54 pages, 2728 KiB  
Review
The Diversity of Escherichia coli Pathotypes and Vaccination Strategies against This Versatile Bacterial Pathogen
by Pravil Pokharel 1,2,†, Sabin Dhakal 1,2,† and Charles M. Dozois 1,2,3,*
1 Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), 531 Boul des Prairies, Laval, QC H7V 1B7, Canada
2 Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, Saint-Hyacinthe, QC J2S 2M2, Canada
3 Pasteur Network, Laval, QC H7V 1B7, Canada
† These authors equally contributed to this work.
Microorganisms 2023, 11(2), 344; https://doi.org/10.3390/microorganisms11020344 - 30 Jan 2023
Cited by 122 | Viewed by 37753
Abstract
Escherichia coli (E. coli) is a gram-negative bacillus and resident of the normal intestinal microbiota. However, some E. coli strains can cause diseases in humans, other mammals and birds ranging from intestinal infections, for example, diarrhea and dysentery, to extraintestinal infections, [...] Read more.
Escherichia coli (E. coli) is a gram-negative bacillus and resident of the normal intestinal microbiota. However, some E. coli strains can cause diseases in humans, other mammals and birds ranging from intestinal infections, for example, diarrhea and dysentery, to extraintestinal infections, such as urinary tract infections, respiratory tract infections, meningitis, and sepsis. In terms of morbidity and mortality, pathogenic E. coli has a great impact on public health, with an economic cost of several billion dollars annually worldwide. Antibiotics are not usually used as first-line treatment for diarrheal illness caused by E. coli and in the case of bloody diarrhea, antibiotics are avoided due to the increased risk of hemolytic uremic syndrome. On the other hand, extraintestinal infections are treated with various antibiotics depending on the site of infection and susceptibility testing. Several alarming papers concerning the rising antibiotic resistance rates in E. coli strains have been published. The silent pandemic of multidrug-resistant bacteria including pathogenic E. coli that have become more difficult to treat favored prophylactic approaches such as E. coli vaccines. This review provides an overview of the pathogenesis of different pathotypes of E. coli, the virulence factors involved and updates on the major aspects of vaccine development against different E. coli pathotypes. Full article
(This article belongs to the Special Issue Virulence Genes, Antimicrobial Resistance Profiles and Genetic Diversity of Escherichia coli)
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21 pages, 3262 KiB  
Article
Exploration of the Nuclear Proteomes in the Ciliate Oxytricha trifallax
by Michael W. Lu 1, Leslie Y. Beh 2, V. Talya Yerlici 2, Wenwen Fang 3, Katarzyna Kulej 4, Benjamin A. Garcia 5 and Laura F. Landweber 1,2,*
1 Department of Biological Sciences, Columbia University, New York, NY 10025, USA
2 Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
3 RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA 01655, USA
4 Division of Protective Immunity and Division of Cancer Pathobiology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
5 Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63130, USA
Microorganisms 2023, 11(2), 343; https://doi.org/10.3390/microorganisms11020343 - 30 Jan 2023
Cited by 1 | Viewed by 2832
Abstract
Nuclear dimorphism is a fundamental feature of ciliated protozoa, which have separate somatic and germline genomes in two distinct organelles within a single cell. The transcriptionally active somatic genome, contained within the physically larger macronucleus, is both structurally and functionally different from the [...] Read more.
Nuclear dimorphism is a fundamental feature of ciliated protozoa, which have separate somatic and germline genomes in two distinct organelles within a single cell. The transcriptionally active somatic genome, contained within the physically larger macronucleus, is both structurally and functionally different from the silent germline genome housed in the smaller micronucleus. This difference in genome architecture is particularly exaggerated in Oxytricha trifallax, in which the somatic genome comprises tens of thousands of gene-sized nanochromosomes maintained at a high and variable ploidy, while the germline has a diploid set of megabase-scale chromosomes. To examine the compositional differences between the nuclear structures housing the genomes, we performed a proteomic survey of both types of nuclei and of macronuclear histones using quantitative mass spectrometry. We note distinct differences between the somatic and germline nuclei, with many functional proteins being highly enriched in one of the two nuclei. To validate our conclusions and the efficacy of nuclear separation, we used protein localization through a combination of transformations and immunofluorescence. We also note that the macronuclear histones strikingly display only activating marks, consistent with the conclusion that the macronucleus is the hub of transcription. These observations suggest that the compartmentalization of different genome features into separate structures has been accompanied by a similar specialization of nuclear components that maintain and facilitate the functions of the genomes specific to each nucleus. Full article
(This article belongs to the Special Issue Ciliates as Model Organisms: From ‘omics’ to Genetics, Ecology and Signaling)
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12 pages, 741 KiB  
Article
Antibiofilm Potential of Coelomic Fluid and Paste of Earthworm Pheretima posthuma (Clitellata, Megascolecidae) against Pathogenic Bacteria
by Mudassar Hussain 1, Iram Liaqat 1,*, Urooj Zafar 2, Sadiah Saleem 2, Muhammad Nauman Aftab 3, Awais Khalid 4, Yosra Modafer 5, Fahdah Ayed Alshammari 6, Abdullah Mashraqi 7 and Ahmed A. El-Mansi 8,9
1 Microbiology Lab, Department of Zoology, Government College University, Lahore 54000, Pakistan
2 Department of Microbiology, University of Karachi, Karachi 75270, Pakistan
3 Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
4 Department of Physics, Hazara University Mansehra, Mansehra 21300, Pakistan
5 Department of Biology, College of Science, Jazan University, Jazan 45142, Saudi Arabia
6 Department of Biology, Faculty of Science and Arts—RAFHA, Northern Border University, Rafha 73213, Saudi Arabia
7 Department of Biology, College of Science, Jazan University, Jazan 82817, Saudi Arabia
8 Department of Biology, Faculty of Science, King Khalid University, Abha 62529, Saudi Arabia
9 Department of Zoology, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
Microorganisms 2023, 11(2), 342; https://doi.org/10.3390/microorganisms11020342 - 30 Jan 2023
Cited by 7 | Viewed by 3414
Abstract
Antibiotic drug resistance is a global public health issue that demands new and novel therapeutic molecules. To develop new agents, animal secretions or products are used as an alternative agent to overcome this problem. In this study, earthworm (Pheretima posthuma) coelomic [...] Read more.
