Gut microbiota (GM) often exhibit variation between different host species and co-divergence with hosts' phylogeny. Identifying these patterns is a key for understanding the mechanisms that shaped symbiosis between GM and its hosts. Therefore, both GM-host species specificity and GM-host co-divergence have been investigated by numerous studies. However, most of them neglected a possibility that different groups of bacteria within GM can vary in the tightness of their association with the host. Consequently, unlike most of these studies, we aimed to directly address how the strength of GM-host species specificity and GM-host co-divergence vary across different GM clades. We decomposed GM communities of 52 passerine species (394 individuals), characterized by 16S rRNA amplicon sequence variant (ASV) profiles, into monophyletic Binned Taxonomic units (BTUs). Subsequently, we analyzed strength of host species specificity and correlation with host phylogeny separately for resulting BTUs. We found that most BTUs exhibited significant host-species specificity in their composition. Notably, BTUs exhibiting high host-species specificity comprised bacterial taxa known to impact host's physiology and immune system. However, BTUs rarely displayed significant co-divergence with host phylogeny, suggesting that passerine GM evolution is not shaped primarily through a shared evolutionary history between the host and its gut microbes.

• Klíčová slova
• 16S rRNA, co‐divergence, gut microbiota, metabarcoding, passerines,
• Publikační typ
• časopisecké články MeSH

Bile acids (BAs) are important steroidal molecules with a rapidly growing span of applications across a variety of fields such as supramolecular chemistry, pharmacy, and biomedicine. This work provides a systematic review on their transport processes within the enterohepatic circulation and related processes. The focus is laid on the description of specific or less-specific BA transport proteins and their localization. Initially, the reader is provided with essential information about BAs' properties, their systemic flow, metabolism, and functions. Later, the transport processes are described in detail and schematically illustrated, moving step by step from the liver via bile ducts to the gallbladder, small intestine, and colon; this description is accompanied by descriptions of major proteins known to be involved in BA transport. Spillage of BAs into systemic circulation and urine excretion are also discussed. Finally, the review also points out some of the less-studied areas of the enterohepatic circulation, which can be crucial for the development of BA-related drugs, prodrugs, and drug carrier systems.

• Klíčová slova
• ASBT, IBABP, MDR, MRP, NTCP, OATP, bile acid, bile salt, drug delivery, enterohepatic circulation, transport protein,
• MeSH
• enterohepatická cirkulace * MeSH
• játra metabolismus   MeSH
• transportní proteiny metabolismus   MeSH
• žlučové cesty MeSH
• žlučové kyseliny a soli * metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• systematický přehled MeSH
• Názvy látek
• transportní proteiny MeSH
• žlučové kyseliny a soli * MeSH

Insects nurture a panoply of microbial populations that are often obligatory and exist mutually with their hosts. Symbionts not only impact their host fitness but also shape the trajectory of their phenotype. This co-constructed niche successfully evolved long in the past to mark advanced ecological specialization. The resident microbes regulate insect nutrition by controlling their host plant specialization and immunity. It enhances the host fitness and performance by detoxifying toxins secreted by the predators and abstains them. The profound effect of a microbial population on insect physiology and behaviour is exploited to understand the host-microbial system in diverse taxa. Emergent research of insect-associated microbes has revealed their potential to modulate insect brain functions and, ultimately, control their behaviours, including social interactions. The revelation of the gut microbiota-brain axis has now unravelled insects as a cost-effective potential model to study neurodegenerative disorders and behavioural dysfunctions in humans. This article reviewed our knowledge about the insect-microbial system, an exquisite network of interactions operating between insects and microbes, its mechanistic insight that holds intricate multi-organismal systems in harmony, and its future perspectives. The demystification of molecular networks governing insect-microbial symbiosis will reveal the perplexing behaviours of insects that could be utilized in managing insect pests.

• Klíčová slova
• arthropod vector, detoxification, gut microbiome, holobiont, host immunity, insect symbiosis, nutrition provisioning, omics technology,
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

