of a combined action of 4 mM ATZ and 4 mM DDC on the membrane potential. Small arrows indicate stirring for aeration. Panel (B): trace a shows 100 μM Ca2+ uptake. The medium was the same as that in Panel (A); instead of 20 μM safranin, 50 μM murexide was added; trace b shows 100 μM Ca2+ uptake in the same medium as that in trace a. The red arrow indicates the Ca2+ addition. Panel (C) incubation medium was the same as that in Panel (A). Trace a shows the effect of the addition of 4 mM DDC and 4 mM ATZ; trace b shows the effect of the addition of 100 μM Ca2+ followed by a combined action of 5 μM ETH129, 4 mM DDC, and 4 mM ATZ. Small arrows indicate the stirring for aeration. Panel (D): Micro-images of the potential-dependent stained’ mitochondria in the E. magnusii cells raised in the mid-exponential growth phase using Rh123. The regions of high mitochondrial polarization are bright red due to concentrated dye. a—control, magnification 100×; b, c—cells were pre-treated with both 4 mM ATZ and 4 mM DDC for 30 min, magnification 100×; c—the incubation medium contained 1 mM Ca2+; d—incubation medium contained 2 mM KCN. To examine the Rh123-stained preparations, filters of 02 and 15 (Zeiss) were used (magnification ×100). The photos were taken using an AxioCamMR camera. <a href="#microbiolres-12-00029-f001" class="html-fig">Figure 1</a>A has been published in [<a href="#B37-microbiolres-12-00029" class="html-bibr">37</a>]. Full article ">Figure 1 Cont.
Effects of Ca2+, ATZ, and DDC on the ∆Ψ generated by the E. magnusii mitochondria respiring on a pyruvate + malate system. Additions and amounts are given in the figure by large arrows. Panel (A): Incubation medium contained 0.4 M mannitol, 0.1 M KCl, 20 mM Tris-acetate, 20 μM safranin, pH 7.4, and 0.4 mg of mitochondria protein. Trace a—control; trace b shows the effect of the addition of 500 μM Ca2+ on the ∆Ψ if the ions are taken up; trace c—the effect of a combined action of 4 mM ATZ and 4 mM DDC on the membrane potential. Small arrows indicate stirring for aeration. Panel (B): trace a shows 100 μM Ca2+ uptake. The medium was the same as that in Panel (A); instead of 20 μM safranin, 50 μM murexide was added; trace b shows 100 μM Ca2+ uptake in the same medium as that in trace a. The red arrow indicates the Ca2+ addition. Panel (C) incubation medium was the same as that in Panel (A). Trace a shows the effect of the addition of 4 mM DDC and 4 mM ATZ; trace b shows the effect of the addition of 100 μM Ca2+ followed by a combined action of 5 μM ETH129, 4 mM DDC, and 4 mM ATZ. Small arrows indicate the stirring for aeration. Panel (D): Micro-images of the potential-dependent stained’ mitochondria in the E. magnusii cells raised in the mid-exponential growth phase using Rh123. The regions of high mitochondrial polarization are bright red due to concentrated dye. a—control, magnification 100×; b, c—cells were pre-treated with both 4 mM ATZ and 4 mM DDC for 30 min, magnification 100×; c—the incubation medium contained 1 mM Ca2+; d—incubation medium contained 2 mM KCN. To examine the Rh123-stained preparations, filters of 02 and 15 (Zeiss) were used (magnification ×100). The photos were taken using an AxioCamMR camera. <a href="#microbiolres-12-00029-f001" class="html-fig">Figure 1</a>A has been published in [<a href="#B37-microbiolres-12-00029" class="html-bibr">37</a>]. Full article ">Figure 2
Recording of ∆Ψ generated by the E. magnusii mitochondria respiring on a 20 mM α-ketoglutarate (Panel (A)), 10 mM succinate (Panel (B)), 10 mM NADPH (Panel (C)), and 10 mM NADH (Panel (D)). The incubation medium contained 0.4 M mannitol, 0.1 M KCl, 20 mM Tris-acetate, 0.4 mg of mitochondria protein, and pH 7.4. Additions and amounts are indicated by large arrows. Trace a—control (solid line); trace b indicates the effect of the addition of 4 mM DDC, and of 4 mM ATZ (dashed line). The additions are indicated by arrows: the solid one for protonophore, 1 μM CCCP; the dashed one for ATZ and DDC. Small arrows indicate stirring for aeration. Full article ">Figure 3
