Journal Description
Microorganisms
Microorganisms
is a scientific, peer-reviewed, open access journal of microbiology, published monthly online by MDPI. The Hellenic Society Mikrobiokosmos (MBK), the Spanish Society for Nitrogen Fixation (SEFIN) and the Society for Microbial Ecology and Disease (SOMED) are affiliated with the Microorganisms, and their members receive a discount on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, PMC, PubAg, CAPlus / SciFinder, AGRIS, and other databases.
- Journal Rank: JCR - Q2 (Microbiology) / CiteScore - Q2 (Microbiology (medical))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 15.1 days after submission; acceptance to publication is undertaken in 2.8 days (median values for papers published in this journal in the second half of 2023).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
- Testimonials: See what our editors and authors say about the Microorganisms.
- Companion journal: Applied Microbiology.
Impact Factor:
4.5 (2022);
5-Year Impact Factor:
4.8 (2022)
Latest Articles
Lactiplantibacillus plantarum ST-III and Lacticaseibacillus rhamnosus KF7 Enhance the Intestinal Epithelial Barrier in a Dual-Environment In Vitro Co-Culture Model
Microorganisms 2024, 12(5), 873; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050873 - 26 Apr 2024
Abstract
Intestinal barrier hyperpermeability, which is characterised by impaired tight junction proteins, is associated with a variety of gastrointestinal and systemic diseases. Therefore, maintaining intestinal barrier integrity is considered one of the effective strategies to reduce the risk of such disorders. This study aims
[...] Read more.
Intestinal barrier hyperpermeability, which is characterised by impaired tight junction proteins, is associated with a variety of gastrointestinal and systemic diseases. Therefore, maintaining intestinal barrier integrity is considered one of the effective strategies to reduce the risk of such disorders. This study aims to investigate the potential benefits of two probiotic strains (Lactiplantibacillus plantarum ST-III and Lacticaseibacillus rhamnosus KF7) on intestinal barrier function by using a physiologically relevant in vitro model of the intestinal epithelium. Our results demonstrate that both strains increased transepithelial electrical resistance, a measure of intestinal barrier integrity. Immunolocalisation studies indicated that this improvement in barrier function was not due to changes in the co-localisation of the tight junction (TJ) proteins ZO-1 and occludin. However, we observed several modifications in TJ-related genes in response to the probiotics, including the upregulation of transmembrane and cytosolic TJ proteins, as well as TJ signalling proteins. Gene expression modulation was strain- and time-dependent, with a greater number of differentially expressed genes and higher fold-change being observed in the L. plantarum ST-III group and at the latter timepoint. Further studies to investigate how the observed gene expression changes can lead to enhanced barrier function will aid in the development of probiotic foods to help improve intestinal barrier function.
Full article
(This article belongs to the Special Issue The Impact of Probiotics on Gut Health)
Open AccessArticle
Bacteria–Fungi Interactions in Multiple Sclerosis
by
Miriam Gorostidi-Aicua, Iraia Reparaz, Ane Otaegui-Chivite, Koldo García, Leire Romarate, Amaya Álvarez de Arcaya, Idoia Mendiburu, Maialen Arruti, Tamara Castillo-Triviño, Laura Moles and David Otaegui
Microorganisms 2024, 12(5), 872; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050872 - 26 Apr 2024
Abstract
Multiple sclerosis (MS) arises from a complex interplay between host genetic factors and environmental components, with the gut microbiota emerging as a key area of investigation. In the current study, we used ion torrent sequencing to delve into the bacteriome (bacterial microbiota) and
[...] Read more.
Multiple sclerosis (MS) arises from a complex interplay between host genetic factors and environmental components, with the gut microbiota emerging as a key area of investigation. In the current study, we used ion torrent sequencing to delve into the bacteriome (bacterial microbiota) and mycobiome (fungal microbiota) of people with MS (pwMS), and compared them to healthy controls (HC). Through principal coordinate, diversity, and abundance analyses, as well as clustering and cross-kingdom microbial correlation assessments, we uncovered significant differences in the microbial profiles between pwMS and HC. Elevated levels of the fungus Torulaspora and the bacterial family Enterobacteriaceae were observed in pwMS, whereas beneficial bacterial taxa, such as Prevotelladaceae and Dialister, were reduced. Notably, clustering analysis revealed overlapping patterns in the bacteriome and mycobiome data for 74% of the participants, with weakened cross-kingdom interactions evident in the altered microbiota of pwMS. Our findings highlight the dysbiosis of both bacterial and fungal microbiota in MS, characterized by shifts in biodiversity and composition. Furthermore, the distinct disease-associated pattern of fungi–bacteria interactions suggests that fungi, in addition to bacteria, contribute to the pathogenesis of MS. Overall, our study sheds light on the intricate microbial dynamics underlying MS, paving the way for further investigation into the potential therapeutic targeting of the gut microbiota in MS management.
Full article
(This article belongs to the Section Gut Microbiota)
►▼
Show Figures
Figure 1
Open AccessArticle
Gender Impacted Gut Microbiota and Growth Performance in the Blotched Snakehead (Channa maculata)
by
Chang Fang, Fang Zeng, Shijun Chen, Shuisheng Li, Yuting Yang, Wanjing Lin, Yun Liu, Cheng Peng and Huirong Yang
Microorganisms 2024, 12(5), 871; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050871 - 26 Apr 2024
Abstract
The blotched snakehead Channa maculata is an important economical freshwater species in East Asia. However, there has been relatively little research conducted on the correlation between gender and gut microbes. In this study, 36 of 1000 blotched snakeheads were randomly selected for growth
[...] Read more.