Antibiotic drug resistance is a global public health issue that demands new and novel therapeutic molecules. To develop new agents, animal secretions or products are used as an alternative agent to overcome this problem. In this study, earthworm (Pheretima posthuma) coelomic fluid (PCF), and body paste (PBP) were used to analyze their effects as antibiofilm agents against four bacterial isolates MH1 (Pseudomonas aeruginosa MT448672), MH2 (Escherichia coli MT448673), MH3 (Staphylococcus aureus MT448675), and MH4 (Klebsiella pneumoniae MT448676). Coelomic fluid extraction and body paste formation were followed by minimum inhibitory concentrations (MICs), biofilm formation time kinetics, and an antibiofilm assay, using heat and cold shock, sunlight exposure auto-digestion, and test tube methods. The results showed that the MIC values of PCF and PBP against S. aureus, P. aeruginosa, K. pneumoniae, and E. coli bacterial isolates ranged from 50 to 100 μg/mL, while, the results related to biofilm formation for P. aeruginosa, S. aureus, and K. pneumoniae strains were observed to be highly significantly increased (p < 0.005) after 72 h. E. coli produced a significant (p < 0.004) amount of biofilm after 48 h. Following time kinetics, the antibiofilm activity of PCF and PBP was tested at different concentrations (i.e., 25–200 μg/mL) against the aforementioned four strains (MH1–MH4). The findings of this study revealed that both PBP (5.61 ± 1.0%) and PCF (5.23 ± 1.5%) at the lowest concentration (25 μg/mL) showed non-significant (p > 0.05) antibiofilm activity against all the selected strains (MH1-MH4). At 50 μg/mL concentration, both PCF and PBP showed significant (p < 0.05) biofilm inhibition (<40%) for all isolates. Further, the biofilm inhibitory potential was also found to be more significant (p < 0.01) at 100 μg/mL of PCF and PBP, while it showed highly significant (p < 0.001) biofilm inhibition at 150 and 200 μg/mL concentrations. Moreover, more than 90% biofilm inhibition was observed at 200 μg/mL of PCF, while in the case of the PBP, <96% biofilm reduction (i.e., 100%) was also observed by all selected strains at 200 μg/mL. In conclusion, earthworm body fluid and paste have biologically active components that inhibit biofilm formation by various pathogenic bacterial strains. For future investigations, there is a need for further study to explore the potential bioactive components and investigate in depth their molecular mechanisms from a pharmaceutical perspective for effective clinical utilization. Full article
(This article belongs to the Special Issue Antimicrobial Activities of Natural Products)
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17 pages, 1801 KiB  
Review
Epigenetic Targets and Pathways Linked to SARS-CoV-2 Infection and Pathology
by Ali A. Rabaan 1,2,3,*, Mohammed Aljeldah 4, Basim R. Al Shammari 4, Roua A. Alsubki 5, Jawaher Alotaibi 6, Yousef N. Alhashem 7, Neda A. Alali 8, Tarek Sulaiman 9, Zainab Alsalem 10, Huda A. Bajunaid 11, Mohammed Garout 12, Heba A. Alsaffar 13, Souad A. Almuthree 14, Doha Hudhaiah 15, Azhar M. Alzaher 16, Fatimah A. Alshaikh 17, Amer Alshengeti 18,19, Mustafa A. Najim 20, Ramadan Abdelmoez Farahat 21 and Ranjan K. Mohapatra 22,*
1 Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
2 College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
3 Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
4 Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
5 Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia
6 Infectious Diseases Unit, Department of Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
7 Clinical Laboratory Science Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia
8 Pediatric Department, Security Force Hospital, Riyadh 13526, Saudi Arabia
9 Infectious Diseases Section, Medical Specialties Department, King Fahad Medical City, Riyadh 12231, Saudi Arabia
10 Department of Epidemic Diseases Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
11 Makkah Specialized Laboratory, Fakeeh Care Group, Hadda 25321, Saudi Arabia
12 Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
13 Department of Azizia Primary Health Care, Ministry of Health, Dammam 32211, Saudi Arabia
14 Department of Infectious Disease, King Abdullah Medical City, Makkah 43442, Saudi Arabia
15 Microbiology Laboratory, King Fahad University Hospital, Al Khobar 34445, Saudi Arabia
16 Improvement of Operation Department, Qatif Health Network, Qatif 31911, Saudi Arabia
17 Infection Prevention and Control Department, Qatif Central Hospital, Qatif 32654, Saudi Arabia
18 Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia
19 Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah 41491, Saudi Arabia
20 Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah 41411, Saudi Arabia
21 Faculty of Medicine, Kafrelsheikh University, Kafrelsheikh 33511, Egypt
22 Department of Chemistry, Government College of Engineering, Keonjhar 758002, India
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Microorganisms 2023, 11(2), 341; https://doi.org/10.3390/microorganisms11020341 - 30 Jan 2023
Cited by 2 | Viewed by 3142
Abstract
The scale at which the SARS-CoV-2/COVID-19 pandemic has spread remains enormous. Provided the genetic makeup of the virus and humans is readily available, the quest for knowing the mechanism and epidemiology continues to prevail across the entire scientific community. Several aspects, including immunology, [...] Read more.
