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Topic Review
Resistome, Mobilome and Nichome
There are three concepts linked to the growing resistance to antibiotics, namely (i) the Resistome, which refers to the collection of bacterial genes that confer resistance to antibiotics, (ii) the Mobilome, which includes all the mobile genetic elements that participate in the spreading of antibiotic resistance among bacteria by horizontal gene transfer processes, and (iii) the Nichome, which refers to the set of genes that are expressed when bacteria try to colonize new niches. 
  • 1.0K
  • 24 Oct 2023
Topic Review
Cigarette Smoking and Human Gut Microbiota
The intestinal microbiota is a crucial regulator of human health and disease because of its interactions with the immune system. Tobacco smoke also influences the human ecosystem with implications for disease development. This entry aims to analyze the available evidence, until June 2021, on the relationship between traditional and/or electronic cigarette smoking and intestinal microbiota in healthy human adults.
  • 1.0K
  • 07 Mar 2022
Topic Review
Microbiota-Derived Butyrate in Colorectal Cancer
Butyrate is one of the main short chain fatty acids (SCFAs) with anti-inflammatory and anti-tumor properties in colorectal cancer (CRC). Increased daily intake of omega-3 polyunsaturated fatty acids (PUFAs) significantly increases the density of bacteria that are known to produce butyrate. Omega-3 PUFAs have been proposed as a treatment to prevent gut microbiota dysregulation and lower the risk or progression of CRC.
  • 1.0K
  • 17 Mar 2022
Topic Review
The Bacterial Urban Resistome
Cities that are densely populated are reservoirs of antibiotic resistant genes (ARGs). The overall presence of all resistance genes in a specific environment is defined as a resistome. Spatial proximity of surfaces and different hygienic conditions leads to the transfer of antibiotic resistant bacteria (ARB) within urban environments. Built environments, public transportation, green spaces, and citizens’ behaviors all support persistence and transfer of antimicrobial resistances (AMR). 
  • 1.0K
  • 14 Jun 2022
Topic Review
Helicobacter pylori in oral cavity from ITP patient
Immune thrombocytopenic purpura (ITP) is an autoimmune disease characterized by isolated cryptogenic thrombocytopenia due to a transient or persistent reduction in platelet count.　However, there have been no studies regarding H. pylori in the oral cavity of patients with ITP. Here, we describe a patient with ITP whose oral samples exhibited H. pylori. A 64-year-old woman with ITP came to our hospital with chief complaints that required oral surgery, including tooth extraction and cystectomy. Bacterial DNA of H. pylori was confirmed on the extracted tooth, but was not detected in saliva taken at the time. Bacterial DNA of H. pylori was detected on the suture around the extraction socket, which was removed at 10 days postoperatively. However, H. pylori DNA was not detected in other oral samples at 10 or 30 days postoperatively. The urea breath test was carried out in the gastrointestinal clinic at 60 days postoperatively, which revealed no presence of H. pylori in the gastrointestinal tract. These results suggest that teeth with severe bacterial infections may be a potential reservoir of H. pylori of patients with ITP.
  • 1.0K
  • 15 Nov 2022
Topic Review
Immunogenic Proteins of Group B Streptococcus
Streptococcus agalactiae (Group B Streptococcus, GBS) is an opportunistic pathogen, which asymptomatically colonizes the gastrointestinal and genitourinary tract of up to one third of healthy adults. Nevertheless, GBS carriage in pregnant women may lead to several health issues in newborns causing life threatening infection, such as sepsis, pneumonia or meningitis. Recommended GBS screening in pregnant women significantly reduced morbidity and mortality in infants. Nevertheless, intrapartum antibiotic prophylaxis, recommended following the detection of carriage or in case of lack of a carriage test result for pregnant women who demonstrate certain risk factors, led to the expansion of the adverse phenomenon of bacterial resistance to antibiotics.
  • 1.0K
  • 05 Jan 2022
Topic Review
Dietary Modulation of Bacteriophages
The role and function of bacteriophages (phages) has been underestimated so far. Natural compounds such as essential oils and tea have been used successfully in naturopathy and folk medicine for hundreds of years. Current research is unveiling the molecular role of their antibacterial, anti-inflammatory, and anticancer properties. The current interdisciplinary review summarizes current knowledge on dietary compounds as to their capacity to modulate the activity of phages, thus potentially contributing to (the modulation of) several gastrointestinal diseases, such as (chronic) inflammation, and even cancer.
