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Microorganisms
Volume 11
Issue 2
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Microorganisms, Volume 11, Issue 2 (February 2023) – 310 articles

Cover Story (view full-size image): Pasteurella multocida (P. multocida) is a commensal and opportunistic zoonotic pathogen, which causes pneumonia and hemorrhagic septicemia in goats and sheep. In clinical cases, necropsies have shown that P. multocida also infects the heart. Therefore, to investigate the immune response of P. multocida-infected hearts, animal infection models were established by two P. multocida strains isolated from goats and sheep. Histopathological studies suggested that mice challenged with serotype D strains presented significant pathological heart damage. Moreover, TLR signaling was significantly activated by serotype A strains but not by serotype D strains. This study is the first to reveal a vital pathway by which the heart recognizes and defends against P. multocida. View this paper
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19 pages, 3537 KiB  
Article
The Pathogen Aeromonas salmonicida achromogenes Induces Fast Immune and Microbiota Modifications in Rainbow Trout
by Baptiste Redivo, Nicolas Derôme, Patrick Kestemont and Valérie Cornet
Microorganisms 2023, 11(2), 539; https://doi.org/10.3390/microorganisms11020539 - 20 Feb 2023
Cited by 3 | Viewed by 1763
Abstract
Environmental stressors can disrupt the relationship between the microbiota and the host and lead to the loss of its functions. Among them, bacterial infection caused by Aeromonas salmonicida, the causative agent of furunculosis, results in high mortality in salmonid aquaculture. Here, rainbow [...] Read more.
Environmental stressors can disrupt the relationship between the microbiota and the host and lead to the loss of its functions. Among them, bacterial infection caused by Aeromonas salmonicida, the causative agent of furunculosis, results in high mortality in salmonid aquaculture. Here, rainbow trout were exposed to A. salmonicida achromogenes and its effects on the taxonomic composition and structure of the microbiota was assessed on different epithelia (gills, skin, and caudal fin) at 6 and 72 h post-infection (hpi) using the V1–V3 region of the 16S rRNA sequencing. Moreover, the infection by the pathogen and immune gene responses were evaluated in the head kidney by qPCR. Our results suggested that α-diversity was highly diverse but predominated by a few taxa while β-diversity was affected very early by infection in the gills after 6 h, subsequently affecting the microbiota of the skin and caudal fin. A dysbiosis of the microbiota and an increase in genera known to be opportunistic pathogens (Aeromonas, Pseudomonas) were also identified. Furthermore, an increase in pro-inflammatory cytokines and virulence protein array (vapa) was observed in trout head kidney as soon as 6 hpi and remained elevated until 72 hpi, while the anti-inflammatory genes seemed repressed. This study suggests that the infection by A. salmonicida achromogenes can alter fish microbiota of gills in the few hours post-infection. This result can be useful to develop a non-invasive technique to prevent disease outbreak in aquaculture. Full article
(This article belongs to the Special Issue Microorganisms and Diseases Associated with Aquatic Animals)
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17 pages, 1632 KiB  
Review
Protoplast Preparation for Algal Single-Cell Omics Sequencing
by Junran Ye, Cuiqiyun Yang, Luojia Xia, Yinjie Zhu, Li Liu, Huansheng Cao and Yi Tao
Microorganisms 2023, 11(2), 538; https://doi.org/10.3390/microorganisms11020538 - 20 Feb 2023
Cited by 4 | Viewed by 2603
Abstract
Single-cell sequencing (SCS) is an evolutionary technique for conducting life science research, providing the highest genome-sale throughput and single-cell resolution and unprecedented capabilities in addressing mechanistic and operational questions. Unfortunately, the current SCS pipeline cannot be directly applied to algal research as algal [...] Read more.
Single-cell sequencing (SCS) is an evolutionary technique for conducting life science research, providing the highest genome-sale throughput and single-cell resolution and unprecedented capabilities in addressing mechanistic and operational questions. Unfortunately, the current SCS pipeline cannot be directly applied to algal research as algal cells have cell walls, which makes RNA extraction hard for the current SCS platforms. Fortunately, effective methods are available for producing algal protoplasts (cells without cell walls), which can be directly fed into current SCS pipelines. In this review, we first summarize the cell wall structure and chemical composition of algal cell walls, particularly in Chlorophyta, then summarize the advances made in preparing algal protoplasts using physical, chemical, and biological methods, followed by specific cases of algal protoplast production in some commonly used eukaryotic algae. This review provides a timely primer to those interested in applying SCS in eukaryotic algal research. Full article
(This article belongs to the Section Microbial Biotechnology)
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3 pages, 220 KiB  
Editorial
The Gut Microbiota in Infants: Focus on Bifidobacterium
by Gonzalo Solís and Miguel Gueimonde
Microorganisms 2023, 11(2), 537; https://doi.org/10.3390/microorganisms11020537 - 20 Feb 2023
Cited by 2 | Viewed by 1142
Abstract
A long time has passed since the initial pioneering works were carried out on the composition of infant microbiota by Thedore Escherich (1857–1911) and Ernst Moro (1874–1951), and since the observations of Henry Tissier (1866–1916) which linked “Bacillus bifidus” to the health of [...] Read more.
A long time has passed since the initial pioneering works were carried out on the composition of infant microbiota by Thedore Escherich (1857–1911) and Ernst Moro (1874–1951), and since the observations of Henry Tissier (1866–1916) which linked “Bacillus bifidus” to the health of babies [...] Full article
(This article belongs to the Special Issue The Gut Microbiota in Infants: Focus on Bifidobacterium)
19 pages, 7933 KiB  
Article
Changes of In Situ Prokaryotic and Eukaryotic Communities in the Upper Sanya River to the Sea over a Nine-Hour Period
by Shijie Bai, Jian Zhang, Xiaoxue Qi, Juntao Zeng, Shijun Wu and Xiaotong Peng
Microorganisms 2023, 11(2), 536; https://doi.org/10.3390/microorganisms11020536 - 20 Feb 2023
Cited by 1 | Viewed by 1545
Abstract
The transition areas of riverine, estuarine, and marine environments are particularly valuable for the research of microbial ecology, biogeochemical processes, and other physical–chemical studies. Although a large number of microbial-related studies have been conducted within such systems, the vast majority of sampling have [...] Read more.