The blotched snakehead Channa maculata is an important economical freshwater species in East Asia. However, there has been relatively little research conducted on the correlation between gender and gut microbes. In this study, 36 of 1000 blotched snakeheads were randomly selected for growth performance measurement and gut microbiota high-throughput sequencing. Results showed that microbial diversity, composition, and metabolic functions were altered by gender and growth performance except the microbial network. In our study, Proteobacteria were the most abundant phylum, with Fusobacteria showing enrichment in males and Bacteroidetes in females. Notably, phylum Deinococcus-Thermus was identified as a significant biomarker. The Cetobacterium was the most abundant genus-level taxon. Furthermore, gut microbes specializing in the production of gut-healthy substances, such as coenzymes and vitamins, were identified as biomarkers in the fast-growing group. Our investigation highlighted the impact of gender on the composition and abundance of gut microbial biomarkers in both males and females, thereby influencing differential growth performance through the modulation of specific metabolic functions.
Full article
(This article belongs to the Special Issue Beneficial Microorganisms in Aquaculture)
►▼
Show Figures
Figure 1
Open AccessArticle
Plant Growth-Promoting Bacteria Influence Microbial Community Composition and Metabolic Function to Enhance the Efficiency of Hybrid pennisetum Remediation in Cadmium-Contaminated Soil
by
Zhao-Jin Chen, Meng-Lu Li, Shan-Shan Gao, Yu-Bo Sun, Hui Han, Bai-Lian Li and Yu-Ying Li
Microorganisms 2024, 12(5), 870; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050870 - 26 Apr 2024
Abstract
The green and efficient remediation of soil cadmium (Cd) is an urgent task, and plant-microbial joint remediation has become a research hotspot due to its advantages. High-throughput sequencing and metabolomics have technical advantages in analyzing the microbiological mechanism of plant growth-promoting bacteria in
[...] Read more.
The green and efficient remediation of soil cadmium (Cd) is an urgent task, and plant-microbial joint remediation has become a research hotspot due to its advantages. High-throughput sequencing and metabolomics have technical advantages in analyzing the microbiological mechanism of plant growth-promoting bacteria in improving phytoremediation of soil heavy metal pollution. In this experiment, a pot trial was conducted to investigate the effects of inoculating the plant growth-promoting bacterium Enterobacter sp. VY on the growth and Cd remediation efficiency of the energy plant Hybrid pennisetum. The test strain VY-1 was analyzed using high-throughput sequencing and metabolomics to assess its effects on microbial community composition and metabolic function. The results demonstrated that Enterobacter sp. VY-1 effectively mitigated Cd stress on Hybrid pennisetum, resulting in increased plant biomass, Cd accumulation, and translocation factor, thereby enhancing phytoremediation efficiency. Analysis of soil physical-chemical properties revealed that strain VY-1 could increase soil total nitrogen, total phosphorus, available phosphorus, and available potassium content. Principal coordinate analysis (PCoA) indicated that strain VY-1 significantly influenced bacterial community composition, with Proteobacteria, Firmicutes, Chloroflexi, among others, being the main differential taxa. Redundancy analysis (RDA) revealed that available phosphorus, available potassium, and pH were the primary factors affecting bacterial communities. Partial Least Squares Discriminant Analysis (PLS-DA) demonstrated that strain VY-1 modulated the metabolite profile of Hybrid pennisetum rhizosphere soil, with 27 differential metabolites showing significant differences, including 19 up-regulated and eight down-regulated expressions. These differentially expressed metabolites were primarily involved in metabolism and environmental information processing, encompassing pathways such as glutamine and glutamate metabolism, α-linolenic acid metabolism, pyrimidine metabolism, and purine metabolism. This study utilized 16S rRNA high-throughput sequencing and metabolomics technology to investigate the impact of the plant growth-promoting bacterium Enterobacter sp. VY-1 on the growth and Cd enrichment of Hybrid pennisetum, providing insights into the regulatory role of plant growth-promoting bacteria in microbial community structure and metabolic function, thereby improving the microbiological mechanisms of phytoremediation.
Full article
(This article belongs to the Topic Microbe-Induced Abiotic Stress Alleviation in Plants)
►▼
Show Figures
Figure 1
Open AccessArticle
The Contributions of Sub-Communities to the Assembly Process and Ecological Mechanisms of Bacterial Communities along the Cotton Soil–Root Continuum Niche Gradient
by
Shaodong Liu, Ruihua Liu, Siping Zhang, Qian Shen, Jing Chen, Huijuan Ma, Changwei Ge, Lidong Hao, Jinshan Zhang, Shubing Shi and Chaoyou Pang
Microorganisms 2024, 12(5), 869; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050869 - 26 Apr 2024
Abstract
Soil microbes are crucial in shaping the root-associated microbial communities. In this study, we analyzed the effect of the soil–root niche gradient on the diversity, composition, and assembly of the bacterial community and co-occurrence network of two cotton varieties. The results revealed that
[...] Read more.
Soil microbes are crucial in shaping the root-associated microbial communities. In this study, we analyzed the effect of the soil–root niche gradient on the diversity, composition, and assembly of the bacterial community and co-occurrence network of two cotton varieties. The results revealed that the bacterial communities in cotton soil–root compartment niches exhibited a skewed species abundance distribution, dominated by abundant taxa showing a strong spatial specificity. The assembly processes of the rhizosphere bacterial communities were mainly driven by stochastic processes, dominated by the enrichment pattern and supplemented by the depletion pattern to recruit bacteria from the bulk soil, resulting in a more stable bacterial community. The assembly processes of the endosphere bacterial communities were determined by processes dominated by the depletion pattern and supplemented by the enrichment pattern to recruit species from the rhizosphere, resulting in a decrease in the stability and complexity of the community co-occurrence network. The compartment niche shaped the diversity of the bacterial communities, and the cotton variety genotype was an important source of diversity in bacterial communities within the compartment niche. We suggest that the moderate taxa contribute to significantly more changes in the diversity of the bacterial community than the rare and abundant taxa during the succession of bacterial communities in the cotton root–soil continuum.