Effects of phosphate (Pi) and mersalyl on non-specific permeability transition induction in the E. magnusii mitochondria respiring on a pyruvate and malate system in the presence of the antioxidant enzyme inhibitors. The incubation medium was the same as that in <a href="#microbiolres-12-00029-f001" class="html-fig">Figure 1</a>, Panel (A): incubation medium contained also 2 mM Pi (trace a), 4 mM Pi (trace b), and 5 mM Pi (trace c); Panel (B): 100 μM mersalyl was added into the medium before the inhibitors. Addition of the inhibitors mixture (4 mM DDC and 4 mM ATZ) is indicated by the arrow. Full article ">Figure 4
Effects of AN and the inhibitors of the ANT on the non-specific permeability transition induction in the E. magnusii mitochondria respiring on a pyruvate and malate system. (Panel (A)); αketoglutarate (Panel (B)), and succinate (Panel (C)) in the presence of the antioxidant enzyme inhibitors. The basic incubation medium also contained 150 μM ATP (trace a) and 150 μM ADP (trace b). (Panel (D)) the incubation medium also contained 0.4 μM CATR (trace a) and 40 μM BA (trace b). The addition of the inhibitors mixture (4 mM DDC and 4 mM ATZ) is indicated by the arrows. Full article ">Figure 5
Effects of Mg2+ ions, polyamines, and the GSH on the induction of the non-specific permeability transition in the E. magnusii mitochondria promoted by the application of the antioxidant enzyme inhibitors. Panel (A): the basic incubation medium also contained 5 mM Mg2+ (trace a), 40 or 100 μM spermidine (trace b and c, respectively), or 5 mM GSH. The ΔΨ was generated by the application of the substrate system (pyruvate + malate) (Panel (B)); α-ketoglutarate (Panel (C)); trace a—control; trace b—5 mM GSH was incubated with the 28 mitochondria and applied before the inhibitors’ addition. Addition of the inhibitors mixture (4 mM DDC and 4 mM ATZ) is indicated by the dashed arrows. Full article ">Figure 6
Estimates of total ROS level in E. magnusii mitochondria. The dynamics of intracellular ROS production were monitored using a spectroscopic fluorescence probe of AR. The incubation medium contained 0.4 M mannitol, 0.1 M KCl, 20 mM Tris-acetate, 0.4 mg of mitochondria protein, and pH 7.4. The incubation medium has been amended to indicate 4 mM ATZ, 4 mM DDC, 5 mM Pi, 5 mM GSH, 5 mM Mg, 10 mM NAD(P)H, 100 μM mersalyl, 5 μM BA, 150 μM ATP, 150 μM ADP, and 500 μM Ca2+. Values are mean ±S.E.M from 5–6 independent experiments. The intensity of ROS production in the version of “positive control” made up 5.89 pmols × min−1 × mg of protein−1. Values with different letters within a column are significantly different at p < 0.05. Full article ">Figure 7
Micro-images of transmission electron microscopy of the E. magnusii mitochondria. (A) —control, (B)—after a 3-min incubation with the antioxidant enzyme inhibitors of 4 mM ATZ and 4 mM DDC; (C)—after a 1-min incubation with 5 mM Mg2+ and 5 mM Pi followed by a 3-min treatment with the antioxidant enzyme inhibitors of 4 mM ATZ and 4 mM DDC; (D)—after a 1-min incubation with10 mM NADH followed by a 3-min treatment with the antioxidant enzyme inhibitors of 4 mM ATZ and 4 mM DDC; (E)—after a 1-minute incubation with 5 mM GSH followed by a 3-min treatment with the antioxidant enzyme inhibitors of 4 mM ATZ and 4 mM DDC. Full article ">Figure 8
Hypothetic scheme of the yPTP in the E. magnusii mitochondria. Full article ">