The transition areas of riverine, estuarine, and marine environments are particularly valuable for the research of microbial ecology, biogeochemical processes, and other physical–chemical studies. Although a large number of microbial-related studies have been conducted within such systems, the vast majority of sampling have been conducted over a large span of time and distance, which may lead to separate batches of samples receiving interference from different factors, thus increasing or decreasing the variability between samples to some extent. In this study, a new in situ filtration system was used to collect membrane samples from six different sampling sites along the Sanya River, from upstream freshwater to the sea, over a nine-hour period. We used high-throughput sequencing of 16S and 18S rRNA genes to analyze the diversity and composition of prokaryotic and eukaryotic communities. The results showed that the structures of these communities varied according to the different sampling sites. The α-diversity of the prokaryotic and eukaryotic communities both decreased gradually along the downstream course. The structural composition of prokaryotic and eukaryotic communities changed continuously with the direction of river flow; for example, the relative abundances of Rhodobacteraceae and Flavobacteriaceae increased with distance downstream, while Sporichthyaceae and Comamonadaceae decreased. Some prokaryotic taxa, such as Phycisphaeraceae and Chromobacteriaceae, were present nearly exclusively in pure freshwater environments, while some additional prokaryotic taxa, including the SAR86 clade, Clade I, AEGEAN-169 marine group, and Actinomarinaceae, were barely present in pure freshwater environments. The eukaryotic communities were mainly composed of the Chlorellales X, Chlamydomonadales X, Sphaeropleales X, Trebouxiophyceae XX, Annelida XX, and Heteroconchia. The prokaryotic and eukaryotic communities were split into abundant, common, and rare communities for NCM analysis, respectively, and the results showed that assembly of the rare community assembly was more impacted by stochastic processes and less restricted by species dispersal than that of abundant and common microbial communities for both prokaryotes and eukaryotes. Overall, this study provides a valuable reference and new perspectives on microbial ecology during the transition from freshwater rivers to estuaries and the sea. Full article
(This article belongs to the Special Issue Unveiling the Multiple Aspects of Microbial Ecology)
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7 pages, 1050 KiB  
Communication
Extraction Bottleneck in the Diagnosis of SARS-CoV-2: Evaluation of an Alternative Protocol Derived from Veterinary Use
by Paolo Bottino, Elisa Zanotto, Francesca Sidoti, Lisa Pastrone, Roberto Piva, Elisabetta Mereu, Cristina Costa and Rossana Cavallo
Microorganisms 2023, 11(2), 535; https://doi.org/10.3390/microorganisms11020535 - 20 Feb 2023
Cited by 1 | Viewed by 1128
Abstract
The COVID-19 pandemic represented a challenge for health-care systems, and a major bottleneck in SARS-CoV-2 diagnosis was the unavailability of extraction reagents. To overcome this limitation, we performed a comparative analysis to evaluate the performance of an alternative extraction protocol derived from veterinary [...] Read more.
The COVID-19 pandemic represented a challenge for health-care systems, and a major bottleneck in SARS-CoV-2 diagnosis was the unavailability of extraction reagents. To overcome this limitation, we performed a comparative analysis to evaluate the performance of an alternative extraction protocol derived from veterinary use adapted to an open robotic platform (Testing method). A total of 73 nasopharyngeal swabs collected for diagnosis of SARS-CoV-2 infection were simultaneously extracted with the Testing protocol and the laboratory Standard of Care in order to assess the performance of the first one. The Cohen’s coefficient between both procedures was excellent (K Value = 0.955). Analysis of cycle threshold and linear regression showed a significant correlation between the two methods for each tested genetic target. Although validated for veterinary applications, the Testing method showed excellent performances in RNA extraction, with several advantages: lower sample input volume, the possibility to overcome the lack of deep-well plates and adaptability to robotic liquid handlers. Full article
(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)
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10 pages, 793 KiB  
Communication
Antiviral Effect of Ephedrine Alkaloids-Free Ephedra Herb Extract against SARS-CoV-2 In Vitro
by Masashi Uema, Masashi Hyuga, Kenzo Yonemitsu, Sumiko Hyuga, Yoshiaki Amakura, Nahoko Uchiyama, Kazushige Mizoguchi, Hiroshi Odaguchi and Yukihiro Goda
Microorganisms 2023, 11(2), 534; https://doi.org/10.3390/microorganisms11020534 - 20 Feb 2023
Cited by 4 | Viewed by 2070
Abstract
We report for the first time that ephedrine alkaloids-free Ephedra Herb extract (EFE) directly inhibits the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vitro and that the addition of EFE to the culture medium before viral infection reduces virus titers [...] Read more.
We report for the first time that ephedrine alkaloids-free Ephedra Herb extract (EFE) directly inhibits the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vitro and that the addition of EFE to the culture medium before viral infection reduces virus titers in the culture supernatant of SARS-CoV-2, including those of variant strains, by more than 99%, 24 h after infection. The addition of Ephedra Herb macromolecule condensed-tannin, which is the main active ingredient responsible for the anticancer, pain suppression, and anti-influenza effects of EFE, similarly suppressed virus production in the culture supernatant by 99% before infection and by more than 90% after infection. Since EFE does not have the side effects caused by ephedrine alkaloids, such as hypertension, palpitations, and insomnia, our results showed the potential of EFE as a safe therapeutic agent against coronavirus disease 2019. Full article
(This article belongs to the Special Issue The New Advance on Disinfectant of Virus and Microorganisms)
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31 pages, 4782 KiB  
Article
Gut Microbiota as Well as Metabolomes of Wistar Rats Recover within Two Weeks after Doripenem Antibiotic Treatment
by Aishwarya Murali, Franziska Maria Zickgraf, Philipp Ternes, Varun Giri, Hunter James Cameron, Saskia Sperber, Volker Haake, Peter Driemert, Hennicke Kamp, Dorothee Funk Weyer, Shana J. Sturla, Ivonne M. G. M. Rietjens and Bennard van Ravenzwaay
Microorganisms 2023, 11(2), 533; https://doi.org/10.3390/microorganisms11020533 - 20 Feb 2023
Viewed by 1744
Abstract
An understanding of the changes in gut microbiome composition and its associated metabolic functions is important to assess the potential implications thereof on host health. Thus, to elucidate the connection between the gut microbiome and the fecal and plasma metabolomes, two poorly bioavailable [...] Read more.
An understanding of the changes in gut microbiome composition and its associated metabolic functions is important to assess the potential implications thereof on host health. Thus, to elucidate the connection between the gut microbiome and the fecal and plasma metabolomes, two poorly bioavailable carbapenem antibiotics (doripenem and meropenem), were administered in a 28-day oral study to male and female Wistar rats. Additionally, the recovery of the gut microbiome and metabolomes in doripenem-exposed rats were studied one and two weeks after antibiotic treatment (i.e., doripenem-recovery groups). The 16S bacterial community analysis revealed an altered microbial population in all antibiotic treatments and a recovery of bacterial diversity in the doripenem-recovery groups. A similar pattern was observed in the fecal metabolomes of treated animals. In the recovery group, particularly after one week, an over-compensation was observed in fecal metabolites, as they were significantly changed in the opposite direction compared to previously changed metabolites upon 28 days of antibiotic exposure. Key plasma metabolites known to be diagnostic of antibiotic-induced microbial shifts, including indole derivatives, hippuric acid, and bile acids were also affected by the two carbapenems. Moreover, a unique increase in the levels of indole-3-acetic acid in plasma following meropenem treatment was observed. As was observed for the fecal metabolome, an overcompensation of plasma metabolites was observed in the recovery group. The data from this study provides insights into the connectivity of the microbiome and fecal and plasma metabolomes and demonstrates restoration post-antibiotic treatment not only for the microbiome but also for the metabolomes. The importance of overcompensation reactions for health needs further studies. Full article
(This article belongs to the Section Gut Microbiota)
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17 pages, 1737 KiB  
Article
Spent Mushroom Substrate Hydrolysis and Utilization as Potential Alternative Feedstock for Anaerobic Co-Digestion
by Gabriel Vasilakis, Evangelos-Markos Rigos, Nikos Giannakis, Panagiota Diamantopoulou and Seraphim Papanikolaou
Microorganisms 2023, 11(2), 532; https://doi.org/10.3390/microorganisms11020532 - 20 Feb 2023
Cited by 2 | Viewed by 2397
Abstract
Valorization of lignocellulosic biomass, such as Spent Mushroom Substrate (SMS), as an alternative substrate for biogas production could meet the increasing demand for energy. In view of this, the present study aimed at the biotechnological valorization of SMS for biogas production. In the [...] Read more.