Full article
(This article belongs to the Section Plant Microbe Interactions)
►▼
Show Figures
Figure 1
Open AccessArticle
Solotvynia, a New Coccoid Lineage among the Ulvophyceae (Chlorophyta)
by
Tatyana Darienko and Thomas Pröschold
Microorganisms 2024, 12(5), 868; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050868 - 26 Apr 2024
Abstract
Coccoid Ulvophyceae are often overlooked despite their wide distribution. They occur as epiphytes on marine seaweeds or grow on stones or on shells of mussels and corals. Most of the species are not easy to identify based solely on morphology. However, they form
[...] Read more.
Coccoid Ulvophyceae are often overlooked despite their wide distribution. They occur as epiphytes on marine seaweeds or grow on stones or on shells of mussels and corals. Most of the species are not easy to identify based solely on morphology. However, they form two groups based on the flagellated cells during asexual reproduction. The biflagellated coccoids are monophyletic and represent the genus Sykidion (Sykidiales). In contrast, the quadriflagellated taxa are polyphyletic and belong to different genera and orders. The newly investigated strains NIES-1838 and NIES-1839, originally identified as Halochlorococcum, belong to the genus Chlorocystis (C. john-westii) among the order Chlorocystidales. The unidentified strain CCMP 1293 had almost an identical SSU and ITS-2 sequence to Symbiochlorum hainanense (Ignatiales) but showed morphological differences (single chloroplast, quadriflagellated zoospores) compared with the original description of this species (multiple chloroplasts, aplanospores). Surprisingly, the strain SAG 2662 (= ULVO-129), together with the published sequence of MBIC 10461, formed a new monophyletic lineage among the Ulvophyceae, which is highly supported in all of the bootstrap and Bayesian analyses and approximately unbiased tests of user-defined trees. This strain is characterized by a spherical morphology and also form quadriflagellated zoospores, have a unique ITS-2 barcode, and can tolerate a high variation of salinities. Considering our results, we emend the diagnosis of Symbiochlorum and propose the new genus Solotvynia among the new order Solotvyniales.
Full article
(This article belongs to the Section Environmental Microbiology)
►▼
Show Figures
Figure 1
Open AccessArticle
Effects of Microtopography on Soil Microbial Community Structure and Abundance in Permafrost Peatlands
by
Man Zhang, Lingyu Fu, Dalong Ma, Xu Wang and Anwen Liu
Microorganisms 2024, 12(5), 867; https://doi.org/10.3390/microorganisms12050867 - 26 Apr 2024
Abstract
Soil microorganisms play crucial roles in the stability of the global carbon pool, particularly in permafrost peatlands that are highly sensitive to climate change. Microtopography is a unique characteristic of peatland ecosystems, but how microtopography affects the microbial community structures and their functions
[...] Read more.
Soil microorganisms play crucial roles in the stability of the global carbon pool, particularly in permafrost peatlands that are highly sensitive to climate change. Microtopography is a unique characteristic of peatland ecosystems, but how microtopography affects the microbial community structures and their functions in the soil is only partially known. We characterized the bacterial and fungal community compositions by amplicon sequencing and their abundances via quantitative PCR at different soil depths in three microtopographical positions (hummocks, flats, and hollows) in permafrost peatland of the Greater Xing’an Mountains in China. The results showed that the soil of hummocks displayed a higher microbial diversity compared to hollows. Microtopography exerted a strong influence on bacterial community structure, while both microtopography and soil depth greatly impacted the fungal community structure with variable effects on fungal functional guilds. Soil water content, dissolved organic carbon, total phosphorus, and total nitrogen levels of the soil mostly affected the bacterial and fungal communities. Microtopography generated variations in the soil water content, which was the main driver of the spatial distribution of microbial abundances. This information stressed that the hummock–flat–hollow microtopography of permafrost peatlands creates heterogeneity in soil physicochemical properties and hydrological conditions, thereby influencing soil microbial communities at a microhabitat scale. Our results imply that changes to the water table induced by climate warming inducing permafrost degradation will impact the composition of soil microbes in peatlands and their related biogeochemical functions, eventually providing feedback loops into the global climate system.
Full article
(This article belongs to the Section Environmental Microbiology)
►▼
Show Figures
Figure 1
Open AccessReview
A Review on the Methodology and Use of the Pregnant Mouse Model in the Study of Brucella Reproductive Pathogenesis and Its Abortifacient Effect
by
Aitor Elizalde-Bielsa, Pilar M. Muñoz, Amaia Zúñiga-Ripa and Raquel Conde-Álvarez
Microorganisms 2024, 12(5), 866; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050866 - 26 Apr 2024
Abstract
Brucellosis is one of the most common and widespread bacterial zoonoses and is caused by Gram-negative bacteria belonging to the genus Brucella. These organisms are able to infect and replicate within the placenta, resulting in abortion, one of the main clinical signs
[...] Read more.