The scale at which the SARS-CoV-2/COVID-19 pandemic has spread remains enormous. Provided the genetic makeup of the virus and humans is readily available, the quest for knowing the mechanism and epidemiology continues to prevail across the entire scientific community. Several aspects, including immunology, molecular biology, and host-pathogen interaction, are continuously being dug into for preparing the human race for future pandemics. The exact reasons for vast differences in symptoms, pathophysiological implications of COVID-infections, and mortality differences remain elusive. Hence, researchers are also looking beyond traditional genomics, proteomics, and transcriptomics approach, especially entrusting the environmental regulation of the genetic landscape of COVID–human interactions. In line with these questions lies a critical process called epigenetics. The epigenetic perturbations in both host and parasites are a matter of great interest to unravel the disparities in COVID-19 mortalities and pathology. This review provides a deeper insight into current research on the epigenetic landscape of SARS-CoV-2 infection in humans and potential targets for augmenting the ongoing investigation. It also explores the potential targets, pathways, and networks associated with the epigenetic regulation of processes involved in SARS-CoV-2 pathology. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection)
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10 pages, 1166 KiB  
Article
Genomic Characterization of Three Novel Bartonella Strains in a Rodent and Two Bat Species from Mexico
by Jonathan Gonçalves-Oliveira 1, Ricardo Gutierrez 2, Cory Lee Schlesener 3, David A. Jaffe 3, Alvaro Aguilar-Setién 4, Henri-Jean Boulouis 5, Yaarit Nachum-Biala 1, Bihua C. Huang 3, Bart C. Weimer 3, Bruno B. Chomel 3 and Shimon Harrus 1,*
1 Laboratory of Zoonotic Vector-Borne Diseases—The Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot 76100, Israel
2 National Reference Center for Bacteriology, Costa Rican Institute for Research and Teaching in Nutrition and Health (INCIENSA), Tres Rios 4-2250, Costa Rica
3 Department of Population Health and Reproduction, 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
4 Unidad de Investigación Médica en Inmunología, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, Mexico City 06720, Mexico
5 Équipe Vecteurs et Agents Microbiens Pathogènes ENVA–Anses–INRA–UMR BIPAR, École Nationale Vétérinaire d’Alfort, 7, Avenue du Général de Gaulle, Maisons-Alfort, CEDEX, 94704 Paris, France
Microorganisms 2023, 11(2), 340; https://doi.org/10.3390/microorganisms11020340 - 30 Jan 2023
Cited by 5 | Viewed by 2855
Abstract
Rodents and bats are the most diverse mammal group that host Bartonella species. In the Americas, they were described as harboring Bartonella species; however, they were mostly characterized to the genotypic level. We describe here Bartonella isolates obtained from blood samples of one [...] Read more.
Rodents and bats are the most diverse mammal group that host Bartonella species. In the Americas, they were described as harboring Bartonella species; however, they were mostly characterized to the genotypic level. We describe here Bartonella isolates obtained from blood samples of one rodent (Peromyscus yucatanicus from San José Pibtuch, Yucatan) and two bat species (Desmodus rotundus from Progreso, and Pteronotus parnellii from Chamela-Cuitzmala) from Mexico. We sequenced and described the genomic features of three Bartonella strains and performed phylogenomic and pangenome analyses to decipher their phylogenetic relationships. The mouse-associated genome was closely related to Bartonella vinsonii. The two bat-associated genomes clustered into a single distinct clade in between lineages 3 and 4, suggesting to be an ancestor of the rodent-associated Bartonella clade (lineage 4). These three genomes showed <95% OrthoANI values compared to any other Bartonella genome, and therefore should be considered as novel species. In addition, our analyses suggest that the B. vinsonii complex should be revised, and all B. vinsonii subspecies need to be renamed and considered as full species. The phylogenomic clustering of the bat-associated Bartonella strains and their virulence factor profile (lack of the Vbh/TraG conjugation system remains of the T4SS) suggest that it should be considered as a new lineage clade (L5) within the Bartonella genus. Full article
(This article belongs to the Special Issue Domestic Animals and Wildlife Zoonotic Microorganisms)
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22 pages, 3873 KiB  
Article
A 7-Week Summer Camp in Antarctica Induces Fluctuations on Human Oral Microbiome, Pro-Inflammatory Markers and Metabolic Hormones Profile
by Michele M. Moraes 1,2, Thiago T. Mendes 3, Leandro Borges 4, Alice L. Marques 5, Cristian Núñez-Espinosa 6,7,8, Dawit A. P. Gonçalves 9,10, Carolina B. Simões 9,10, Tales S. Vieira 9, Roberto V. P. Ladeira 2, Talita G. B. Lourenço 11, Danielle V. Ribeiro 12,13, Elaine Hatanaka 4, Debora Heller 12,13,14 and Rosa M. E. Arantes 1,2,*