Valorization of lignocellulosic biomass, such as Spent Mushroom Substrate (SMS), as an alternative substrate for biogas production could meet the increasing demand for energy. In view of this, the present study aimed at the biotechnological valorization of SMS for biogas production. In the first part of the study, two SMS chemical pretreatment processes were investigated and subsequently combined with thermal treatment of the mentioned waste streams. The acidic chemical hydrolysate derived from the hydrothermal treatment, which yielded in the highest concentration of free sugars (≈36 g/100 g dry SMS, hydrolysis yield ≈75% w/w of holocellulose), was used as a potential feedstock for biomethane production in a laboratory bench-scale improvised digester, and 52 L biogas/kg of volatile solids (VS) containing 65% methane were produced in a 15-day trial of anaerobic digestion. As regards the alkaline hydrolysate, it was like a pulp due to the lignocellulosic matrix disruption, without releasing additional sugars, and the biogas production was delayed for several days. The biogas yield value was 37 L/kg VS, and the methane content was 62%. Based on these results, it can be concluded that SMS can be valorized as an alternative medium employed for anaerobic digestion when pretreated with both chemical and hydrothermal hydrolysis. Full article
(This article belongs to the Special Issue Advances in Microbial Metabolites)
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19 pages, 4647 KiB  
Article
Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome
by Nazima Habibi, Saif Uddin, Hanan Al-Sarawi, Ahmed Aldhameer, Anisha Shajan, Farhana Zakir, Nasreem Abdul Razzack and Faiz Alam
Microorganisms 2023, 11(2), 531; https://doi.org/10.3390/microorganisms11020531 - 20 Feb 2023
Cited by 8 | Viewed by 2957
Abstract
Coastal sediments in the proximity of wastewater and emergency outfalls are often sinks of pharmaceutical compounds and other organic and inorganic contaminants that are likely to affect the microbial community. The metabolites of these contaminants affect microbial diversity and their metabolic processes, resulting [...] Read more.
Coastal sediments in the proximity of wastewater and emergency outfalls are often sinks of pharmaceutical compounds and other organic and inorganic contaminants that are likely to affect the microbial community. The metabolites of these contaminants affect microbial diversity and their metabolic processes, resulting in undesirable effects on ecosystem functioning, thus necessitating the need to understand their composition and functions. In the present investigation, we studied the metagenomes of 12 coastal surface sediments through whole genome shot-gun sequencing. Taxonomic binning of the genes predicted about 86% as bacteria, 1% as archaea, >0.001% as viruses and Eukaryota, and 12% as other communities. The dominant bacterial, archaeal, and fungal genera were Woeseia, Nitrosopumilus, and Rhizophagus, respectively. The most prevalent viral families were Myoviridae and Siphoviridae, and the T4 virus was the most dominant bacteriophage. The unigenes further aligned to 26 clusters of orthologous genes (COGs) and five carbohydrate-active enzymes (CAZy) classes. Glycoside hydrolases (GH) and glycoside transferase (GT) were the highest-recorded CAzymes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) level 3 functions were subjugated by purine metabolism > ABC transporters > oxidative phosphorylation > two-component system > pyrimidine metabolism > pyruvate metabolism > quorum sensing > carbon fixation pathways > ribosomes > and glyoxalate and dicarboxylate metabolism. Sequences allying with plasmids, integrons, insertion sequences and antibiotic-resistance genes were also observed. Both the taxonomies and functional abundances exhibited variation in relative abundances, with limited spatial variability (ANOVA p > 0.05; ANOSIM-0.05, p > 0.05). This study underlines the dominant microbial communities and functional genes in the marine sediments of Kuwait as a baseline for future biomonitoring programs. Full article
(This article belongs to the Collection Biodegradation and Environmental Microbiomes)
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2 pages, 185 KiB  
Editorial
Special Issue “Nutritional Regulation on Gut Microbiota”: Editorial
by Garry X. Shen
Microorganisms 2023, 11(2), 530; https://doi.org/10.3390/microorganisms11020530 - 19 Feb 2023
Viewed by 978
Abstract
Accumulated lines of evidence demonstrate that the gut microbiota plays a critical role in metabolism, inflammation and the pathophysiology of many chronic diseases [...] Full article
(This article belongs to the Special Issue Nutritional Regulation on Gut Microbiota)
10 pages, 960 KiB  
Article
An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology
by Hon S. Ip, Sarah Uhm, Mary Lea Killian and Mia K. Torchetti
Microorganisms 2023, 11(2), 529; https://doi.org/10.3390/microorganisms11020529 - 19 Feb 2023
Cited by 4 | Viewed by 3562
Abstract
As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian [...] Read more.
As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian influenza virus in Europe, North America, and elsewhere raises the need for similarly rapid sequencing to aid in appropriate response and mitigation activities. To facilitate this objective, we investigate a next-generation sequencing platform that uses a portable nanopore sequencing device to generate and present data in real time. This platform offers the potential to extend in-house sequencing capacities to laboratories that may otherwise lack resources to adopt sequencing technologies requiring large benchtop instruments. We evaluate this platform for routine use in a diagnostic laboratory. In this study, we evaluate different primer sets for the whole genome amplification of influenza A virus and evaluate five different library preparation approaches for sequencing on the nanopore platform using the MinION flow cell. A limited amplification procedure and a rapid procedure are found to be best among the approaches taken. Full article
(This article belongs to the Special Issue Viral Metagenomic Analysis in Animals)
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4 pages, 214 KiB  
Editorial
Probiotics and Their Antimicrobial Effect
by Sabina Fijan
Microorganisms 2023, 11(2), 528; https://doi.org/10.3390/microorganisms11020528 - 19 Feb 2023
Cited by 13 | Viewed by 4262
Abstract
This Special Issue of the journal Microorganisms highlights the importance of the antimicrobial effect of probiotics [...] Full article
(This article belongs to the Special Issue Probiotics and Antimicrobial Effect)
20 pages, 2639 KiB  
Article
Partial Substitution of Urea with Biochar Induced Improvements in Soil Enzymes Activity, Ammonia-Nitrite Oxidizers, and Nitrogen Uptake in the Double-Cropping Rice System
by Saif Ullah, Izhar Ali, Mei Yang, Quan Zhao, Anas Iqbal, Xiaoyan Wu, Shakeel Ahmad, Ihsan Muhammad, Abdullah Khan, Muhammad Adnan, Pengli Yuan and Ligeng Jiang
Microorganisms 2023, 11(2), 527; https://doi.org/10.3390/microorganisms11020527 - 19 Feb 2023
Cited by 6 | Viewed by 1752
Abstract
Biochar is an important soil amendment that can enhance the biological properties of soil, as well as nitrogen (N) uptake and utilization in N-fertilized crops. However, few studies have characterized the effects of urea and biochar application on soil biochemical traits and its [...] Read more.