16 pages, 684 KiB

Open AccessReview

A Review on the Prevalence of Poxvirus Disease in Free-Living and Captive Wild Birds

by Richard A. J. Williams, Daniel A. Truchado and Laura Benitez

Microbiol. Res. 2021, 12(2), 403-418; https://doi.org/10.3390/microbiolres12020028 - 30 Apr 2021

Cited by 24 | Viewed by 4652

Abstract

Avian pox is a widespread infection in birds caused by genus Avipoxvirus pathogens. It is a noteworthy, potentially lethal disease to wild and domestic hosts. It can produce two different conditions: cutaneous pox, and diphtheritic pox. Here, we carry out an exhaustive review [...] Read more.

Avian pox is a widespread infection in birds caused by genus Avipoxvirus pathogens. It is a noteworthy, potentially lethal disease to wild and domestic hosts. It can produce two different conditions: cutaneous pox, and diphtheritic pox. Here, we carry out an exhaustive review of all cases of avian pox reported from wild birds to analyze the effect and distribution in different avian species. Avian poxvirus strains have been detected in at least 374 wild bird species, a 60% increase on a 1999 review on avian pox hosts. We also analyze epizootic cases and if this disease contributes to wild bird population declines. We frequently observe very high prevalence in wild birds in remote island groups, e.g., Hawaii, Galapagos, etc., representing a major risk for the conservation of their unique endemic avifauna. However, the difference in prevalence between islands and continents is not significant given the few available studies. Morbidity and mortality can also be very high in captive birds, due to high population densities. However, despite the importance of the disease, the current detection rate of new Avipoxvirus strains suggests that diversity is incomplete for this group, and more research is needed to clarify its real extent, particularly in wild birds. Full article

► Show Figures

Figure 1

8 pages, 1743 KiB

Open AccessBrief Report

Virucidal Efficacy of Household Dishwashers

by Ralf Lucassen, Mirko Weide and Dirk Bockmühl

Microbiol. Res. 2021, 12(2), 395-402; https://doi.org/10.3390/microbiolres12020027 - 27 Apr 2021

Cited by 7 | Viewed by 3075

Abstract

Not only since SARS-CoV-2, have transmission routes of viruses been of interest. Noroviruses e.g., can be transmitted via smear infection, are relatively stable in the environment and very resistant to chemical disinfection. Some studies determined the virucidal efficacy of laundering processes, but few [...] Read more.

Not only since SARS-CoV-2, have transmission routes of viruses been of interest. Noroviruses e.g., can be transmitted via smear infection, are relatively stable in the environment and very resistant to chemical disinfection. Some studies determined the virucidal efficacy of laundering processes, but few studies focused on the virucidal efficacy of dishwashing processes. Here, especially consumer related conditions are of interest. Households for example are a hotspot of norovirus infection and thus a sufficient reduction of these and other viruses from dishes must be insured to avoid an infection via this route. The likelihood of such an event should not be underestimated, since it was shown that the washing machine can be a reservoir for the transmission of extended spectrum beta-lactamase producing bacteria in newborns. Although viruses do not replicate in these devices a transmission via contaminated cutlery e.g., cannot be excluded. Using a consumer related approach to determine the virucidal efficacy of dishwashers, we found a combination of a bleach containing dishwasher detergent, a cleaning temperature of 45 °C for 45 min and a rinsing temperature of 50 °C, to be sufficient to reduces viral titer of bovine corona virus, murine norovirus and modified vaccinia virus by 4.8, 4.2 and 3.8 logarithmic stages respectively. Full article

► Show Figures

Figure 1

12 pages, 869 KiB

Open AccessReview

Genetic Environments of Plasmid-Mediated bla_CTXM-15 Beta-Lactamase Gene in Enterobacteriaceae from Africa

by Babafela B. Awosile and Michael Agbaje

Microbiol. Res. 2021, 12(2), 383-394; https://doi.org/10.3390/microbiolres12020026 - 21 Apr 2021

Cited by 11 | Viewed by 3788

Abstract

The most widely distributed bla_CTX-M gene on a global scale is bla_CTX-M-15. The dissemination has been associated with clonal spread and different types of mobile genetic elements. The objective of this review was to describe the genetic environments of the [...] Read more.

The most widely distributed bla_CTX-M gene on a global scale is bla_CTX-M-15. The dissemination has been associated with clonal spread and different types of mobile genetic elements. The objective of this review was to describe the genetic environments of the bla_CTX-M-15 gene detected from Enterobacteriaceae in published literature from Africa. A literature search for relevant articles was performed through PubMed, AJOL, and Google Scholar electronic databases; 43 articles from 17 African countries were included in the review based on the eligibility criteria. Insertion sequences were reported as part of the genetic environment of bla_CTX-M-15 gene in 32 studies, integrons in 13 studies, and plasmids in 23 studies. In this review, five insertion sequences including ISEcp1, IS26, orf447, IS903, and IS3 have been detected which are associated with the genetic environment of bla_CTX-M-15 in Africa. Seven different genetic patterns were seen in the bla_CTX-M-15 genetic environment. Insertion sequence ISEcp1 was commonly located upstream of the end of the bla_CTX-M-15 gene, while the insertion sequence orf477 was located downstream. In some studies, ISEcp1 was truncated upstream of bla_CTX-M-15 by insertion sequences IS26 and IS3. The class 1 integron (Intl1) was most commonly reported to be associated with bla_CTX-M-15 (13 studies), with Intl1/dfrA17–aadA5 being the most common gene cassette array. IncFIA-FIB-FII multi-replicons and IncHI2 replicon types were the most common plasmid replicon types that horizontally transferred the bla_CTX-M-15 gene. Aminoglycoside-modifying enzymes, and plasmid-mediated quinolone resistance genes were commonly collocated with the bla_CTX-M-15 gene on plasmids. This review revealed the predominant role of ISEcp1, Intl1 and IncF plasmids in the mobilization and continental dissemination of the bla_CTX-M-15 gene in Africa. Full article