Brucellosis is one of the most common and widespread bacterial zoonoses and is caused by Gram-negative bacteria belonging to the genus Brucella. These organisms are able to infect and replicate within the placenta, resulting in abortion, one of the main clinical signs of brucellosis. Although the mouse model is widely used to study Brucella virulence and, more recently, to evaluate the protection of new vaccines, there is no clear consensus on the experimental conditions (e.g., mouse strains, doses, routes of inoculation, infection/pregnancy time) and the natural host reproducibility of the pregnant mouse model for reproductive brucellosis. This lack of consensus calls for a review that integrates the major findings regarding the effect of Brucella wild-type and vaccine strains infections on mouse pregnancy. We found sufficient evidence on the utility of the pregnant mouse model to study Brucella-induced placentitis and abortion and propose suitable experimental conditions (dose, time of infection) and pregnancy outcome readouts for B. abortus and B. melitensis studies. Finally, we discuss the utility and limitations of the pregnant mouse as a predictive model for the abortifacient effect of live Brucella vaccines.
Full article
(This article belongs to the Section Veterinary Microbiology)
►▼
Show Figures
Figure 1
Open AccessEditorial
Editorial for the Special Issue “Advances in Acanthamoeba”
by
Daniele Corsaro
Microorganisms 2024, 12(5), 865; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050865 - 26 Apr 2024
Abstract
Some free-living amoebae can behave as opportunistic parasites, causing rare but dangerous diseases in humans and animals, primarily amoebic keratitis, with loss of vision, and encephalitis, which is almost always fatal [...]
Full article
(This article belongs to the Special Issue Advances in Acanthamoeba)
Open AccessArticle
Isolation and Identification of Indole Alkaloids from Aspergillus amstelodami BSX001 and Optimization of Ultrasound-Assisted Extraction of Neoechinulin A
by
Shuyao Li, Xiaobo Liu, Qiuya Gu and Xiaobin Yu
Microorganisms 2024, 12(5), 864; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050864 - 26 Apr 2024
Abstract
This study aimed to investigate the alkaloid secondary metabolites of Aspergillus amstelodami BSX001, a fungus isolated from Anhua dark tea, and to improve the extraction yield of the active ingredients by optimizing the extraction process. The structural characterization of the compounds was investigated
[...] Read more.
This study aimed to investigate the alkaloid secondary metabolites of Aspergillus amstelodami BSX001, a fungus isolated from Anhua dark tea, and to improve the extraction yield of the active ingredients by optimizing the extraction process. The structural characterization of the compounds was investigated using mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. The antioxidant activity of echinulin-related alkaloids was evaluated by determining the total reducing power and DPPH radical scavenging capacity. The extraction process of the compound with optimum activity was optimized by a single-factor test and response surface methodology (RSM) combined with Box–Behnken design (BBD). The optimized result was validated. Finally, a new alkaloid 8-hydroxyechinulin (1), and four known alkaloids, variecolorin G (2), echinulin (3), neoechinulin A (4), and eurocristatine (5), were isolated. Echinulin-related compounds 1, 3, and 4 possessed certain antioxidant activities, with IC50 values of 0.587 mg/mL, 1.628 mg/mL, and 0.219 mg/mL, respectively, against DPPH radicals. Their total reducing power at a concentration of 0.5 mg/mL was 0.29 mmol/L, 0.17 mmol/L, and 4.25 mmol/L. The extraction process of neoechinulin A was optimized with the optimum extraction parameters of 72.76% methanol volume fraction, 25 mL/g solid–liquid ratio, and 50.8 °C soaking temperature. Under these conditions, the extraction yield of neoechinulin A was up to 1.500 mg/g.
Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms 3.0)
►▼
Show Figures
Figure 1
Open AccessArticle
Alkaline-Tolerant Bacillus cereus 12GS: A Promising Polyhydroxybutyrate (PHB) Producer Isolated from the North of Mexico
by
Gustavo de J. San Miguel-González, María E. Alemán-Huerta, Raul E. Martínez-Herrera, Isela Quintero-Zapata, Susana de la Torre-Zavala, Hamlet Avilés-Arnaut, Fátima L. Gandarilla-Pacheco and Erick de J. de Luna-Santillana
Microorganisms 2024, 12(5), 863; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050863 - 26 Apr 2024
Abstract
Environmental pollution caused by petroleum-derived plastics continues to increase annually. Consequently, current research is interested in the search for eco-friendly bacterial polymers. The importance of Bacillus bacteria as producers of polyhydroxyalkanoates (PHAs) has been recognized because of their physiological and genetic qualities. In
[...] Read more.
Environmental pollution caused by petroleum-derived plastics continues to increase annually. Consequently, current research is interested in the search for eco-friendly bacterial polymers. The importance of Bacillus bacteria as producers of polyhydroxyalkanoates (PHAs) has been recognized because of their physiological and genetic qualities. In this study, twenty strains of Bacillus genus PHA producers were isolated. Production was initially evaluated qualitatively to screen the strains, and subsequently, the strain B12 or Bacillus sp. 12GS, with the highest production, was selected through liquid fermentation. Biochemical and molecular identification revealed it as a novel isolate of Bacillus cereus. Production optimization was carried out using the Taguchi methodology, determining the optimal parameters as 30 °C, pH 8, 150 rpm, and 4% inoculum, resulting in 87% and 1.91 g/L of polyhydroxybutyrate (PHB). Kinetic studies demonstrated a higher production within 48 h. The produced biopolymer was analyzed using Fourier-transform infrared spectroscopy (FTIR), confirming the production of short-chain-length (scl) polyhydroxyalkanoate, named PHB, and differential scanning calorimetry (DSC) analysis revealed thermal properties, making it a promising material for various applications. The novel B. cereus isolate exhibited a high %PHB, emphasizing the importance of bioprospecting, study, and characterization for strains with biotechnological potential.