Biochar is an important soil amendment that can enhance the biological properties of soil, as well as nitrogen (N) uptake and utilization in N-fertilized crops. However, few studies have characterized the effects of urea and biochar application on soil biochemical traits and its effect on paddy rice. Therefore, a field trial was conducted in the early and late seasons of 2020 in a randomized complete block design with two N levels (135 and 180 kg ha−1) and four levels of biochar (0, 10, 20, and 30 t ha−1). The treatment combinations were as follows: 135 kg N ha−1 + 0 t B ha−1 (T1), 135 kg N ha−1 + 10 t B ha−1 (T2), 135 kg N ha−1 + 20 t B ha−1 (T3), 135 kg N ha−1 + 30 t B ha−1 (T4), 180 kg N ha−1 + 0 t B ha−1 (T5), 180 kg N ha−1 + 10 t B ha−1 (T6), 180 kg N ha−1 + 20 t B ha−1 (T7) and 180 kg N ha−1 + 30 t B ha−1 (T8). The results showed that soil amended with biochar had higher soil pH, soil organic carbon content, total nitrogen content, and mineral nitrogen (NH4+-N and NO3−-N) than soil that had not been amended with biochar. In both seasons, the 20 t ha−1 and 30 t ha−1 biochar treatments had the highest an average concentrations of NO3–-N (10.54 mg kg−1 and 10.25 mg kg−1, respectively). In comparison to soil that had not been treated with biochar, the average activity of the enzymes urease, polyphenol oxidase, dehydrogenase, and chitinase was, respectively, 25.28%, 14.13%, 67.76%, and 22.26% greater; however, the activity of the enzyme catalase was 15.06% lower in both seasons. Application of biochar considerably increased the abundance of ammonia-oxidizing bacteria (AOB), which was 48% greater on average in biochar-amended soil than in unamended soil. However, there were no significant variations in the abundances of ammonia-oxidizing archaea (AOA) or nitrite-oxidizing bacteria (NOB) across treatments. In comparison to soil that had not been treated with biochar, the average N content was 24.46%, 20.47%, and 19.08% higher in the stem, leaves, and panicles, respectively. In general, adding biochar at a rate of 20 to 30 t ha−1 with low-dose urea (135 kg N ha−1) is a beneficial technique for improving the nutrient balance and biological processes of soil, as well as the N uptake and grain yield of rice plants. Full article
(This article belongs to the Special Issue Advances in Microbial and Plant Biotechnology)
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18 pages, 6631 KiB  
Article
Diversity of Microbial Communities, PAHs, and Metals in Road and Leaf Dust of Functional Zones of Moscow and Murmansk
by Anna A. Vetrova, Olesya I. Sazonova, Anastasia A. Ivanova, Rostislav A. Streletskii, Dmitriy A. Sarzhanov, Maria V. Korneykova, Andrey I. Novikov, Viacheslav I. Vasenev, Kristina V. Ivashchenko, Marina V. Slukovskaya and Olga Gavrichkova
Microorganisms 2023, 11(2), 526; https://doi.org/10.3390/microorganisms11020526 - 18 Feb 2023
Cited by 1 | Viewed by 1702
Abstract
The impact of geographical factors, functional zoning, and biotope type on the diversity of microbial communities and chemical components in the dust of urban ecosystems was studied. Comprehensive analyses of bacterial and fungal communities, polycyclic aromatic hydrocarbons (PAHs), and metals in road and [...] Read more.
The impact of geographical factors, functional zoning, and biotope type on the diversity of microbial communities and chemical components in the dust of urban ecosystems was studied. Comprehensive analyses of bacterial and fungal communities, polycyclic aromatic hydrocarbons (PAHs), and metals in road and leaf dust in three urban zones of Murmansk and Moscow with contrasting anthropogenic load were conducted. We found that the structure of bacterial communities affected the functional zoning of the city, biotope type, and geographical components. Fungal communities were instead impacted only by biotope type. Our findings revealed that the structure of fungal communities was mostly impacted by PAHs whereas bacterial communities were sensitive to metals. Bacteria of the genus Sphingomonas in road and leaf dust as indicators of the ecological state of the urban ecosystems were proposed. Full article
(This article belongs to the Special Issue Microbial Communities in a Changing World: Composition, Metabolism, and Environmental Adaptation)
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17 pages, 1677 KiB  
Article
Genomic Characterization of Multidrug-Resistant Extended Spectrum β-Lactamase-Producing Klebsiella pneumoniae from Clinical Samples of a Tertiary Hospital in South Kivu Province, Eastern Democratic Republic of Congo
by Leonid M. Irenge, Jérôme Ambroise, Bertrand Bearzatto, Jean-François Durant, Maxime Bonjean and Jean-Luc Gala
Microorganisms 2023, 11(2), 525; https://doi.org/10.3390/microorganisms11020525 - 18 Feb 2023
Viewed by 1760
Abstract
Multidrug-resistant (MDR) and extended spectrum β-lactamase (ESBL)-producing extra-intestinal K. pneumoniae are associated with increased morbidity and mortality. This study aimed to characterize the resistance and virulence profiles of extra-intestinal MDR ESBL-producing K. pneumoniae associated with infections at a tertiary hospital in South-Kivu province, [...] Read more.
Multidrug-resistant (MDR) and extended spectrum β-lactamase (ESBL)-producing extra-intestinal K. pneumoniae are associated with increased morbidity and mortality. This study aimed to characterize the resistance and virulence profiles of extra-intestinal MDR ESBL-producing K. pneumoniae associated with infections at a tertiary hospital in South-Kivu province, DRC. Whole-genome sequencing (WGS) was carried out on 37 K. pneumoniae isolates displaying MDR and ESBL-producing phenotype. The assembled genomes were analysed for phylogeny, virulence factors and antimicrobial resistance genes (ARG) determinants. These isolates were compared to sub-Saharan counterparts. K. pneumoniae isolates displayed a high genetic variability with up to 16 sequence types (ST). AMR was widespread against β-lactamases (including third and fourth-generation cephalosporins, but not carbapenems), aminoglycosides, ciprofloxacin, tetracycline, erythromycin, nitrofurantoin, and cotrimoxazole. The blaCTX-M-15 gene was the most common β-lactamase gene among K. pneumoniae isolates. No carbapenemase gene was found. ARG for aminoglycosides, quinolones, phenicols, tetracyclines, sulfonamides, nitrofurantoin were widely distributed among the isolates. Nine isolates had the colistin-resistant R256G substitution in the pmrB efflux pump gene without displaying reduced susceptibility to colistin. Despite carrying virulence genes, none had hypervirulence genes. Our results highlight the genetic diversity of MDR ESBL-producing K. pneumoniae isolates and underscore the importance of monitoring simultaneously the evolution of phenotypic and genotypic AMR in Bukavu and DRC, while calling for caution in administering colistin and carbapenem to patients. Full article
(This article belongs to the Special Issue Advances in Antibiotic and Drug-Resistance Mechanisms)
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15 pages, 2880 KiB  
Article
Phenol Degradation by Pseudarthrobacter phenanthrenivorans Sphe3
by Stamatia Asimakoula, Orfeas Marinakos, Epameinondas Tsagogiannis and Anna-Irini Koukkou
Microorganisms 2023, 11(2), 524; https://doi.org/10.3390/microorganisms11020524 - 18 Feb 2023
Cited by 12 | Viewed by 2046
Abstract
Phenol poses a threat as one of the most important industrial environmental pollutants that must be removed before disposal. Biodegradation is a cost-effective and environmentally friendly approach for phenol removal. This work aimed at studying phenol degradation by Pseudarthrobacter phenanthrenivorans Sphe3 cells and also, [...] Read more.