► Show Figures

Figure 1

7 pages, 594 KiB

Open AccessArticle

Effect of Bromination on the Quorum Sensing-Inhibiting Properties of Indole-3-Carboxaldehydes in Chromobacterium violaceum AHL System

by Chesley A. Kemp, Donna K. McCullough, Dobrusia Bialonska and Paul J. T. Johnson

Microbiol. Res. 2021, 12(2), 376-382; https://doi.org/10.3390/microbiolres12020025 - 12 Apr 2021

Cited by 4 | Viewed by 2215

Abstract

Quorum sensing (QS) is a form of bacterial communication involved in the production of virulence factors in many species. As a result, inhibition of quorum sensing may be of use in mitigating pathogenesis. The signaling molecule indole is currently being investigated as a [...] Read more.

Quorum sensing (QS) is a form of bacterial communication involved in the production of virulence factors in many species. As a result, inhibition of quorum sensing may be of use in mitigating pathogenesis. The signaling molecule indole is currently being investigated as a target for quorum sensing inhibition (QSI) and the indole derivative indole-3-carboxaldehyde (ICA) has been shown to inhibit quorum sensing-mediated behaviors in Escherichia coli. In this study, we investigate bromination as a method of increasing the QSI capabilities of indole carboxaldehydes. The IC₅₀ values of three monobrominated indole carboxaldehydes (5-bromoindole-3-carboxaldehyde, 6-bromoindole-3-carboxaldehyde, and 7-bromoindole-3-carboxaldehyde) were determined and compared to the IC₅₀ value of ICA. The bromination of these indole carboxaldehydes reduced the IC₅₀ values between 2- and 13-fold, indicating that bromination significantly increases the potency of these indole carboxaldehydes. Full article

► Show Figures

Figure 1

22 pages, 1211 KiB

Open AccessReview

Insights on Cadmium Removal by Bioremediation: The Case of Haloarchaea

by Mónica Vera-Bernal and Rosa María Martínez-Espinosa

Microbiol. Res. 2021, 12(2), 354-375; https://doi.org/10.3390/microbiolres12020024 - 11 Apr 2021

Cited by 11 | Viewed by 4458

Abstract

Although heavy metals are naturally found in the environment as components of the earth’s crust, environmental pollution by these toxic elements has increased since the industrial revolution. Some of them can be considered essential, since they play regulatory roles in different biological processes; [...] Read more.

Although heavy metals are naturally found in the environment as components of the earth’s crust, environmental pollution by these toxic elements has increased since the industrial revolution. Some of them can be considered essential, since they play regulatory roles in different biological processes; but the role of other heavy metals in living tissues is not clear, and once ingested they can accumulate in the organism for long periods of time causing adverse health effects. To mitigate this problem, different methods have been used to remove heavy metals from water and soil, such as chelation-based processes. However, techniques like bioremediation are leaving these conventional methodologies in the background for being more effective and eco-friendlier. Recently, different research lines have been promoted, in which several organisms have been used for bioremediation approaches. Within this context, the extremophilic microorganisms represent one of the best tools for the treatment of contaminated sites due to the biochemical and molecular properties they show. Furthermore, since it is estimated that 5% of industrial effluents are saline and hypersaline, halophilic microorganisms have been suggested as good candidates for bioremediation and treatment of this kind of samples. These microorganisms, and specifically the haloarchaea group, are of interest to design strategies aiming the removal of polluting compounds due to the efficiency of their metabolism under extreme conditions and their significant tolerance to highly toxic compounds such as heavy metals, bromate, nitrite, chlorate, or perchlorate ions. However, there are still few trials that have proven the bioremediation of environments contaminated with heavy metals using these microorganisms. This review analyses scientific literature focused on metabolic capabilities of haloarchaea that may allow these microbes to tolerate and eliminate heavy metals from the media, paying special attention to cadmium. Thus, this work will shed light on potential uses of haloarchaea in bioremediation of soils and waters negatively affected by heavy metals, and more specifically by cadmium. Full article

► Show Figures

Figure 1

19 pages, 1651 KiB

Open AccessReview

Manipulating the Microbiome: An Alternative Treatment for Bile Acid Diarrhoea

by Evette B. M. Hillman, Sjoerd Rijpkema, Danielle Carson, Ramesh P. Arasaradnam, Elizabeth M. H. Wellington and Gregory C. A. Amos

Microbiol. Res. 2021, 12(2), 335-353; https://doi.org/10.3390/microbiolres12020023 - 9 Apr 2021

Cited by 1 | Viewed by 10116

Abstract

Bile acid diarrhoea (BAD) is a widespread gastrointestinal disease that is often misdiagnosed as irritable bowel syndrome and is estimated to affect 1% of the United Kingdom (UK) population alone. BAD is associated with excessive bile acid synthesis secondary to a gastrointestinal or [...] Read more.