Full article
(This article belongs to the Special Issue The Role of Microbial Biotechnology in the Development of Sustainable Biopolymers)
►▼
Show Figures
Figure 1
Open AccessArticle
Time to Positivity in Blood Culture Bottles Inoculated with Sonication Fluid from Fracture-Related Infections
by
Leopold Henssler, Lena Schellenberger, Susanne Baertl, Lisa Klute, Robert Heyd, Maximilian Kerschbaum, Volker Alt and Daniel Popp
Microorganisms 2024, 12(5), 862; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050862 - 26 Apr 2024
Abstract
The timely and accurate identification of causative agents is crucial for effectively managing fracture-related infections (FRIs). Among various diagnostic methods, the “time to positivity” (TTP) of cultures has emerged as a valuable predictive factor in infectious diseases. While sonication of implants and inoculation
[...] Read more.
The timely and accurate identification of causative agents is crucial for effectively managing fracture-related infections (FRIs). Among various diagnostic methods, the “time to positivity” (TTP) of cultures has emerged as a valuable predictive factor in infectious diseases. While sonication of implants and inoculation of blood culture bottles with sonication fluid have enhanced sensitivity, data on the TTP of this microbiological technique remain limited. Therefore, patients with ICM criteria for confirmed FRI treated at our institution between March 2019 and March 2023 were retrospectively identified and their microbiological records were analyzed. The primary outcome parameter was TTP for different microorganism species cultured in a liquid culture collected from patients with confirmed FRI. A total of 155 sonication fluid samples from 126 patients (average age 57.0 ± 17.4 years, 68.3% males) was analyzed. Positive bacterial detection was observed in 78.7% (122/155) of the liquid culture pairs infused with sonication fluid. Staphylococcus aureus was the most prevalent organism (42.6%). Streptococcus species exhibited the fastest TTP (median 11.9 h), followed by Staphylococcus aureus (median 12.1 h) and Gram-negative bacteria (median 12.5 h), all of which had a 100% detection rate within 48 h after inoculation. Since all Gram-negative pathogens yielded positive culture results within 24 h, it could be discussed if empirical antibiotic therapy could be de-escalated early and limited towards the Gram-positive germ spectrum if no Gram-negative pathogens are detected up to this time point in the context of antibiotic stewardship.
Full article
(This article belongs to the Special Issue Device-Related Infections and Bacterial Biofilms)
►▼
Show Figures
Figure 1
Open AccessArticle
Immune Response after Anti-SARS-CoV-2 mRNA Vaccination in Relation to Cellular Immunity, Vitamin D and Comorbidities in Hemodialysis Patients
by
Egle Dalinkeviciene, Brigita Gradauskiene, Sandra Sakalauskaite, Kristina Petruliene, Ruta Vaiciuniene, Inga Skarupskiene, Daina Bastyte, Jolanta Sauseriene, Leonas Valius, Inga Arune Bumblyte and Edita Ziginskiene
Microorganisms 2024, 12(5), 861; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050861 - 25 Apr 2024
Abstract
In the global threat of SARS-CoV-2, individuals undergoing maintenance dialysis represent a vulnerable population with an increased risk of severe COVID-19 outcomes. Therefore, immunization against SARS-CoV-2 is an essential component of healthcare strategy for these patients. Existing data indicate that they tend to
[...] Read more.
In the global threat of SARS-CoV-2, individuals undergoing maintenance dialysis represent a vulnerable population with an increased risk of severe COVID-19 outcomes. Therefore, immunization against SARS-CoV-2 is an essential component of healthcare strategy for these patients. Existing data indicate that they tend to exhibit a reduced immune response to vaccines compared to the general population. Our study aimed to assess both humoral and cellular immune responses following two doses of an anti-SARS-CoV-2 mRNA vaccine, an ability to maintain adequate antibody titers over time, and potential relations with vitamin D, comorbidities and other factors in hemodialysis patients based on a single center experience. A total of 41/45 patients (91.1%) responded to the second dose of the anti-SARS-CoV-2 mRNA vaccine. The titer of anti-SARS-CoV-2 IgG class antibodies and levels of T cells three to four weeks after vaccination were lower in dialysis patients than in healthy controls. Antibodies titer in dialysis patients had a positive correlation with B lymphocytes and was related to cardiovascular diseases. The level of CD4+ cells had a negative correlation with hemodialysis vintage, as did the vitamin D level with post-vaccination seroconversion and decline in anti-SARS-CoV-2 antibodies titer during six months after vaccination. Hemodialysis patients had decreased amounts of CD4+ and CD8+ cells and lower levels of anti-SARS-CoV-2 antibodies than healthy controls. Therefore, chronic hemodialysis could lead to diminished cellular immunity and humoral immune response to the anti-SARS-CoV-2 mRNA vaccination and reduced protection from COVID-19. Comorbidity in cardiovascular diseases was associated with a lower level of specific anti-SARS-CoV-2 antibody titer. Vitamin D may be important in maintaining stable levels of anti-SARS-CoV-2 antibodies, while the duration of dialysis treatment could be one of the factors decreasing anti-SARS-CoV-2 antibody titer and determining lower CD4+ cell counts.
Full article
(This article belongs to the Special Issue Immune Modulation to SARS-CoV-2 Vaccination and Infection)
►▼
Show Figures
Figure 1
Open AccessArticle
Multi-Omics of Campylobacter jejuni Growth in Chicken Exudate Reveals Molecular Remodelling Associated with Altered Virulence and Survival Phenotypes
by
Lok Man, Pamela X. Y. Soh, Tess E. McEnearney, Joel A. Cain, Ashleigh L. Dale and Stuart J. Cordwell
Microorganisms 2024, 12(5), 860; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050860 - 25 Apr 2024
Abstract
Campylobacter jejuni is the leading cause of foodborne human gastroenteritis in the developed world. Infections are largely acquired from poultry produced for human consumption and poor food handling is thus a major risk factor. Chicken exudate (CE) is a liquid produced from defrosted
[...] Read more.