Phenol poses a threat as one of the most important industrial environmental pollutants that must be removed before disposal. Biodegradation is a cost-effective and environmentally friendly approach for phenol removal. This work aimed at studying phenol degradation by Pseudarthrobacter phenanthrenivorans Sphe3 cells and also, investigating the pathway used by the bacterium for phenol catabolism. Moreover, alginate-immobilized Sphe3 cells were studied in terms of phenol degradation efficiency compared to free cells. Sphe3 was found to be capable of growing in the presence of phenol as the sole source of carbon and energy, at concentrations up to 1500 mg/L. According to qPCR findings, both pathways of ortho- and meta-cleavage of catechol are active, however, enzymatic assays and intermediate products identification support the predominance of the ortho-metabolic pathway for phenol degradation. Alginate-entrapped Sphe3 cells completely degraded 1000 mg/L phenol after 192 h, even though phenol catabolism proceeds slower in the first 24 h compared to free cells. Immobilized Sphe3 cells retain phenol-degrading capacity even after 30 days of storage and also can be reused for at least five cycles retaining more than 75% of the original phenol-catabolizing capacity. Full article
(This article belongs to the Special Issue Microbial Biodegradation and Biotransformation 2.0)
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9 pages, 681 KiB  
Communication
Mobile Phones: Reservoirs of Resistant Bacteria during the COVID-19 Pandemic in Abu Dhabi, United Arab Emirates
by Kawthar Kayed, Ghalia Khoder, Joviana Farhat and Rose Ghemrawi
Microorganisms 2023, 11(2), 523; https://doi.org/10.3390/microorganisms11020523 - 18 Feb 2023
Cited by 1 | Viewed by 5179
Abstract
Background: Mobile phones are excessively used even though microbes’ ability to survive on phone surfaces was confirmed. During the COVID-19 pandemic, heavy hygiene practices have been applied to mobile surfaces. Therefore, it is interesting to evaluate the emergence of antimicrobial-resistant bacteria on mobile [...] Read more.
Background: Mobile phones are excessively used even though microbes’ ability to survive on phone surfaces was confirmed. During the COVID-19 pandemic, heavy hygiene practices have been applied to mobile surfaces. Therefore, it is interesting to evaluate the emergence of antimicrobial-resistant bacteria on mobile phone surfaces. Methods: A random sampling technique was utilized on residents in Abu Dhabi, UAE between May and June 2021. A swab sample from each participant’s mobile phone was collected and transported to the microbiology laboratory for bacterial culture and antimicrobial susceptibility tests. Furthermore, a cross-sectional study was conducted via a self-administered questionnaire filled by participants. The questionnaire was used to collect sociodemographic data, phone frequency usage and cleaning methods. Results: One hundred two-sample swabs and data have been included in the study. The majority of participants (91.1%) reported cleaning their mobile phones with wipes and alcohol. However, 100% of participants had a mobile phone contaminated by bacteria such as S. aureus, E. coli, Coagulase-negative staphylococci, Micrococcus, Bacillus, Streptococcus, Citrobacter, Proteus, Enterococcus, klebsiella, Pseudomonas and Actinobacteria. Interestingly, most of these potentially pathogenic bacteria were found to be resistant to ampicillin, ceftazidime and cefotaxime. Conclusion: The continuous hand and mobile disinfectant have contributed to the emergence of resistant bacteria. Full article
(This article belongs to the Special Issue Infectious Diseases, New Approaches to Old Problems 2.0)
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14 pages, 1247 KiB  
Article
Bioremediation of Oil-Contaminated Soil of the Republic of Kazakhstan Using a New Biopreparation
by Tatiana Vyacheslavovna Funtikova, Lenar Imametdinovich Akhmetov, Irina Filippovna Puntus, Pavel Alexeevich Mikhailov, Nurbol Orynbasaruly Appazov, Roza Abdibekovna Narmanova, Andrey Evgenievich Filonov and Inna Petrovna Solyanikova
Microorganisms 2023, 11(2), 522; https://doi.org/10.3390/microorganisms11020522 - 18 Feb 2023
Cited by 4 | Viewed by 2257
Abstract
A new biopreparation is developed to clean soils from oil pollution in the arid climate of the Republic of Kazakhstan. The biopreparation includes bacterial strains R. qingshengii F2-1, R. qingshengii F2-2, and P. alloputida BS3701. When using the biopreparation in a liquid mineral [...] Read more.
A new biopreparation is developed to clean soils from oil pollution in the arid climate of the Republic of Kazakhstan. The biopreparation includes bacterial strains R. qingshengii F2-1, R. qingshengii F2-2, and P. alloputida BS3701. When using the biopreparation in a liquid mineral medium with 15% crude oil, laboratory studies have revealed degradation of 48% n-alkanes and 39% of PAHs after 50 days. The effectiveness of the biopreparation has been demonstrated in field experiments in the soil contaminated with 10% crude oil at the K-Kurylys landfill, Republic of Kazakhstan. During the six-month field experiment, the number of oil degraders reached 107 CFU/g soil, which degraded 70% of crude oil by the end of the experiment. Full article
(This article belongs to the Special Issue Microbial Biodegradation and Biotransformation 2.0)
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16 pages, 753 KiB  
Article
Prevalence, Virulence Potential, and Growth in Cheese of Bacillus cereus Strains Isolated from Fresh and Short-Ripened Cheeses Sold on the Italian Market
by Erica Tirloni, Cristian Bernardi, Francesco Celandroni, Diletta Mazzantini, Mariacristina Massimino, Simone Stella and Emilia Ghelardi
Microorganisms 2023, 11(2), 521; https://doi.org/10.3390/microorganisms11020521 - 18 Feb 2023
Cited by 5 | Viewed by 1849
Abstract
This study investigated B. cereus presence in 122 samples belonging to 34 typologies of fresh or short-ripened cheeses made from cow, sheep, goat, or buffalo pasteurized milk, and sold on the Italian market. B. cereus was isolated at a prevalence of 9.8%, with [...] Read more.
This study investigated B. cereus presence in 122 samples belonging to 34 typologies of fresh or short-ripened cheeses made from cow, sheep, goat, or buffalo pasteurized milk, and sold on the Italian market. B. cereus was isolated at a prevalence of 9.8%, with a marked variability among cheese categories, and at low counts (always below 2.26 Log CFU/g). Twelve isolates were identified by MALDI-TOF analysis and typified by RAPD PCR as belonging to different B. cereus strains. All the strains were tested for the production of hemolysin BL, phosphatidylcholine-specific phospholipase C, proteases, and biofilm formation, and for the presence of chromosomal toxin-encoding genes (sph, plcA, cytK, entFM, bcet, nheA, nheB, nheC). Overall, 92% of strains harbored bcet, 75% the three genes nheA, nheB, and nheC, as well as plcA and sph, 67% entFM, and 33% cytK. All strains showed biofilm-forming ability. A chemical-physical characterization of the cheeses was also performed to show their suitability as substrates for B. cereus growth, showing high heterogeneity in terms of pH, aw, salt content, and concentration of organic acids. Finally, the ability to support spore germination and vegetative cell growth of a selected cheese was investigated in spores-inoculated samples maintained at 10 °C and 15 °C, showing the inhibitory effect of low storage temperatures. Full article
(This article belongs to the Special Issue Microbial Ecology of Dairy Products: From Diversity to Functions)
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14 pages, 2593 KiB  
Article
Assessing the Effects of Rotifer Feed Enrichments on Turbot (Scophthalmus maximus) Larvae and Post-Larvae Gut-Associated Bacterial Communities
by Antonio Louvado, Carolina Castro, Davide A. M. Silva, Vanessa Oliveira, Luís E. C. Conceição, Daniel F. R. Cleary and Newton C. M. Gomes
Microorganisms 2023, 11(2), 520; https://doi.org/10.3390/microorganisms11020520 - 17 Feb 2023
Cited by 1 | Viewed by 1576
Abstract
Live feed enrichments are often used in fish larvicultures as an optimized source of essential nutrients to improve larval growth and survival. In addition to this, they may also play an important role in structuring larval-associated microbial communities and may help improve their [...] Read more.