Bile acid diarrhoea (BAD) is a widespread gastrointestinal disease that is often misdiagnosed as irritable bowel syndrome and is estimated to affect 1% of the United Kingdom (UK) population alone. BAD is associated with excessive bile acid synthesis secondary to a gastrointestinal or idiopathic disorder (also known as primary BAD). Current licensed treatment in the UK has undesirable effects and has been the same since BAD was first discovered in the 1960s. Bacteria are essential in transforming primary bile acids into secondary bile acids. The profile of an individual’s bile acid pool is central in bile acid homeostasis as bile acids regulate their own synthesis. Therefore, microbiome dysbiosis incurred through changes in diet, stress levels and the introduction of antibiotics may contribute to or be the cause of primary BAD. This literature review focuses on primary BAD, providing an overview of bile acid metabolism, the role of the human gut microbiome in BAD and the potential options for therapeutic intervention in primary BAD through manipulation of the microbiome. Full article

► Show Figures

Figure 1

Figure 1
The schematic molecular structure of common bile acids found in humans annotated to show its relationship to other bile acids. α (represented by a dashed line) indicates a steric downwards orientation and β (represented by a solid line) indicates a steric upwards orientation. Full article ">Figure 2
Host and bacterial primary and secondary bile acid metabolisms. Host transformation from cholesterol by enzymes (boxed) cytochrome P450 family 7 subfamily A member 1 (CYP7A1), in the classical pathway and CYP27A1 in the alternative pathway produces cholic acid and chenodeoxycholic acid, which are conjugated with taurine or glycine. Bacterial transformation often requires deconjugation via bile salt hydrolases (BSH), which exposes the bile acid to a range of further modifications. For simplicity, only deoxycholic acid and lithocholic acid are shown here, following dehydroxylation by enzymes encoded in the bile acid-inducible (bai) operon. Full article ">Figure 3
Bile acids regulate their own expression as primary and secondary bile acids bind as agonists and antagonists to the nuclear receptor FXR, which transcriptionally activates the hormone FGF19 that inhibits CYP7A1 thus inhibiting bile acid synthesis. FXR, farnesoid X receptor; FGF19, fibroblast growth factor 19; CPY7A1, cholesterol-7α-hydroxylase; CYP27A1, Sterol-27-hydroxylase; C4, 7α-hydroxy-4-cholesten-3-one; BA, bile acid. Full article ">Figure 4
Intestinal bacterial homeostasis maintained by primary and secondary bile acids. Stress, diet and antibiotics induced dysbiosis are treated by manipulating the microbiome via faecal microbiota transplantation (FMT); faecal filtrate transfer (FFT); and live biotherapeutic products (LBP). Full article ">

18 pages, 2460 KiB

Open AccessArticle

Software Benchmark—Classification Tree Algorithms for Cell Atlases Annotation Using Single-Cell RNA-Sequencing Data

by Omar Alaqeeli, Li Xing and Xuekui Zhang

Microbiol. Res. 2021, 12(2), 317-334; https://doi.org/10.3390/microbiolres12020022 - 7 Apr 2021

Cited by 2 | Viewed by 2469

Abstract

Classification tree is a widely used machine learning method. It has multiple implementations as R packages; rpart, ctree, evtree, tree and C5.0. The details of these implementations are not the same, and hence their performances differ from one application to another. We are [...] Read more.

Classification tree is a widely used machine learning method. It has multiple implementations as R packages; rpart, ctree, evtree, tree and C5.0. The details of these implementations are not the same, and hence their performances differ from one application to another. We are interested in their performance in the classification of cells using the single-cell RNA-Sequencing data. In this paper, we conducted a benchmark study using 22 Single-Cell RNA-sequencing data sets. Using cross-validation, we compare packages’ prediction performances based on their Precision, Recall,

F_{1}

-score, Area Under the Curve (AUC). We also compared the Complexity and Run-time of these R packages. Our study shows that rpart and evtree have the best Precision; evtree is the best in Recall,

F_{1}

-score and AUC; C5.0 prefers more complex trees; tree is consistently much faster than others, although its complexity is often higher than others. Full article