Campylobacter jejuni is the leading cause of foodborne human gastroenteritis in the developed world. Infections are largely acquired from poultry produced for human consumption and poor food handling is thus a major risk factor. Chicken exudate (CE) is a liquid produced from defrosted commercial chicken products that facilitates C. jejuni growth. We examined the response of C. jejuni to growth in CE using a multi-omics approach. Changes in the C. jejuni proteome were assessed by label-based liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). We quantified 1328 and 1304 proteins, respectively, in experiments comparing 5% CE in Mueller–Hinton (MH) medium and 100% CE with MH-only controls. These proteins represent 81.8% and 80.3% of the predicted C. jejuni NCTC11168 proteome. Growth in CE induced profound remodelling of the proteome. These changes were typically conserved between 5% and 100% CE, with a greater magnitude of change observed in 100% CE. We confirmed that CE induced C. jejuni biofilm formation, as well as increasing motility and resistance against oxidative stress, consistent with changes to proteins representing those functions. Assessment of the C. jejuni metabolome showed CE also led to increased intracellular abundances of serine, proline, and lactate that were correlated with the elevated abundances of their respective transporters. Analysis of carbon source uptake showed prolonged culture supernatant retention of proline and succinate in CE-supplemented medium. Metabolomics data provided preliminary evidence for the uptake of chicken-meat-associated dipeptides. C. jejuni exposed to CE showed increased resistance to several antibiotics, including polymyxin B, consistent with changes to tripartite efflux system proteins and those involved in the synthesis of lipid A. The C. jejuni CE proteome was also characterised by very large increases in proteins associated with iron acquisition, while a decrease in proteins containing iron–sulphur clusters was also observed. Our data suggest CE is both oxygen- and iron-limiting and provide evidence of factors required for phenotypic remodelling to enable C. jejuni survival on poultry products.
Full article
(This article belongs to the Special Issue Foodborne Bacteria–Host Interactions 2.0)
►▼
Show Figures
Figure 1
Open AccessEditorial
Editorial: Impact of Special Issue “The Microbial Population of the Gastrointestinal Tract of Animals: Impacts on Host Physiology”
by
Jeferson M. Lourenco and Todd R. Callaway
Microorganisms 2024, 12(5), 859; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050859 - 25 Apr 2024
Abstract
In recent years, there has been an exponential increase in the number of papers that have investigated the microbiome of animals and humans [...]
Full article
(This article belongs to the Special Issue The Microbial Population of the Gastrointestinal Tract of Animals: Impacts on Host Physiology)
Open AccessArticle
Temporal Dynamics of Fungal Communities in Alkali-Treated Round Bamboo Deterioration under Natural Weathering
by
Shuaibo Han, Xiaojiao An, Xiaolong He, Xin Ren, John Sichone, Xinxing Wu, Yan Zhang, Hui Wang and Fangli Sun
Microorganisms 2024, 12(5), 858; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050858 - 25 Apr 2024
Abstract
Microbes naturally inhabit bamboo-based materials in outdoor environments, sequentially contributing to their deterioration. Fungi play a significant role in deterioration, especially in environments with abundant water and favorable temperatures. Alkali treatment is often employed in the pretreatment of round bamboo to change its
[...] Read more.
Microbes naturally inhabit bamboo-based materials in outdoor environments, sequentially contributing to their deterioration. Fungi play a significant role in deterioration, especially in environments with abundant water and favorable temperatures. Alkali treatment is often employed in the pretreatment of round bamboo to change its natural elastic and aesthetic behaviors. However, little research has investigated the structure and dynamics of fungal communities on alkali-treated round bamboo during natural deterioration. In this work, high-throughput sequencing and multiple characterization methods were used to disclose the fungal community succession and characteristic alterations of alkali-treated round bamboo in both roofed and unroofed habitats throughout a 13-week deterioration period. In total, 192 fungal amplicon sequence variants (ASVs) from six phyla were identified. The fungal community richness of roofed bamboo samples declined, whereas that of unroofed bamboo samples increased during deterioration. The phyla Ascomycota and Basidiomycota exhibited dominance during the entire deterioration process in two distinct environments, and the relative abundance of them combined was more than 99%. A distinct shift in fungal communities from Basidiomycota dominant in the early stage to Ascomycota dominant in the late stage was observed, which may be attributed to the increase of moisture and temperature during succession and the effect of alkali treatment. Among all environmental factors, temperature contributed most to the variation in the fungal community. The surface of round bamboo underwent continuous destruction from fungi and environmental factors. The total amount of cell wall components in bamboo epidermis in both roofed and unroofed conditions presented a descending trend. The content of hemicellulose declined sharply by 8.3% and 11.1% under roofed and unroofed environments after 9 weeks of deterioration. In addition, the contact angle was reduced throughout the deterioration process in both roofed and unroofed samples, which might be attributed to wax layer removal and lignin degradation. This study provides theoretical support for the protection of round bamboo under natural weathering.