Live feed enrichments are often used in fish larvicultures as an optimized source of essential nutrients to improve larval growth and survival. In addition to this, they may also play an important role in structuring larval-associated microbial communities and may help improve their resistance to diseases. However, there is limited information available on how larval microbial communities and larviculture water are influenced by different live feed enrichments. In the present study, we investigated the effects of two commercial rotifer enrichments (ER) on turbot (Scophthalmus maximus) larval and post-larval gut-associated bacterial communities during larviculture production. We evaluated their effects on bacterial populations related to known pathogens and beneficial bacteria and their potential influence on the composition of bacterioplankton communities during larval rearing. High-throughput 16S rRNA gene sequencing was used to assess the effects of different rotifer enrichments (ER1 and ER2) on the structural diversity of bacterial communities of the whole turbot larvae 10 days after hatching (DAH), the post-larval gut 30 DAH, and the larviculture water. Our results showed that different rotifer feed enrichments were associated with significant differences in bacterial composition of turbot larvae 10 DAH, but not with the composition of larval gut communities 30 DAH or bacterioplankton communities 10 and 30 DAH. However, a more in-depth taxonomic analysis showed that there were significant differences in the abundance of Vibrionales in both 10 DAH larvae and in the 30 DAH post-larval gut fed different RE diets. Interestingly, the ER1 diet had a higher relative abundance of specific amplicon sequence variants (ASVs) related to potential Vibrio-antagonists belonging to the Roseobacter clade (e.g., Phaeobacter and Ruegeria at 10 DAH and Sulfitobacter at 30 DAH). In line with this, the diet was also associated with a lower relative abundance of Vibrio and a lower mortality. These results suggest that rotifer diets can affect colonization by Vibrio members in the guts of post-larval turbot. Overall, this study indicates that live feed enrichments can have modulatory effects on fish bacterial communities during the early stages of development, which includes the relative abundances of pathogenic and antagonist taxa in larviculture systems. Full article
(This article belongs to the Section Veterinary Microbiology)
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17 pages, 3861 KiB  
Review
Current Methods for the Detection of Antibodies of Varicella-Zoster Virus: A Review
by Dequan Pan, Wei Wang and Tong Cheng
Microorganisms 2023, 11(2), 519; https://doi.org/10.3390/microorganisms11020519 - 17 Feb 2023
Cited by 3 | Viewed by 4581
Abstract
Infection with the varicella-zoster virus (VZV) causes chickenpox and shingles, which lead to significant morbidity and mortality globally. The detection of serum VZV-specific antibodies is important for the clinical diagnosis and sero-epidemiological research of VZV infection, and for assessing the effect of VZV [...] Read more.
Infection with the varicella-zoster virus (VZV) causes chickenpox and shingles, which lead to significant morbidity and mortality globally. The detection of serum VZV-specific antibodies is important for the clinical diagnosis and sero-epidemiological research of VZV infection, and for assessing the effect of VZV vaccine immunization. Over recent decades, a variety of methods for VZV antibody detection have been developed. This review summarizes and compares the current methods for detecting VZV antibodies, and discussed future directions for this field. Full article
(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)
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18 pages, 5136 KiB  
Article
Risk of Exposure to Coccidioides spp. in the Temblor Special Recreation Management Area (SRMA), Kern County, CA
by Antje Lauer, Jocelyne Jassiri Lopez, Michael Chabolla and Carl Kloock
Microorganisms 2023, 11(2), 518; https://doi.org/10.3390/microorganisms11020518 - 17 Feb 2023
Cited by 2 | Viewed by 1328
Abstract
The Temblor Mountain Special Recreation Area (SRMA) on the western flank of the San Joaquin Valley, CA, is located in the endemic area of Coccidioides, a fungal pathogen responsible for the increasing incidence of coccidioidomycosis (Valley fever). Recreationists in the SRMA, such as [...] Read more.
The Temblor Mountain Special Recreation Area (SRMA) on the western flank of the San Joaquin Valley, CA, is located in the endemic area of Coccidioides, a fungal pathogen responsible for the increasing incidence of coccidioidomycosis (Valley fever). Recreationists in the SRMA, such as off-highway vehicle (OHV) drivers and mountain bikers who disturb the soils, are at risk of being exposed to airborne arthroconidia (asexual spores) of the pathogen. To reduce the risk of pathogen exposure for visitors, the Bureau of Land Management (BLM) plans to limit recreational activities to areas with a reduced pathogen presence. They envision an official OHV park in the future, by also restricting access to areas with ongoing restoration efforts and by limiting soil erosion in sensitive areas. To investigate which soils in the Temblor SRMA are most likely to support the growth of Coccidioides spp., soil samples were collected over a 3-year period from dominant soil types in a northern and a southern sampling area and analyzed for the pathogen using a culture-independent PCR-based method. In addition, soil pH and electrical conductivity were determined. The results of this study revealed slight genetic variance in the Coccidioides sequences obtained from the soils of the Temblor SRMA. An analysis of variance (ANOVA) could not confirm differences in soil pH and electrical conductivity (EC) between the different soil types investigated and between sites where the pathogen was detected compared to sites where it could not be found. However, the year of sampling appeared to have an influence on observed soil pH and EC, and the presence of the pathogen. Of all dominant soil types investigated, those belonging to the Littlesignal–Cochora association were the least likely to contain the pathogen, whereas soils of the Beam–Panoza–Hillbrick association appeared more supportive. In addition to pointing out OHV areas with lower pathogen exposure risk in the Temblor SRMA, recommendations were made to educate visitors and BLM workers about the risk of contracting Valley fever. Full article
(This article belongs to the Special Issue Microbial Exposure Assessments in Different Occupational and Indoor Settings)
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14 pages, 2917 KiB  
Article
Vancomycin-Resistant Enterococcus faecium Sterilization and Conductivity Change by Impulse Voltage
by Takahisa Ueno, Takashi Furukawa and Takashi Sakugawa
Microorganisms 2023, 11(2), 517; https://doi.org/10.3390/microorganisms11020517 - 17 Feb 2023
Viewed by 1276
Abstract
Owing to the increased use of antibiotics, drug-resistant strains, including those that are resistant to the antibiotic vancomycin, have emerged, which has become a major problem. In Japan, sewage treatments consist of sterilization with chlorine; however, this may not be sufficient to inactivate [...] Read more.