► Show Figures

Figure 1

18 pages, 3335 KiB

Open AccessArticle

Metabacillus schmidteae sp. nov., Cultivated from Planarian Schmidtea mediterranea Microbiota

by Luis Johnson Kangale, Didier A. Raoult, Eric Ghigo and Pierre-Edouard Fournier

Microbiol. Res. 2021, 12(2), 299-316; https://doi.org/10.3390/microbiolres12020021 - 2 Apr 2021

Cited by 5 | Viewed by 4432

Abstract

Taxonogenomics combines phenotypic assays and genomic analysis as a means of characterizing novel strains. We used this strategy to study Marseille-P9898^T strain, an aerobic, motile, Gram-negative, spore-forming, and rod-shaped bacterium isolated from planarian Schmidtea mediterranea. Marseille-P9898^T is catalase-positive and oxidase-negative. [...] Read more.

Taxonogenomics combines phenotypic assays and genomic analysis as a means of characterizing novel strains. We used this strategy to study Marseille-P9898^T strain, an aerobic, motile, Gram-negative, spore-forming, and rod-shaped bacterium isolated from planarian Schmidtea mediterranea. Marseille-P9898^T is catalase-positive and oxidase-negative. The major fatty acids detected are 12-methyl-tetradecanoic acid, 13-methyl-tetradecanoic acid, and hexadecanoic acid. Marseille-P9898^T strain shared more than 98% sequence similarity with the Metabacillus niabensis strain 4T19^T (98.99%), Metabacillus halosaccharovorans strain E33^T (98.75%), Metabacillus malikii strain NCCP-662^T (98.19%), and Metabacillus litoralis strain SW-211^T (97.15%). Marseille-P9898 strain belongs to Metabacillus genus. Genomic analysis revealed the highest similarities with Ortho-ANI and dDDH, 85.76% with Metabacillus halosaccharovorans, and 34.20% with Bacillus acidicola, respectively. These results show that the Marseille-P9898^T strain is a novel bacterial species from Metabacillus genus, for which we propose the name of Metabacillus schmidteae sp. nov. (Type strain Marseille-P9898^T = CSUR P9898^T = DSM 111480^T). Full article

► Show Figures

Figure 1

Figure 1
Transmission electron microscopy of Marseille-P9898 strain. Bacteria are rod-shaped and exhibit a polar flagellum (black arrow). Scale bar = 10.0 µm. Full article ">Figure 2
Gram staining of Marseille-P9898 strain. Full article ">Figure 3
Phylogenetic tree carried out from a comparative analysis of 16S rRNA gene sequences indicating the relationships between Marseille-P9898 strain and related species. Sequences are aligned using the MUSCLE algorithm with default parameters and phylogenies are inferred by the MEGAX software (version 10.1). Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 1000 times to generate a majority consensus tree. Only bootstrap values ≥ 50% are retained. Scale bare indicates a 0.01% sequence divergence. Full article ">Figure 4
The numeric map is generated with Ortho-ANI values calculated using OAT software between the Marseille-P9898 strain and related species with nomenclature classification. Color code shows closely (in red) to the farthest (in green) related species. Metabacillus halosaccharovorans, Metabacillus litoralis, and Metabacillus niabensis are closely related to Metabacillus schmidteae. Full article ">Figure 5
Comparison of predicted genes according to the COGs of Marseille-P9898 strain and related species. Metabacillus halosaccharovorans, Metabacillus litoralis, and Metabacillus niabensis are closely related to Metabacillus schmidteae. [B] Chromatin structure and dynamics; [C] Energy production and conversion; [D] Cell cycle control, cell division, chromosome partitioning; [E] Amino acid transport and metabolism; [F] Nucleotide transport and metabolism; [G] Carbohydrate transport and metabolism; [H] Coenzyme transport and metabolism; [I] Lipid transport and metabolism; [J] Translation, ribosomal structure, and biogenesis; [K] Transcription; [L] Replication, recombination, and repair; [M] Cell wall/membrane/envelope biogenesis; [N] Cell motility; [O] Posttranslational modification, protein turnover, chaperones; [P] Inorganic ion transport and metabolism; [Q] Secondary metabolites biosynthesis, transport, and catabolism; [R] General function prediction only; [S] Function unknown; [T] Signal transduction mechanisms; [U] Intracellular trafficking, secretion, and vesicular transport; [V] Defense mechanisms; [W] Extracellular structures; [X] Mobilome: prophages, transposons; [Z] Cytoskeleton. Full article ">

11 pages, 1495 KiB

Open AccessArticle

Hurdle Effects of Ethanolic Plant Extracts with Antimicrobials Commonly Used in Food against Foodborne Pathogenic Escherichia coli

by Waraporn Kusalaruk and Hiroyuki Nakano

Microbiol. Res. 2021, 12(2), 288-298; https://doi.org/10.3390/microbiolres12020020 - 2 Apr 2021

Cited by 4 | Viewed by 3564

Abstract

Escherichia coli (E. coli) O157:H7 is a major foodborne pathogen that causes severe human infections. Plant extracts, glycine, and sodium acetate (NaOAc) exert antimicrobial effects that can be used to control pathogenic E. coli. However, their combinations have not been investigated. [...] Read more.