Full article
(This article belongs to the Section Plant Microbe Interactions)
►▼
Show Figures
Figure 1
Open AccessCase Report
From Investigating a Case of Cellulitis to Exploring Nosocomial Infection Control of ST1 Legionella pneumophila Using Genomic Approaches
by
Charlotte Michel, Fedoua Echahidi, Sammy Place, Lorenzo Filippin, Vincent Colombie, Nicolas Yin, Delphine Martiny, Olivier Vandenberg, Denis Piérard and Marie Hallin
Microorganisms 2024, 12(5), 857; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050857 - 25 Apr 2024
Abstract
Legionella pneumophila can cause a large panel of symptoms besides the classic pneumonia presentation. Here we present a case of fatal nosocomial cellulitis in an immunocompromised patient followed, a year later, by a second case of Legionnaires’ disease in the same ward. While
[...] Read more.
Legionella pneumophila can cause a large panel of symptoms besides the classic pneumonia presentation. Here we present a case of fatal nosocomial cellulitis in an immunocompromised patient followed, a year later, by a second case of Legionnaires’ disease in the same ward. While the first case was easily assumed as nosocomial based on the date of symptom onset, the second case required clear typing results to be assigned either as nosocomial and related to the same environmental source as the first case, or community acquired. To untangle this specific question, we applied core-genome multilocus typing (MLST), whole-genome single nucleotide polymorphism and whole-genome MLST methods to a collection of 36 Belgian and 41 international sequence-type 1 (ST1) isolates using both thresholds recommended in the literature and tailored threshold based on local epidemiological data. Based on the thresholds applied to cluster isolates together, the three methods gave different results and no firm conclusion about the nosocomial setting of the second case could been drawn. Our data highlight that despite promising results in the study of outbreaks and for large-scale epidemiological investigations, next-generation sequencing typing methods applied to ST1 outbreak investigation still need standardization regarding both wet-lab protocols and bioinformatics. A deeper evaluation of the L. pneumophila evolutionary clock is also required to increase our understanding of genomic differences between isolates sampled during a clinical infection and in the environment.
Full article
(This article belongs to the Special Issue Clinical and Environmental Surveillance for the Prevention of Legionellosis 2.0)
Open AccessCommunication
Trichinella spiralis Infecting Wild Boars in West, Southwest, and Northwest of Romania: Evidence of an Underrated Risk
by
Ana-Maria Marin, Tudor Rareș Olariu, Dan-Cornel Popovici, Gianluca Marucci, Sorin Morariu, Daian Popa and Narcisa Mederle
Microorganisms 2024, 12(5), 856; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050856 - 25 Apr 2024
Abstract
The species of the genus Trichinella are etiological agents distributed all over the world and are able to infect mammals, birds, and reptiles. Trichinella spiralis is the species most adapted to domestic and wild pigs and is also the most important etiological agent
[...] Read more.
The species of the genus Trichinella are etiological agents distributed all over the world and are able to infect mammals, birds, and reptiles. Trichinella spiralis is the species most adapted to domestic and wild pigs and is also the most important etiological agent of trichinellosis. The wild boar (Sus scrofa) is a nocturnal omnivorous mammal belonging to the Suidae family. S. scrofa has a great appetite and its diet includes a variety of small prey such as mice, rats, and other rodents, as well as carcasses of larger animals. The aim of this study was the identification and the molecular characterization of Trichinella larvae isolated from the muscle tissue of S. scrofa specimens collected in different counties of Romania. The muscle samples were examined by artificial digestion and the larvae identified at the species level by multiplex PCR. T. spiralis, a species that is able to infect a considerable number of different host species including humans, was identified. In Romania, S. scrofa is an important reservoir species for T. spiralis and plays an important role in linking the domestic and the wild cycle of Trichinella, with serious repercussions for human health.
Full article
(This article belongs to the Section Parasitology)
Open AccessReview
Interaction of Trypanosoma cruzi, Triatomines and the Microbiota of the Vectors—A Review
by
Günter A. Schaub
Microorganisms 2024, 12(5), 855; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050855 - 25 Apr 2024
Abstract
This review summarizes the interactions between Trypanosoma cruzi, the etiologic agent of Chagas disease, its vectors, triatomines, and the diverse intestinal microbiota of triatomines, which includes mutualistic symbionts, and highlights open questions. T. cruzi strains show great biological heterogeneity in their development
[...] Read more.
This review summarizes the interactions between Trypanosoma cruzi, the etiologic agent of Chagas disease, its vectors, triatomines, and the diverse intestinal microbiota of triatomines, which includes mutualistic symbionts, and highlights open questions. T. cruzi strains show great biological heterogeneity in their development and their interactions. Triatomines differ from other important vectors of diseases in their ontogeny and the enzymes used to digest blood. Many different bacteria colonize the intestinal tract of triatomines, but only Actinomycetales have been identified as mutualistic symbionts. Effects of the vector on T. cruzi are indicated by differences in the ability of T. cruzi to establish in the triatomines and in colonization peculiarities, i.e., proliferation mainly in the posterior midgut and rectum and preferential transformation into infectious metacyclic trypomastigotes in the rectum. In addition, certain forms of T. cruzi develop after feeding and during starvation of triatomines. Negative effects of T. cruzi on the triatomine vectors appear to be particularly evident when the triatomines are stressed and depend on the T. cruzi strain. Effects on the intestinal immunity of the triatomines are induced by ingested blood-stage trypomastigotes of T. cruzi and affect the populations of many non-symbiotic intestinal bacteria, but not all and not the mutualistic symbionts. After the knockdown of antimicrobial peptides, the number of non-symbiotic bacteria increases and the number of T. cruzi decreases. Presumably, in long-term infections, intestinal immunity is suppressed, which supports the growth of specific bacteria, depending on the strain of T. cruzi. These interactions may provide an approach to disrupt T. cruzi transmission.