1 Department of Pathology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
2 Center for Newborn Screening and Genetics Diagnosis, Faculty of Medicine, Universidade Federal de Minas Gerais, NUPAD-FM/UFMG, Belo Horizonte 30130-100, MG, Brazil
3 Department of Physical Education, Faculty of Education, Universidade Federal da Bahia, Salvador 40170-110, BA, Brazil
4 Interdisciplinary Program in Health Sciences, Universidade Cruzeiro do Sul, São Paulo 01506-000, SP, Brazil
5 Post-Graduation Program in Social Sciences in Development, Culture and Society of the Universidade Federal Rural do Rio de Janeiro, Seropédica 23890-000, RJ, Brazil
6 School of Medicine, Universidad de Magallanes, Punta Arenas 6200000, Chile
7 Austral Integrative Neurophysiology Group, Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6200000, Chile
8 Interuniversity Center for Healthy Aging, Punta Arenas 6200000, Chile
9 Exercise Physiology Laboratory, School of Physical Education, Physiotherapy and Occupational Therapy, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
10 Sports Training Center, School of Physical Education, Physiotherapy and Occupational Therapy, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
11 Oral Microbiology Laboratory, Institute of Microbiology Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
12 Hospital Israelita Albert Einstein, São Paulo 05652-900, SP, Brazil
13 Post-Graduate Studies in Dentistry, Universidade Cruzeiro do Sul, São Paulo 430-0926, SP, Brazil
14 Department of Periodontology, School of Dentistry, UT Health San Antonio, San Antonio, TX 78229, USA
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Microorganisms 2023, 11(2), 339; https://doi.org/10.3390/microorganisms11020339 - 30 Jan 2023
Cited by 4 | Viewed by 3281
Abstract
Antarctic camps pose psychophysiological challenges related to isolated, confined, and extreme (ICE) conditions, including meals composed of sealed food. ICE conditions can influence the microbiome and inflammatory responses. Seven expeditioners took part in a 7-week Antarctic summer camp (Nelson Island) and were evaluated [...] Read more.
Antarctic camps pose psychophysiological challenges related to isolated, confined, and extreme (ICE) conditions, including meals composed of sealed food. ICE conditions can influence the microbiome and inflammatory responses. Seven expeditioners took part in a 7-week Antarctic summer camp (Nelson Island) and were evaluated at Pre-Camp (i.e., at the beginning of the ship travel), Camp-Initial (i.e., 4th and 5th day in camp), Camp-Middle (i.e., 19th–20th, and 33rd–34th days), Camp-Final (i.e., 45th–46th day), and at the Post-Camp (on the ship). At the Pre-Camp, Camp-Initial, and Camp-Final, we assessed microbiome and inflammatory markers. Catecholamines were accessed Pre- and Post-Camp. Heart rate variability (HRV), leptin, thyroid stimulating hormone (TSH), and thyroxine (T4) were accessed at all time points. Students’ t-tests or repeated-measures analysis of variance (one or two-way ANOVA) followed by Student-Newman-Keuls (post hoc) were used for parametric analysis. Kruskal-Wallis test was applied for non-parametric analysis. Microbiome analysis showed a predominance of Pseudomonadota (34.01%), Bacillota (29.82%), and Bacteroidota (18.54%), followed by Actinomycetota (5.85%), and Fusobacteria (5.74%). Staying in a long-term Antarctic camp resulted in microbiome fluctuations with a reduction in Pseudomonadota—a “microbial signature” of disease. However, the pro-inflammatory marker leptin and IL-8 tended to increase, and the angiogenic factor VEGF was reduced during camp. These results suggest that distinct Antarctic natural environments and behavioral factors modulate oral microbiome and inflammation. Full article
(This article belongs to the Special Issue Customized Minimally Invasive Protocols for the Clinical and Microbiological Management of the Oral Microbiota)
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16 pages, 2225 KiB  
Article
A One-Year Systematic Study to Assess the Microbiological Profile in Oysters from a Commercial Harvesting Area in Portugal
by Inês C. Rodrigues 1,†, Nânci Santos-Ferreira 2,†, Daniela Silva 1, Carla Chiquelho da Silva 3, Ângela S. Inácio 4, Maria São José Nascimento 5 and Paulo Martins da Costa 1,6,*
1 ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
2 KU Leuven-Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
3 Department of Quality Control and Food Safety, Grupo Jerónimo Martins, Rua Nossa Sra. do Amparo, 4440-232 Porto, Portugal
4 CNC-Center for Neurosciences and Cell Biology, Faculty of Medicine, University of Coimbra, Rua Larga, Polo I, 3004–504 Coimbra, Portugal
5 Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
6 Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros do Porto, de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
† These authors contributed equally to this work.