Escherichia coli (E. coli) O157:H7 is a major foodborne pathogen that causes severe human infections. Plant extracts, glycine, and sodium acetate (NaOAc) exert antimicrobial effects that can be used to control pathogenic E. coli. However, their combinations have not been investigated. Thus, this study investigates the combination of ethanolic plant extracts with glycine and NaOAc against E. coli at various pH and temperature levels. Clove and rosemary extracts exhibited significant (p ≤ 0.05) antimicrobial activity against E. coli. At neutral pH, the combination of plant extracts with 1.0% glycine or 0.1% NaOAc reduced the minimum inhibitory concentration of clove from 0.4% to 0.2%; at pH 5.5, clove (0.1%) and rosemary (0.2%) extracts supplemented with NaOAc (0.1%) showed an additive effect. The population of E. coli O157:H7 in phosphate-buffered saline with 0.2% clove extract, 2% glycine, and 2% NaOAc showed a more than 5 log reduction after incubation at 15 °C for 96 h, while the combination of 0.1% clove extract with 2% NaOAc at pH 5.5 completely inhibited E. coli within 24 h at 35 °C. Thus, the combination of plant extracts with glycine and NaOAc could serve as a promising hurdle technology in controlling the growth of E. coli. Full article

► Show Figures

Graphical abstract

20 pages, 2587 KiB

Open AccessArticle

Pedobacter ghigonii sp. nov., Isolated from the Microbiota of the Planarian Schmidtea mediterranea

by Luis Johnson Kangale, Didier Raoult and Fournier Pierre-Edouard

Microbiol. Res. 2021, 12(2), 268-287; https://doi.org/10.3390/microbiolres12020019 - 1 Apr 2021

Cited by 2 | Viewed by 2758

Abstract

The planarian S. mediterranea is a platyhelminth with worldwide distribution that can regenerate any part of its body after amputation and has the capacity to eliminate a large spectrum of human bacterial pathogens. Surprisingly, the microbiota of S. mediterranea remains poorly investigated. Using [...] Read more.

The planarian S. mediterranea is a platyhelminth with worldwide distribution that can regenerate any part of its body after amputation and has the capacity to eliminate a large spectrum of human bacterial pathogens. Surprisingly, the microbiota of S. mediterranea remains poorly investigated. Using the culturomics strategy to study the bacterial component of planarians, we isolated a new bacterial strain, Marseille-Q2390, which we characterized with the taxono-genomic approach that associates phenotypic assays and genome sequencing and analysis. Strain Marseille-Q2390 exhibited a 16S rRNA sequence similarity of 99.36% with Pedobacter kyungheensis strain THG-T17^T, the closest phylogenetic neighbor. It is a white-pigmented, Gram-negative, and rod-shaped bacterium. It grows in aerobic conditions and belongs to the family Sphingobacteriaceae. The genome of strain Marseille-Q2390 is 5,919,359 bp-long, with a G + C content of 40.3%. By comparing its genome with other closely related strains, the highest Orthologous Average Nucleotide Identity (Ortho-ANI) and digital DNA-DNA hybridization (dDDH) values were 85.71% and 30.50%, respectively, which were found with Pedobacter soli strain 15-51^T. We conclude that strain Marseille-Q2390^T is sufficiently different from other nearby species to be classified within a new species for which we propose the name Pedobacter ghigonii sp. nov. Full article

► Show Figures

Figure 1

10 pages, 1391 KiB

Open AccessArticle

Sodium Pyruvate Ameliorates Influenza A Virus Infection In Vivo

by Jessica M. Reel and Christopher R. Lupfer

Microbiol. Res. 2021, 12(2), 258-267; https://doi.org/10.3390/microbiolres12020018 - 26 Mar 2021

Cited by 1 | Viewed by 2927

Abstract

Influenza A virus (IAV) causes seasonal epidemics annually and pandemics every few decades. Most antiviral treatments used for IAV are only effective if administered during the first 48 h of infection and antiviral resistance is possible. Therapies that can be initiated later during [...] Read more.