Full article
(This article belongs to the Section Parasitology)
►▼
Show Figures
Figure 1
Open AccessReview
The Impact of Artificial Restoration of Alpine Grasslands in the Qilian Mountains on Vegetation, Soil Bacteria, and Soil Fungal Community Diversity
by
Xiaomei Yang, Qi Feng, Meng Zhu, Jutao Zhang, Linshan Yang and Ruolin Li
Microorganisms 2024, 12(5), 854; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms12050854 - 25 Apr 2024
Abstract
To understand how the soil microbial community structure responds to vegetation restoration in alpine mining areas, this study specifically examines the grassland ecosystem in the Qianmalong mining area of the Qilian Mountains after five years of artificial restoration. High-throughput sequencing methods were employed
[...] Read more.
To understand how the soil microbial community structure responds to vegetation restoration in alpine mining areas, this study specifically examines the grassland ecosystem in the Qianmalong mining area of the Qilian Mountains after five years of artificial restoration. High-throughput sequencing methods were employed to analyze soil bacteria and fungi microbial characteristics in diverse grassland communities. Combined with modifications in vegetation diversity as well as soil physicochemical properties, the impact of vegetation restoration on soil microbiome diversity in this alpine mining area was investigated. The findings indicated that the dominant plants were Cyperus rotundus, Carex spp., and Elymus nutans. As the extent of the grassland’s restoration increased, the number of plant species, importance values, and plant community diversity showed an increasing trend. The plant functional groups were mainly dominated by Cyperaceae, followed by Poaceae. Plant height, density, plant cover, frequency, and aboveground biomass showed an increasing trend, and soil water content (SWC) increased. While soil pH and soil electrical conductivity (EC) exhibited a declining trend, available phosphorus (AP), total phosphorus (TP), total nitrogen (TN), nitrate nitrogen (NO3-N), soil organic carbon (SOC), and soil water content (SWC) showed an increasing trend. The dominant bacterial communities were Actinobacteriota, Proteobacteria, Acidobacteriota, Chloroflexi, Firmicutes, and Gemmatimonadota, while the dominant fungal communities were Ascomycota, Mortierellomycota, Basidiomycota, unclassified_k_Fungi, and Glomeromycota. Significant differences were detected within soil microbial community composition among different degrees of restoration grasslands, with bacteria generally dominating over fungi. SWC, TP, and TN were found to be the main soil physicochemical factors affecting the distribution of soil bacterial communities’ structure; however, SOC, TN, and NO3-N were the primary factors influencing the soil distribution of fungal communities. The results of this study indicate that different degrees of vegetation restoration in alpine mining areas can significantly affect soil bacterial and fungal communities, and the degree of restoration has varying effects on the soil bacteria and fungi community structure in alpine mining areas.
Full article
(This article belongs to the Section Environmental Microbiology)
►▼
Show Figures
Figure 1
Journal Menu
► ▼ Journal Menu-
- Microorganisms Home
- Aims & Scope
- Editorial Board
- Reviewer Board
- Topical Advisory Panel
- Instructions for Authors
- Special Issues
- Topics
- Sections & Collections
- Article Processing Charge
- Indexing & Archiving
- Editor’s Choice Articles
- Most Cited & Viewed
- Journal Statistics
- Journal History
- Journal Awards
- Society Collaborations
- Editorial Office
Journal Browser
► ▼ Journal BrowserHighly Accessed Articles
Latest Books
E-Mail Alert
News
Topics
Topic in
Biology, Ecologies, Forests, Microorganisms, Plants
Litter Decompositions: From Individuals to Ecosystems
Topic Editors: Wen Zhou, Guihua LiuDeadline: 30 April 2024
Topic in
Aquaculture Journal, Fishes, Microorganisms, Water
Women in Aquaculture Research
Topic Editors: Camino Ordás, Patrícia Díaz-RosalesDeadline: 30 June 2024
Topic in
Agronomy, Environments, Microorganisms, Pollutants, Sustainability, Water
Soil and Water Pollution Process and Remediation Technologies, 2nd Volume
Topic Editors: Hongbiao Cui, Ru Wang, Yu Shi, Haiying Lu, Lin ChenDeadline: 15 July 2024
Topic in
Antibiotics, Antioxidants, JoF, Microbiology Research, Microorganisms
Redox in Microorganisms, 2nd Edition
Topic Editors: Michal Letek, Volker BehrendsDeadline: 31 July 2024
Conferences
Special Issues
Special Issue in
Microorganisms
Plant and Human Probiotics: Consequences on the Autochthonous Microbiota
Guest Editors: Elisa Gamalero, Elisa Bona, Giorgia Novello, Francesco VuoloDeadline: 30 April 2024
Special Issue in
Microorganisms
Human Skin Microbiota 2.0
Guest Editors: Holger Brüggemann, Rolf LoodDeadline: 15 May 2024
Special Issue in
Microorganisms
The Urban Microbiome
Guest Editors: Haruo Suzuki, Soojin JangDeadline: 31 May 2024
Special Issue in
Microorganisms
Emerging Pathogens Causing Acute Hepatitis
Guest Editors: Ibrahim M. Sayed, Sayed F. Abdelwahab, Ahmed El-ShamyDeadline: 15 June 2024
Topical Collections
Topical Collection in
Microorganisms
Trends in Yeast Biochemistry and Biotechnology
Collection Editors: Seiji Shibasaki, Mitsuyoshi Ueda
Topical Collection in
Microorganisms
Epidemiology and Pathogenicity of Animal-Adapted Streptococci
Collection Editors: Peter Valentin-Weigand, Marcus Fulde
Topical Collection in
Microorganisms
Biodegradation and Environmental Microbiomes
Collection Editors: Shuangjiang Liu, Hongzhi Tang, Jiandong Jiang, Xiaolei Wu