Owing to the increased use of antibiotics, drug-resistant strains, including those that are resistant to the antibiotic vancomycin, have emerged, which has become a major problem. In Japan, sewage treatments consist of sterilization with chlorine; however, this may not be sufficient to inactivate these bacteria. In this study, impulse voltage was employed instead of chlorine to inactivate drug-resistant bacteria. The results showed that sterilization above 105 CFU/mL is possible with longer application times of applied voltages above 4.5 kV. The effectiveness of impulse-voltage-mediated sterilization increased as the temperature of the bacterial suspension increased. The number of bacteria sterilized via impulse voltage was correlated with conductivity when the number of bacteria sterilized by impulse voltage exceeded 105 CFU/mL. The sterilization rate achieved by the use of impulse voltage could be estimated immediately by measuring the electrical conductivity and without the need for using the culture method. Full article
(This article belongs to the Special Issue Advances in Waterborne Pathogens)
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7 pages, 1040 KiB  
Communication
Diversity of Bacterial Clones and Plasmids of NDM-1 Producing Escherichia coli Clinical Isolates in Central Greece
by Katerina Tsilipounidaki, Zoi Florou, Anargyros Skoulakis, George C. Fthenakis, Vivi Miriagou and Efthymia Petinaki
Microorganisms 2023, 11(2), 516; https://doi.org/10.3390/microorganisms11020516 - 17 Feb 2023
Cited by 3 | Viewed by 1562
Abstract
The objective of the present study was to genetically characterize ten NDM-1 producing Escherichia coli isolates, recovered from patients in a hospital in Central Greece during the period 2017 to 2021.The isolates were studied by whole genome sequencing to obtain multi-locus sequencing typing [...] Read more.
The objective of the present study was to genetically characterize ten NDM-1 producing Escherichia coli isolates, recovered from patients in a hospital in Central Greece during the period 2017 to 2021.The isolates were studied by whole genome sequencing to obtain multi-locus sequencing typing (MLST), identification of blaNDM1-environment, resistome and plasmid content. MLST analysis showed the presence of eight sequence types: ST46* (two isolates), ST46, ST744, ST998, ST410, ST224, ST4380, ST683 and ST12 (one isolate each). Apart of the presence of blaNDM-1, the isolates carried a combination of various to β-lactams encoding resistance genes: blaTEM-1B, blaCTX-15, blaOXA-1, blaVIM-1, blaSHV-5, blaOXA-16, blaOXA-10 and blaVEB-1. Additionally, plurality of resistance genes to aminoglycosides, macrolides, rifamycin, phenicols, sulfonamides and tetracycline was detected. The presence of multiple replicons was observed, with predominance of IncFII and IncFIB. Analysis of blaNDM-1 genetic environment of the isolates showed that seven had 100% identity with the pS-3002cz plasmid (Accession Number KJ 958927), two with the pB-3002cz plasmid (Accession Number KJ958926) and one with the pEc19397-131 plasmid (Accession Number MG878866). Τhis latter plasmid was derived by the fusion of two, previously identified, plasmids, pAMPD2 and pLK75 (Accession Numbers CP078058 and KJ440076, respectively). The diversity of clones and plasmids of NDM-1 producing E. coli isolated from patients in Greece indicates a continuous horizontal gene transfer. Full article
(This article belongs to the Special Issue ß-Lactamases 2.0)
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15 pages, 641 KiB  
Article
Genomic Islands Identified in Highly Resistant Serratia sp. HRI: A Pathway to Discover New Disinfectant Resistance Elements
by Samantha J. McCarlie, Charlotte E. Boucher and Robert R. Bragg
Microorganisms 2023, 11(2), 515; https://doi.org/10.3390/microorganisms11020515 - 17 Feb 2023
Cited by 1 | Viewed by 1673
Abstract
Molecular insights into the mechanisms of resistance to disinfectants are severely limited, together with the roles of various mobile genetic elements. Genomic islands are a well-characterised molecular resistance element in antibiotic resistance, but it is unknown whether genomic islands play a role in [...] Read more.
Molecular insights into the mechanisms of resistance to disinfectants are severely limited, together with the roles of various mobile genetic elements. Genomic islands are a well-characterised molecular resistance element in antibiotic resistance, but it is unknown whether genomic islands play a role in disinfectant resistance. Through whole-genome sequencing and the bioinformatic analysis of Serratia sp. HRI, an isolate with high disinfectant resistance capabilities, nine resistance islands were predicted and annotated within the genome. Resistance genes active against several antimicrobials were annotated in these islands, most of which are multidrug efflux pumps belonging to the MFS, ABC and DMT efflux families. Antibiotic resistance islands containing genes encoding for multidrug resistance proteins ErmB (macrolide and erythromycin resistance) and biclomycin were also found. A metal fitness island harbouring 13 resistance and response genes to copper, silver, lead, cadmium, zinc, and mercury was identified. In the search for disinfectant resistance islands, two genomic islands were identified to harbour smr genes, notorious for conferring disinfectant resistance. This suggests that genomic islands are capable of conferring disinfectant resistance, a phenomenon that has not yet been observed in the study of biocide resistance and tolerance. Full article
(This article belongs to the Special Issue Microbial Diversity and Antimicrobial Resistance Genes in the Environment)
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18 pages, 999 KiB  
Review
SARS-CoV-2 Affects Both Humans and Animals: What Is the Potential Transmission Risk? A Literature Review
by Antonio Santaniello, Giuseppe Perruolo, Serena Cristiano, Ayewa Lawoe Agognon, Serena Cabaro, Alessia Amato, Ludovico Dipineto, Luca Borrelli, Pietro Formisano, Alessandro Fioretti and Francesco Oriente
Microorganisms 2023, 11(2), 514; https://doi.org/10.3390/microorganisms11020514 - 17 Feb 2023
Cited by 4 | Viewed by 1640
Abstract
In March 2020, the World Health Organization Department declared the coronavirus (COVID-19) outbreak a global pandemic, as a consequence of its rapid spread on all continents. The COVID-19 pandemic has been not only a health emergency but also a serious general problem as [...] Read more.
In March 2020, the World Health Organization Department declared the coronavirus (COVID-19) outbreak a global pandemic, as a consequence of its rapid spread on all continents. The COVID-19 pandemic has been not only a health emergency but also a serious general problem as fear of contagion and severe restrictions put economic and social activity on hold in many countries. Considering the close link between human and animal health, COVID-19 might infect wild and companion animals, and spawn dangerous viral mutants that could jump back and pose an ulterior threat to us. The purpose of this review is to provide an overview of the pandemic, with a particular focus on the clinical manifestations in humans and animals, the different diagnosis methods, the potential transmission risks, and their potential direct impact on the human–animal relationship. Full article
(This article belongs to the Special Issue The Ecology and Evolution of SARS-CoV-2)
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20 pages, 2454 KiB  
Article
Effects of Different Types of LAB on Dynamic Fermentation Quality and Microbial Community of Native Grass Silage during Anaerobic Fermentation and Aerobic Exposure
by Jiawei Zhang, Yichao Liu, Zhijun Wang, Jian Bao, Muqier Zhao, Qiang Si, Pengbo Sun, Gentu Ge and Yushan Jia
Microorganisms 2023, 11(2), 513; https://doi.org/10.3390/microorganisms11020513 - 17 Feb 2023
Cited by 3 | Viewed by 1629
Abstract
Silage of native grasses can alleviate seasonal forage supply imbalance in pastures and provide additional sources to meet forage demand. The study aimed to investigate the effects of Lactobacillus plantarum (LP), Lactobacillus buchneri (LB), and Lactobacillus plantarum in combination with Lactobacillus buchneri (PB) [...] Read more.