Influenza A virus (IAV) causes seasonal epidemics annually and pandemics every few decades. Most antiviral treatments used for IAV are only effective if administered during the first 48 h of infection and antiviral resistance is possible. Therapies that can be initiated later during IAV infection and that are less likely to elicit resistance will significantly improve treatment options. Pyruvate, a key metabolite, and an end product of glycolysis, has been studied for many uses, including its anti-inflammatory capabilities. Sodium pyruvate was recently shown by us to decrease inflammasome activation during IAV infection. Here, we investigated sodium pyruvate’s effects on IAV in vivo. We found that nebulizing mice with sodium pyruvate decreased morbidity and weight loss during infection. Additionally, treated mice consumed more chow during infection, indicating improved symptoms. There were notable improvements in pro-inflammatory cytokine production (IL-1β) and lower virus titers on day 7 post-infection in mice treated with sodium pyruvate compared to control animals. As pyruvate acts on the host immune response and metabolic pathways and not directly on the virus, our data demonstrate that sodium pyruvate is a promising treatment option that is safe, effective, and unlikely to elicit antiviral resistance. Full article

► Show Figures

Figure 1

Figure 1
Sodium pyruvate (NaPyr) shows no toxicity in mice. WT C57BL/6J mice were nebulized 3 times daily for 15 min per treatment with 10 mM and 1 M concentrations of NaPyr diluted in phosphate buffered saline (PBS) for 14 days to determine toxicity and weight differences between treatment groups. Data are representative of one experiment with n = 5 mice per treatment group. Full article ">Figure 2
Effects of injection or nebulization of NaPyr on influenza A virus (IAV) infection. WT C57BL/6J mice were infected intranasally with 250 PFU of influenza A/PR/8/34 H1N1. Mice were treated as indicated and monitored daily for 14 days to determine survival and weight differences between treatment groups. (A) Weight loss was examined in mice injected Sub-Q with 55 mg/kg NaPyr twice a day for 14-days compared to PBS injected mice. (B) Average chow intake over the 14-day IAV infection of both Sub-Q NaPyr treated and PBS treated mice. (C) Mice were treated 3 times a day with either nebulized 10 mM NaPyr or nebulized PBS as control. Weight loss differences viewed over the 14-day IAV infection of both NaPyr treated and PBS treated mice. (D) Average chow intake over the 14-day IAV infection of both nebulized 10 mM NaPyr and PBS treated mice. Data are representative of 2–3 individual experiments with n = 4–5 mice per treatment group per independent experiment. Statistical significance was determined using a Two-way ANOVA with Fisher LSD post-hoc for multiple comparisons. * p < 0.05, ** p < 0.01. Full article ">Figure 3
Nebulized N115 improves weight loss and virus titer in mice infected with IAV. WT C57BL/6J mice were treated with either nebulized 20 mM NaPyr (N115) or nebulized PBS as control 3 times a day for 20 min/treatment to test for toxicity (A). WT C57BL/6J mice were infected intranasally with 250 PFU of influenza A/PR/8/34 H1N1. Mice were treated with either nebulized 20 mM NaPyr (N115) or nebulized PBS as control 3 times a day for 20 min/treatment. (B) Mice were monitored daily for 14 days to determine weight differences between treatment groups. (C) Average chow intake over the 14-day IAV infection of both N115 treated and PBS treated mice. (D,E) Viral titer was assessed by plaque assay on day 3 (D) and day 7 (E) p.i. from lung homogenates. Weight loss and chow intake data are representative of 3 independent experiments with n = 4–6 mice per treatment group per independent experiment. Viral titer data are representative of 2 individual experiments with 3–5 mice per treatment group per individual experiment. Statistical significance was determined using a Two-way ANOVA with Fisher LSD post-hoc for multiple comparisons, and Student’s t-test for single comparisons. * p < 0.05, ** p < 0.01, *** p < 0.001. Full article ">Figure 4
N115 treatment modulates inflammatory responses during IAV infection. WT C57BL/6J mice were anesthetized and infected with 250 PFU of influenza A/PR/8/34 H1N1. Mice were treated 3 times a daily for 20 min/treatment with either nebulized 20 mM NaPyr (N115) or nebulized PBS as control. Mice were euthanized on day 3 (A) or day 7 p.i. (B–D) for tissue collection. Lung samples were then homogenized and examined via ELISA for cytokine production (A,B) or cellular infiltration into the lungs by flow cytometry (C,D). Data are combined from 2 independent experiments with n = 3–5 mice per experiment. Statistical significance was determined using a Student’s t-test for single comparisons. * p < 0.05, ** p < 0.01. Full article ">

Journal Menu

Journal Browser

Microbiol. Res., Volume 12, Issue 2 (June 2021) – 19 articles

Further Information

Guidelines

MDPI Initiatives

Follow MDPI