Microorganisms 2023, 11(2), 338; https://doi.org/10.3390/microorganisms11020338 - 29 Jan 2023
Cited by 2 | Viewed by 2837
Abstract
As filter-feeding animals farmed in water bodies exposed to anthropogenic influences, oysters can be both useful bioremediators and high-risk foodstuffs, considering that they are typically consumed raw. Understanding the dynamic of bacterial and viral load in Pacific oyster (Crassostrea gigas) tissues, [...] Read more.
As filter-feeding animals farmed in water bodies exposed to anthropogenic influences, oysters can be both useful bioremediators and high-risk foodstuffs, considering that they are typically consumed raw. Understanding the dynamic of bacterial and viral load in Pacific oyster (Crassostrea gigas) tissues, hemolymph, outer shell surface biofilm, and farming water is therefore of great importance for microbiological risk assessment. A one-year survey of oysters collected from a class B production area (Canal de Mira, on the Portuguese western coast) revealed that these bivalve mollusks have a good depurating capacity with regard to bacteria, as Salmonella spp. and viable enterococci were not detected in any oyster flesh (edible portion) samples, despite the fact that these bacteria have regularly been found in the farming waters. Furthermore, the level of Escherichia coli contamination was clearly below the legal limit in oysters reared in a class B area (>230–≤4600 MPN E. coli/100 g). On the contrary, norovirus was repeatedly detected in the digestive glands of oysters sampled in autumn, winter, and spring. However, their presence in farming waters was only detected during winter. Full article
(This article belongs to the Special Issue Microbiomes of Aquatic Organisms)
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16 pages, 2816 KiB  
Article
Effects of Cellulase and Lactic Acid Bacteria on Ensiling Performance and Bacterial Community of Caragana korshinskii Silage
by Baochao Bai 1,2,†, Rui Qiu 1,2,†, Zhijun Wang 1,2, Yichao Liu 1,2, Jian Bao 1,2, Lin Sun 3, Tingyu Liu 4, Gentu Ge 1,2 and Yushan Jia 1,2,*
1 Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010019, China
2 Key Laboratory of Grassland Resources, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010019, China
3 Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
4 College of Agriculture, Inner Mongolia Minzu University, Tongliao 028000, China
† These authors contributed equally to this work.
Microorganisms 2023, 11(2), 337; https://doi.org/10.3390/microorganisms11020337 - 29 Jan 2023
Cited by 26 | Viewed by 2515
Abstract
The aim of this study was to evaluate the effects of cellulase (CE) and lactic acid bacteria (LAB) on Caragana korshinskii silage by analyzing the fermentation parameters, chemical composition, and bacterial community. The Caragana korshinskii was harvested at the fruiting period and treated [...] Read more.
The aim of this study was to evaluate the effects of cellulase (CE) and lactic acid bacteria (LAB) on Caragana korshinskii silage by analyzing the fermentation parameters, chemical composition, and bacterial community. The Caragana korshinskii was harvested at the fruiting period and treated with cellulase and LAB alone as a control treatment with no additive (CK). The ensiling performance and bacterial community were determined after 3, 7, 15, 30, and 60 days of fermentation process. Compared with the CK group, the pH, dry matter loss, and ammonia nitrogen content were significantly (p < 0.05) decreased in the LAB and CE treatments. Compared with the CK and LAB group, the contents of acid detergent fiber, neutral detergent fiber, and acid detergent lignin in the CE group decreased significantly (p < 0.05), and the water-soluble carbohydrates, acetic acid, and lactic acid concentrations increased significantly (p < 0.05). At the genus level of microorganisms, the addition of cellulase and LAB significantly reduced the microbial diversity. Compared with the CK group (78.05%), the relative abundance of Lactiplantibacillus in the CE group (90.19%) and LAB group (88.40%) significantly (p < 0.05) increased. The relative abundance of Pediococcus in the CE group (3.66%) and LAB group (2.14%) was significantly (p < 0.05) lower than that in the CK group (14.73%). Predicted functional profiling of 16S rRNA genes revealed that the addition of cellulase and LAB increased the pyruvate metabolic pathway during Caragana korshinskii silage, thereby increasing the accumulation of lactic acid concentration. The addition of cellulase expressed a better advantage in the biosynthetic capacity of lysine. In summary, the addition of cellulase and LAB could adjust the bacterial community to improve the silage quality of Caragana korshinskii, and the addition of cellulase exhibited better results than the LAB additives. Full article
(This article belongs to the Section Microbial Biotechnology)
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10 pages, 1045 KiB  
Article
Effect of Savirin or Ticagrelor Treatment on the Expression of Commonly Used Reference Genes in Staphylococcus aureus
by Narayan Pant 1,2,*, Catherine Rush 2, Jeffrey Warner 2 and Damon P. Eisen 1
1 College of Medicine and Dentistry, James Cook University, Townsville, QLD 4811, Australia
2 Australian Institute of Tropical Health and Medicine, Townsville, QLD 4811, Australia
Microorganisms 2023, 11(2), 336; https://doi.org/10.3390/microorganisms11020336 - 29 Jan 2023
Cited by 4 | Viewed by 2207
Abstract
Reference genes are frequently used for the normalization of quantitative reverse transcriptase PCR (qRTPCR) data in gene expression studies. Staphylococcus aureus is one of the most common causes of biofilm-related infections. Savirin and ticagrelor show in vitro as well as in vivo antibiofilm [...] Read more.