Silage of native grasses can alleviate seasonal forage supply imbalance in pastures and provide additional sources to meet forage demand. The study aimed to investigate the effects of Lactobacillus plantarum (LP), Lactobacillus buchneri (LB), and Lactobacillus plantarum in combination with Lactobacillus buchneri (PB) on the nutritional quality, fermentation quality, and microbial community of native grass silage at 2, 7, 15, and 60 days after ensiling and at 4 and 8 days after aerobic exposure. The results showed that dry matter content, crude protein content, the number of lactic acid bacteria, and lactic acid and acetic acid content increased and pH and ammonia nitrogen content decreased after lactic acid bacteria (LAB) inoculation compared with the control group (CK). LP had the lowest pH and highest lactic acid content but did not have greater aerobic stability. LB maintained a lower pH level and acetic acid remained at a higher level after aerobic exposure; aerobic bacteria, coliform bacteria, yeast, and molds all decreased in number, which effectively improved aerobic stability. The effect of the compound addition of LAB was in between the two other treatments, having higher crude protein content, lactic acid and acetic acid content, lower pH, and ammonia nitrogen content. At the phylum level, the dominant phylum changed from Proteobacteria to Firmicutes after ensiling, and at the genus level, Lactiplantibacillus and Lentilactobacillus were the dominant genera in both LAB added groups, while Limosilactobacillus was the dominant genus in the CK treatment. In conclusion, the addition of LAB can improve native grass silage quality by changing bacterial community structure. LP is beneficial to improve the fermentation quality in the ensiling stage, LB is beneficial to inhibit silage deterioration in the aerobic exposure stage, and compound LAB addition is more beneficial to be applied in native grass silage. Full article
(This article belongs to the Section Microbial Biotechnology)
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19 pages, 2824 KiB  
Article
Spray Drying Is a Viable Technology for the Preservation of Recombinant Proteins in Microalgae
by Anaëlle Vilatte, Xenia Spencer-Milnes, Harry Oliver Jackson, Saul Purton and Brenda Parker
Microorganisms 2023, 11(2), 512; https://doi.org/10.3390/microorganisms11020512 - 17 Feb 2023
Cited by 7 | Viewed by 2582
Abstract
Microalgae are promising host organisms for the production of encapsulated recombinant proteins such as vaccines. However, bottlenecks in bioprocess development, such as the drying stage, need to be addressed to ensure feasibility at scale. In this study, we investigated the potential of spray [...] Read more.
Microalgae are promising host organisms for the production of encapsulated recombinant proteins such as vaccines. However, bottlenecks in bioprocess development, such as the drying stage, need to be addressed to ensure feasibility at scale. In this study, we investigated the potential of spray drying to produce a recombinant vaccine in microalgae. A transformant line of Chlamydomonas reinhardtii carrying a subunit vaccine against salmonid alphavirus was created via chloroplast engineering. The integrity of the recombinant protein after spray drying and its stability after 27 months storage at –80 °C, +4 °C and room temperature were assessed by immunoblotting. The protein withstood spray drying without significant losses. Long-term storage at +4 °C and room temperature resulted in 50% and 92% degradation, respectively. Optimizing spray drying and storage conditions should minimize degradation and favour short-term storage at positive temperatures. Using data on yield and productivity, the economics of spray drying- and freeze drying-based bioprocesses were compared. The drying stage corresponded to 41% of the total production cost. Process optimization, genetic engineering and new market strategies were identified as potential targets for cost reduction. Overall, this study successfully demonstrates the suitability of spray drying as a process option for recombinant protein production in microalgae at the industrial scale. Full article
(This article belongs to the Special Issue Production of Recombinant Molecules in Algal Chloroplasts)
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13 pages, 1245 KiB  
Article
Short Course of Antibiotic Therapy for Gram-Negative Bacilli Bacteremia in Patients with Cancer and Hematopoietic Stem Cell Transplantation: Less Is Possible
by Fabián Herrera, Diego Torres, Alberto Carena, Federico Nicola, Andrés Rearte, Elena Temporiti, Laura Jorge, Ricardo Valentini, Florencia Bues, Silvia Relloso and Pablo Bonvehí
Microorganisms 2023, 11(2), 511; https://doi.org/10.3390/microorganisms11020511 - 17 Feb 2023
Cited by 1 | Viewed by 1789
Abstract
Data about short courses of antibiotic therapy for Gram-negative bacilli (GNB) bacteremia in immunosuppressed patients are limited. This is a prospective observational study performed on adult patients with cancer and hematopoietic stem cell transplant (HSCT) who developed GNB bacteremia and received appropriate empirical [...] Read more.
Data about short courses of antibiotic therapy for Gram-negative bacilli (GNB) bacteremia in immunosuppressed patients are limited. This is a prospective observational study performed on adult patients with cancer and hematopoietic stem cell transplant (HSCT) who developed GNB bacteremia and received appropriate empirical antibiotic therapy (EAT), had a clinical response within 7 days and survived 48 h after the end of therapy. They received antibiotic therapy in the range of 7–15 days and were divided into short course, with a median of 7 days (SC), or long course, with a median of 14 days (LC). Seventy-four patients were included (SC: 36 and LC: 38). No differences were observed in baseline characteristics or in the presence of neutropenia: 58.3% vs. 60.5% (p = 0.84). Clinical presentation and microbiological characteristics were similar in SC and LC, respectively: clinical source of bacteremia 72.2% vs. 76.3% (p = 0.68); shock 2.8% vs. 10.5% (p = 0.35) and multidrug-resistant GNB 27.8% vs. 21.1% (p = 0.50). Overall, mortality was 2.8% vs. 7.9% (p = 0.61), and bacteremia relapse was 2.8% vs. 0 (p = 0.30). The length of hospitalization since bacteremia was 7 days (interquartile range (IQR), 6–15) for SC and 12 days (IQR, 7–19) (p = 0.021) for LC. In the case of patients with cancer or HSCT and GNB bacteremia who receive appropriate EAT with clinical response, 7 days of antibiotic therapy might be adequate. Full article
(This article belongs to the Special Issue Bacterial Pathogens Associated with Bacteremia)
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26 pages, 1610 KiB  
Review
The Recent Advances in the Utility of Microbial Lipases: A Review
by Sajid Ali, Sumera Afzal Khan, Muhammad Hamayun and In-Jung Lee
Microorganisms 2023, 11(2), 510; https://doi.org/10.3390/microorganisms11020510 - 17 Feb 2023
Cited by 21 | Viewed by 4437
Abstract
Lipases are versatile biocatalysts and are used in different bioconversion reactions. Microbial lipases are currently attracting a great amount of attention due to the rapid advancement of enzyme technology and its practical application in a variety of industrial processes. The current review provides [...] Read more.
Lipases are versatile biocatalysts and are used in different bioconversion reactions. Microbial lipases are currently attracting a great amount of attention due to the rapid advancement of enzyme technology and its practical application in a variety of industrial processes. The current review provides updated information on the different sources of microbial lipases, such as fungi, bacteria, and yeast, their classical and modern purification techniques, including precipitation and chromatographic separation, the immunopurification technique, the reversed micellar system, aqueous two-phase system (ATPS), aqueous two-phase flotation (ATPF), and the use of microbial lipases in different industries, e.g., the food, textile, leather, cosmetics, paper, and detergent industries. Furthermore, the article provides a critical analysis of lipase-producing microbes, distinguished from the previously published reviews, and illustrates the use of lipases in biosensors, biodiesel production, and tea processing, and their role in bioremediation and racemization. Full article
(This article belongs to the Section Microbial Biotechnology)
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