  • 1.0K
  • 27 Apr 2021
Topic Review
Antibiotic Resistance among Gastrointestinal Bacteria in Broilers
Chickens can acquire bacteria at different stages, and bacterial diversity can occur due to production practices, diet, and environment. The changes in consumer trends have led to increased animal production, and chicken meat is one of the most consumed meats. To ensure high levels of production, antimicrobials have been used in livestock for therapeutic purposes, disease prevention, and growth promotion, contributing to the development of antimicrobial resistance across the resident microbiota. Enterococcus spp. and Escherichia coli are normal inhabitants of the gastrointestinal microbiota of chickens that can develop strains capable of causing a wide range of diseases, i.e., opportunistic pathogens. Enterococcus spp. isolated from broilers have shown resistance to at least seven classes of antibiotics, while E. coli have shown resistance to at least four. 
  • 1.0K
  • 23 Apr 2023
Topic Review
Tetracycline Resistance in Acid Bacterial Species
By comparing phenotypes with genotypes based on genome-wide annotations, five tetracycline resistance genes, tet(M), tet(W/N/W), tet(L), tet(S), and tet(45), were detected in LAB. Multiple LAB strains without tetracycline resistance genes were found to be resistant to tetracycline at the currently recommended cutoff values. 
  • 1.0K
  • 24 Nov 2021
Topic Review
Factors Affecting Microbiome Establishment in Rumens
Within the ruminant intestines, a diverse array of microbiota predominates, predominantly comprised of bacteria with a specialized role in breaking down intricate nutrients like cellulose and hemicellulose. This breakdown results in the conversion of these complex compounds into simpler constituents, such as glucose, which ultimately facilitates the assimilation of nutrients. The composition of these microbial communities within the rumen is contingent on a multitude of factors. These include breed, age, external environment, diet, and nutritional factors. Moreover, other variables, such as the process of weaning, energy requirements, and the presence of potentially toxic metabolic byproducts, can also exert an impact on the microbial composition and abundance within the rumen. External factors, including heat stress, psychological stress, environmental conditions, and dietary patterns, can likewise pose threats to the stability of rumen microflora.
  • 1.0K
  • 27 Oct 2023
Topic Review
Helicobacter pylori Biofilms
Microbial biofilm is defined as a structured consortium of cells immersed in a self-produced matrix. It is worth mentioning, however, that the biofilm may also include host components, e.g., fibrin, antibodies, platelets, or leukocytes. Biofilms can be attached to an abiotic or biotic surface, but they can also constitute a mobile, non-adhered structure floating in culture broth or body fluids.
  • 1.0K
  • 14 Jan 2021
Topic Review
Physiology of Methylotrophic Yeasts
Methanol is abundant in the phyllosphere, the surface of the above-ground parts of plants, and its concentration oscillates diurnally. The phyllosphere is one of the major habitats for a group of microorganisms, the so-called methylotrophs, that utilize one-carbon (C1) compounds, such as methanol and methane, as their sole source of carbon and energy. Among phyllospheric microorganisms, methanol-utilizing yeasts can proliferate and survive in the phyllosphere by using unique molecular and cellular mechanisms to adapt to the stressful phyllosphere environment. 
  • 1.0K
  • 26 Apr 2021
Topic Review
Influencing Factors on Root Exudate-Rhizobacteria Interactions
The rhizosphere, the narrow zone of soil influenced by the plant root system, is a dynamic environment where complex interplay between plants and soil microbes occurs, and it may contain up to 1011 cells/g of root, with more than 30,000 bacterial species. There are various signals in the rhizosphere, including QS signals among microorganisms and root exudate signals from plants to microorganisms.
  • 1.0K
  • 08 Feb 2024
Topic Review
Genome-Based Phylogeny of the Genus Thiothrix
Representatives of the genus Thiothrix are filamentous, sulfur-oxidizing bacteria, capable of lithoauto-, lithohetero- and organoheterotrophic growth. They are often found in flowing waters with counter-oriented sulfide and oxygen gradients. They were first described at the end of the 19th century, but the first pure cultures of this species only became available 100 years later. An increase in the number of described Thiothrix species at the beginning of the 21st century shows that the classical phylogenetic marker, 16S rRNA gene, is not informative for species differentiation, which is possible based on genome analysis.
  • 1.0K
  • 01 Sep 2022
Topic Review
Toxicity of Mycotoxins to Intestinal Epithelial Cells
Mycotoxin is a naturally occurring substance produced by fungi. Consumption of low concentrations of mycotoxins in animals would result in severe hazardous symptoms.