Reference genes are frequently used for the normalization of quantitative reverse transcriptase PCR (qRTPCR) data in gene expression studies. Staphylococcus aureus is one of the most common causes of biofilm-related infections. Savirin and ticagrelor show in vitro as well as in vivo antibiofilm activity against S. aureus. The main aim of this study was to identify the most stably expressed reference genes to study the effect of these molecules on genes in a strong biofilm producing S. aureus isolate isolated from biofilm-related infection. Quantitative real-time PCR was performed by using relative quantification method. Four different algorithms, delta Ct, normfinder, bestkeeper, and genorm, followed by a comprehensive analysis was used to identify the most stable reference genes from a list of sixteen different candidate reference genes. All four algorithms reported different results, with some comparable findings among some methods. In the comprehensive analysis of the results of all the algorithms used, the most stable reference genes found were spa, rpoD, and pyk for savirin treatment experiment and gapdH, gyrA, and gmk for ticagrelor treatment experiment. The optimal number of reference genes required was two for both the experimental conditions. Despite having some drawbacks, each algorithm can reliably determine an appropriate reference gene independently. However, based on consensus ranking and the required optimal number of reference genes reported, spa and rpoD were the most appropriate reference genes for savirin treatment experiment, and gapdH and gyrA were most appropriate for ticagrelor treatment experiment. This study provides baseline data on reference genes to study the effect of savirin or ticagrelor treatment on the expression of potential reference genes in S. aureus. We recommend prior re-validation of reference genes on a case-by-case basis before they can be used. Full article
(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)
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16 pages, 3491 KiB  
Article
Diversity of Bacterial Soft Rot-Causing Pectobacterium Species Affecting Cabbage in Serbia
by Aleksandra Jelušić 1,*, Petar Mitrović 2, Sanja Marković 1, Renata Iličić 3, Predrag Milovanović 4, Slaviša Stanković 5 and Tatjana Popović Milovanović 6,*
1 Institute for Multidisciplinary Research, University of Belgrade, Kneza Višeslava 1, 11030 Belgrade, Serbia
2 Institute for Field and Vegetable Crops, National Institute of the Republic of Serbia, Maksima Gorkog 30, 21000 Novi Sad, Serbia
3 Faculty of Agriculture, University of Novi Sad, Trg Dositeja Obradovića 8, 21000 Novi Sad, Serbia
4 Agrosava doo, Palmira Toljatija 5, 11070 Belgrade, Serbia
5 Faculty of Biology, University of Belgrade, Studentski Trg 16, 11000 Belgrade, Serbia
6 Institute for Plant Protection and Environment, Teodora Drajzer 9, 11040 Belgrade, Serbia
Microorganisms 2023, 11(2), 335; https://doi.org/10.3390/microorganisms11020335 - 29 Jan 2023
Cited by 5 | Viewed by 3682
Abstract
The aim of this work was to identify and characterize the pectolytic bacteria responsible for the emergence of bacterial soft rot on two summer cabbage hybrids (Cheers F1 and Hippo F1) grown in the Futog locality (Bačka, Vojvodina), known for the five-century-long tradition [...] Read more.
The aim of this work was to identify and characterize the pectolytic bacteria responsible for the emergence of bacterial soft rot on two summer cabbage hybrids (Cheers F1 and Hippo F1) grown in the Futog locality (Bačka, Vojvodina), known for the five-century-long tradition of cabbage cultivation in Serbia. Symptoms manifesting as soft lesions on outer head leaves were observed during August 2021, while the inner tissues were macerated, featuring cream to black discoloration. As the affected tissue decomposed, it exuded a specific odor. Disease incidence ranged from 15% to 25%. A total of 67 isolates producing pits on crystal violet pectate (CVP) medium were characterized for their phenotypic and genotypic features. The pathogenicity was confirmed on cabbage heads. Findings yielded by the repetitive element palindromic-polymerase chain reaction (rep-PCR) technique confirmed interspecies diversity between cabbage isolates, as well as intraspecies genetic diversity within the P. carotovorum group of isolates. Based on multilocus sequence typing (MLST) using genes dnaX, mdh, icdA, and proA, five representative isolates were identified as Pectobacterium carotovorum (Cheers F1 and Hippo F1), while two were identified as Pectobacterium versatile (Hippo F1) and Pectobacterium odoriferum (Hippo F1), respectively, indicating the presence of diverse Pectobacterium species even in combined infection in the same field. Among the obtained isolates, P. carotovorum was the most prevalent species (62.69%), while P. versatile and P. odoriferum were less represented (contributing by 19.40% and 17.91%, respectively). Multilocus sequence analysis (MLSA) performed with concatenated sequences of four housekeeping genes (proA, dnaX, icdA, and mdh) and constructed a neighbor-joining phylogenetic tree enabled insight into the phylogenetic position of the Serbian cabbage Pectobacterium isolates. Bacterium P. odoriferum was found to be the most virulent species for cabbage, followed by P. versatile, while all three species had comparable virulence with respect to potato. The results obtained in this work provide a better understanding of the spreading routes and abundance of different Pectobacterium spp. in Serbia. 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, 2232 KiB  
Review
Weeds: An Insidious Enemy or a Tool to Boost Mycorrhization in Cropping Systems?
by Alessandra Trinchera * and Dylan Warren Raffa
Council for Agricultural Research and Economics (CREA), Research Centre for Agriculture and Environment, Via della Navicella, 2, 00184 Rome, Italy
Microorganisms 2023, 11(2), 334; https://doi.org/10.3390/microorganisms11020334 - 29 Jan 2023
Cited by 8 | Viewed by 2718
Abstract
Weeds have always been considered an insidious enemy, capable of reducing crop production. Conversely, the agroecological vision attributes a key role to the spontaneous flora in promoting plant diversity and belowground interactions, which may improve the ecological performance of agroecosystems. We summarized the [...] Read more.
Weeds have always been considered an insidious enemy, capable of reducing crop production. Conversely, the agroecological vision attributes a key role to the spontaneous flora in promoting plant diversity and belowground interactions, which may improve the ecological performance of agroecosystems. We summarized the literature on the weeds’ arbuscular–mycorrhizae (AM) interaction and we analyzed evidence on the: (i) AM suppressive/selective effect on weed communities; (ii) effect of weeds on AM colonization, and (iii) positive role of AM-supporting weeds on forming shared mycorrhizal hyphal connections in agroecosystems. While some authors conceptualized AM as a weed control tool, others underlined their selective effect on weed communities. Recent studies suggest that AM-host weeds can participate in the development of a common mycorrhizal mycelial network (MMN) among different plants species. Nevertheless, direct evidence of the actual exchange of nutrients and C between coexisting plants through MMN in agroecosystems is missing. Although the effect of agricultural practices on plant community-AM interactions are complex, more conservative farming management seems to foster AM populations. Future studies should focus on: (i) field studies, (ii) weed communities and their traits, rather than on the most abundant species, and (iii) the use of advanced analytical techniques, able to monitor MMN development and functionality. Full article
(This article belongs to the Special Issue Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems 2.0)
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9 pages, 1791 KiB  
Case Report
Isolation and Identification of Aeromonas veronii in Sheep with Fatal Infection in China: A Case Report
by Yongqiang Miao, Xueliang Zhao, Fathalrhman Eisa Addoma Adam, Qingfang Xie, Hang Feng, Jingru Ding, Xindong Bai, Juan Wang * and Zengqi Yang *
College of Veterinary Medicine, Northwest A&F University, Yangling, Xianyang 712100, China
Microorganisms 2023, 11(2), 333; https://doi.org/10.3390/microorganisms11020333 - 29 Jan 2023
Cited by 6 | Viewed by 2833
Abstract
According to the findings of a sheep breeding farm in Shaanxi, China, 2.53% (15/594) of sheep exhibited respiratory (clinical) symptoms such as dyspnoea, nasal discharge, wet cough, fever, and progressive emaciation. Although multi-drug treatment strategies (including ampicillin, tylosin, florfenicol, and ceftiofur) have been [...] Read more.
According to the findings of a sheep breeding farm in Shaanxi, China, 2.53% (15/594) of sheep exhibited respiratory (clinical) symptoms such as dyspnoea, nasal discharge, wet cough, fever, and progressive emaciation. Although multi-drug treatment strategies (including ampicillin, tylosin, florfenicol, and ceftiofur) have been attempted to improve clinical outcomes, they have only been met with limited success, with a mortality rate of 40%. Ultimately, Aeromonas veronii (A. veronii) was identified as the causative pathogen for respiratory disease. The rates of symptomatic and asymptomatic sheep positive to A. veronii were 64.28% (95% CI 52.25–76.31%) and 8.02% (95% CI 6.96–9.08%), respectively. Pathogenicity tests demonstrated that the A. veronii is pathogenic to sheep and mice. The results of the antibiotic susceptibility tests revealed that the strain was sensitive to cefotaxime, gentamicin, and enrofloxacin and resistant to ampicillin, ceftiofur, amoxicillin, kanamycin, neomycin, streptomycin, tetracycline, florfenicol, and tylosin. We suggest that the combination of cefotaxime and gentamicin is an effective treatment based on the results of an antimicrobial susceptibility test, which exhibited good therapeutic efficacy. To the best of our knowledge, this is the first report in which pathogenic A. veronii has been documented as the cause of death in sheep in China. We concluded that pathogenic A. veronii poses a potential risk to the industry of sheep husbandry. This study’s findings can help guide prevention and treatment plans for A. veronii infection in sheep. Full article
(This article belongs to the Special Issue Domestic Animals and Wildlife Zoonotic Microorganisms)
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15 pages, 2393 KiB  
Article
eDNA Provides a Scaffold for Autoaggregation of B. subtilis in Bacterioplankton Suspension
by Iztok Dogsa, Rok Kostanjšek and David Stopar *
Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
Microorganisms 2023, 11(2), 332; https://doi.org/10.3390/microorganisms11020332 - 28 Jan 2023
Cited by 6 | Viewed by 2165
Abstract
The self-binding of bacterial cells, or autoaggregation, is, together with surface colonization, one of the first steps in the formation of a mature biofilm. In this work, the autoaggregation of B. subtilis in dilute bacterial suspensions was studied. The dynamics of cell lysis, [...] Read more.