  • 1.0K
  • 26 Dec 2022
Topic Review
Porphyromonas gingivalis during Periodontitis Pathogenesis
Periodontitis is a non-communicable chronic inflammatory disease characterized by the progressive and irreversible breakdown of the soft periodontal tissues and resorption of teeth-supporting alveolar bone. The etiology of periodontitis involves dysbiotic shifts in the diversity of microbial communities inhabiting the subgingival crevice, which is dominated by anaerobic Gram-negative bacteria, including Porphyromonas gingivalis. Indeed, P. gingivalis is a keystone pathogen with a repertoire of attributes that allow it to colonize periodontal tissues and influence the metabolism, growth rate, and virulence of other periodontal bacteria. The pathogenic potential of P. gingivalis has been traditionally analyzed using classical biochemical and molecular approaches.
  • 1.0K
  • 31 Jan 2023
Topic Review
Metabolic Engineering of Yeast for Bioethanol Production
Increased human population and the rapid decline of fossil fuels resulted in a global tendency to look for alternative fuel sources. Ethanol has been the primary fossil fuel alternative due to its low carbon emission rates, high octane content and comparatively facile microbial production processes. As a well-known platform microorganism and native ethanol producer, baker’s yeast Saccharomyces cerevisiae has been the primary subject of interest for both academic and industrial perspectives in terms of enhanced ethanol production processes. Metabolic engineering strategies have been primarily adopted for direct manipulation of genes of interest responsible in mainstreams of ethanol metabolism. To overcome limitations of rational metabolic engineering, an alternative bottom-up strategy called inverse metabolic engineering has been widely used. In this context, evolutionary engineering, also known as adaptive laboratory evolution (ALE), which is based on random mutagenesis and systematic selection, is a powerful strategy to improve bioethanol production of S. cerevisiae. Metabolic and evolutionary engineering strategies are intertwined and many metabolically engineered strains for bioethanol production can be further improved by powerful evolutionary engineering strategies as well as the recent advancements in directed genome evolution, including CRISPR-Cas9 technology.
  • 1.0K
  • 16 Oct 2023
Topic Review
Microbiota Alterations in Pancreatic Cancer
The human microbiome is a key factor in many malignancies, having the ability to alter host metabolism and immune responses and participate in tumorigenesis. Gut microbes have an influence on physiological functions of the healthy pancreas and are themselves controlled by pancreatic secretions. An altered oral microbiota may colonize the pancreas and cause local inflammation by the action of its metabolites, which may lead to carcinogenesis. The mechanisms behind dysbiosis and pancreatic cancer (PC) development are not completely clear. An altered microbiota may induce oncogenomic changes, or, on the other hand, cancer mutations may have an impact on microbiota composition. Altered microbiota can also influence drug efficacy in PC chemo- and immunotherapies. Possible future scenarios are the intentional manipulation of the gut microbiota in combination with therapy or the utilization of microbial profiles for the noninvasive screening and monitoring of PC.
  • 1.0K
  • 13 Dec 2021
Topic Review
Occurrence of β-N-Methylamino-L-alanine
One interesting compound in the spectrum of cyanobacterial metabolites is the non-proteinogenic amino acid β-N-methylamino-L-alanine, abbreviated BMAA. In total, the presence of BMAA and/or its isomers was linked to more than 200 findings related to cyanobacteria from nature (freshwaters, marine and brackish environment, terrestrial habitats and plant symbionts), market samples and specimens from culture collections. Although BMAA and its isomers are found in many ecosystems, the occurrence of these compounds is not ubiquitous. 
  • 1.0K
  • 29 Dec 2022
Topic Review
Clostridioides difficile
Clostridioides difficile is an increasingly common pathogen both within and outside the hospital and is responsible for a large clinical spectrum from asymptomatic carriage to complicated infection associated with a high mortality. While diagnostic methods have considerably progressed over the years, the optimal diagnostic algorithm is still debated and there is no single diagnostic test that can be used as a standalone test. More importantly, the heterogeneity in diagnostic practices between centers along with the lack of robust surveillance systems in all countries and an important degree of underdiagnosis due to lack of clinical suspicion in the community, hinder a more accurate evaluation of the burden of disease. Our improved understanding of the physiopathology of CDI has allowed some significant progress in the treatment of CDI, including a broader use of fidaxomicine, the use of fecal microbiota transplantation for multiples recurrences and newer approaches including antibodies, vaccines and new molecules, already developed or in the pipeline.
  • 1.0K
  • 12 Oct 2021
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