The self-binding of bacterial cells, or autoaggregation, is, together with surface colonization, one of the first steps in the formation of a mature biofilm. In this work, the autoaggregation of B. subtilis in dilute bacterial suspensions was studied. The dynamics of cell lysis, eDNA release, and bacterial autoaggregate assembly were determined and related to the spatial autocorrelation of bacterial cells in dilute planktonic bacterial suspensions. The non-random distribution of cells was associated with an eDNA network, which stabilized the initial bacterial cell-cell aggregates. Upon the addition of DNase I, the aggregates were dispersed. The release of eDNA during cell lysis allows for the entrapment of bacterial drifters at a radius several times the size of the dying bacteria. The size of bacterial aggregates increased from 2 to about 100 μm in diameter in dilute bacterial suspensions. The results suggest that B. subtilis cells form previously unnoticed continuum of autoaggregate structures during planktonic growth. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Biofilms)
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15 pages, 2687 KiB  
Article
Mapping Genetic Variation in Arabidopsis in Response to Plant Growth-Promoting Bacterium Azoarcus olearius DQS-4T
by Fernanda Plucani do Amaral 1,2, Juexin Wang 3,4, Jacob Williams 5, Thalita R. Tuleski 6, Trupti Joshi 3,7, Marco A. R. Ferreira 5 and Gary Stacey 1,*
1 Divisions of Plant Sciences and Technology, C. S. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA
2 Ginkgo Bioworks, Ag Biologicals, 890 Embarcadero Dr., West Sacramento, CA 95605, USA
3 Department of Electrical Engineering and Computer Science, C. S. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA
4 Departemnt of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianopolis, Indianopolis, IN 46202, USA
5 Department of Statistics, Virginia Tech, Blacksburg, VA 24060, USA
6 Department of Biochemistry and Molecular Biology, Federal University of Parana, Curitiba 19046, Brazil
7 Department of Health Management and Informatics, MU Institute for Data Science and Informatics, C. S. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA
Microorganisms 2023, 11(2), 331; https://doi.org/10.3390/microorganisms11020331 - 28 Jan 2023
Cited by 6 | Viewed by 2591
Abstract
Plant growth-promoting bacteria (PGPB) can enhance plant health by facilitating nutrient uptake, nitrogen fixation, protection from pathogens, stress tolerance and/or boosting plant productivity. The genetic determinants that drive the plant–bacteria association remain understudied. To identify genetic loci highly correlated with traits responsive to [...] Read more.
Plant growth-promoting bacteria (PGPB) can enhance plant health by facilitating nutrient uptake, nitrogen fixation, protection from pathogens, stress tolerance and/or boosting plant productivity. The genetic determinants that drive the plant–bacteria association remain understudied. To identify genetic loci highly correlated with traits responsive to PGPB, we performed a genome-wide association study (GWAS) using an Arabidopsis thaliana population treated with Azoarcus olearius DQS-4T. Phenotypically, the 305 Arabidopsis accessions tested responded differently to bacterial treatment by improving, inhibiting, or not affecting root system or shoot traits. GWA mapping analysis identified several predicted loci associated with primary root length or root fresh weight. Two statistical analyses were performed to narrow down potential gene candidates followed by haplotype block analysis, resulting in the identification of 11 loci associated with the responsiveness of Arabidopsis root fresh weight to bacterial inoculation. Our results showed considerable variation in the ability of plants to respond to inoculation by A. olearius DQS-4T while revealing considerable complexity regarding statistically associated loci with the growth traits measured. This investigation is a promising starting point for sustainable breeding strategies for future cropping practices that may employ beneficial microbes and/or modifications of the root microbiome. Full article
(This article belongs to the Section Plant Microbe Interactions)
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21 pages, 2746 KiB  
Article
Interaction between Illite and a Pseudomonas stutzeri-Heavy Oil Biodegradation Complex
by Lei Li, Yun Yang Wan *, Hong Mei Mu, Sheng Bao Shi and Jian Fa Chen
State Key Laboratory of Petroleum Resources and Prospecting, Research Centre for Geomicrobial Resources and Application, Unconventional Petroleum Research Institute, College of Geosciences, China University of Petroleum, Beijing 102249, China
Microorganisms 2023, 11(2), 330; https://doi.org/10.3390/microorganisms11020330 - 28 Jan 2023
Cited by 2 | Viewed by 2347
Abstract
Illite is a widely distributed clay mineral with huge reserves in Earth’s crust, but its effect on heavy oil biodegradation is rarely reported. This study made an investigation of the interactions between illite and a Pseudomonas stutzeri-heavy oil complex (PstHO). [...] Read more.
Illite is a widely distributed clay mineral with huge reserves in Earth’s crust, but its effect on heavy oil biodegradation is rarely reported. This study made an investigation of the interactions between illite and a Pseudomonas stutzeri-heavy oil complex (PstHO). Results showed that, although illite exerted a negative effect on P. stutzeri degrading heavy oil by inhibiting the biodegradation of 64 saturated hydrocarbons (SHs) and 50 aromatic hydrocarbons (AHs), it selectively stimulated the biodegradation of 45 AHs with a specific structure, and its biogenic kaolinization at room temperature (35 °C) and pressure (1 atm) was observed in PstHO for the first time. The finding points out for the first time that, in PstHO, illite may change the quasi-sequential of AHs biodegradation of heavy oil, as well as its kaolinization without clay intermediate. Full article
(This article belongs to the Special Issue Petroleum Microbiology 2.0)
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