BACKGROUND: In the last twenty years, new methodologies have made possible the gathering of large amounts of data concerning the genetic information and metabolic functions associated to the human gut microbiome. In spite of that, processing all this data available might not be the simplest of tasks, which could result in an excess of information awaiting proper annotation. This assessment intended on evaluating how well respected databases could describe a mock human gut microbiome. METHODS: In this work, we critically evaluate the output of the cross-reference between the Uniprot Knowledge Base (Uniprot KB) and the Kyoto Encyclopedia of Genes and Genomes Orthologs (KEGG Orthologs) or the evolutionary genealogy of genes: Non-supervised Orthologous groups (EggNOG) databases regarding a list of species that were previously found in the human gut microbiome. RESULTS: From a list which contemplates 131 species and 52 genera, 53 species and 40 genera had corresponding entries for KEGG Database and 82 species and 47 genera had corresponding entries for EggNOG Database. Moreover, we present the KEGG Orthologs (KOs) and EggNOG Orthologs (NOGs) entries associated to the search as their distribution over species and genera and lists of functions that appeared in many species or genera, the "core" functions of the human gut microbiome. We also present the relative abundance of KOs and NOGs throughout phyla and genera. Lastly, we expose a variance found between searches with different arguments on the database entries. Inferring functionality based on cross-referencing UniProt and KEGG or EggNOG can be lackluster due to the low number of annotated species in Uniprot and due to the lower number of functions affiliated to the majority of these species. Additionally, the EggNOG database showed greater performance for a cross-search with Uniprot about a mock human gut microbiome. Notwithstanding, efforts targeting cultivation, single-cell sequencing or the reconstruction of high-quality metagenome-assembled genomes (MAG) and their annotation are needed to allow the use of these databases for inferring functionality in human gut microbiome studies.

• Klíčová slova
• Database, EggNOG, Functional diversity, Gut microbiome, Human Microbiome, KEGG, Uniprot,
• Publikační typ
• časopisecké články MeSH

Environmental pollutants, including antibiotics (ATBs), have become an increasingly common health hazard in the last several decades. Overdose and abuse of ATBs led to the emergence of antibiotic-resistant genes (ARGs), which represent a serious health threat. Moreover, water bodies and reservoirs are places where a wide range of bacterial species with ARGs originate, owing to the strong selective pressure from presence of ATB residues. In this regard, graphene oxide (GO) has been utilised in several fields including remediation of the environment. In this review, we present a brief overview of resistant genes of frequently used ATBs, their occurrence in the environment and their behaviour. Further, we discussed the factors influencing the binding of nucleic acids and the response of ARGs to GO, including the presence of salts in the water environment or water pH, because of intrinsic properties of GO of not only binding to nucleic acids but also catalysing their decomposition. This would be helpful in designing new types of water treatment facilities.

• Klíčová slova
• Antibiotics, Environment, Genes, Graphene oxide, Nanomaterials, Pollution, Wastewater,
• MeSH
• antibakteriální látky analýza   MeSH
• bakteriální geny * MeSH
• bakteriální léková rezistence genetika   MeSH
• chemické látky znečišťující vodu analýza   MeSH
• čištění vody MeSH
• grafit chemie   MeSH
• odpadní voda chemie   mikrobiologie   MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• antibakteriální látky MeSH
• chemické látky znečišťující vodu MeSH
• grafit MeSH
• graphene oxide MeSH Prohlížeč
• odpadní voda MeSH

Severe oral mucositis occurs frequently in patients receiving hematopoietic stem cell transplantation (HCT). Oral mucosal bacteria can be associated with progression of oral mucositis, and systemic infection may occur via ulcerative oral mucositis. However, little information is available regarding the oral microbiota after HCT. Here, PCR-denaturing gradient gel electrophoresis (DGGE) was performed to characterize the oral mucosal microbiota, which can be affected by antibiotics, before and after HCT. Sixty reduced-intensity HCT patients were enrolled. Three patients with the least antibiotic use (quinolone prophylaxis and/or β-lactam monotherapy group) and three patients with the most antibiotic use (β-lactam-glycopeptide combination therapy group) were selected. Bacterial DNA samples obtained from the oral mucosa before and after HCT were subjected to PCR-DGGE. The trajectory of oral mucositis was evaluated. The oral mucosal microbiota in the β-lactam-glycopeptide combination therapy group was different from that in the quinolone prophylaxis and/or β-lactam monotherapy group, and Staphylococcus spp. and Enterococcus spp. were identified. Lautropia mirabilis was dominant in one patient. Ulcerative oral mucositis was observed only in the β-lactam-glycopeptide combination therapy group. In conclusion, especially with the use of strong antibiotics, such as glycopeptides, the oral mucosal microbiota differed completely from that under normal conditions and consisted of Staphylococcus spp., Enterococcus spp., and unexpectedly L. mirabilis. The normal oral microbiota consists not only of bacteria, but these unexpected bacteria could be involved in the pathophysiology as well as systemic infection via oral mucositis. Our results can be used as the basis for future studies in larger patient populations.

• MeSH
• antibakteriální látky škodlivé účinky   terapeutické užití   MeSH
• beta-laktamy škodlivé účinky   terapeutické užití   MeSH
• chinolony škodlivé účinky   terapeutické užití   MeSH
• DNA bakterií genetika   MeSH
• dospělí MeSH
• glykopeptidy škodlivé účinky   terapeutické užití   MeSH
• lidé středního věku MeSH
• lidé MeSH
• mikrobiota účinky léků   MeSH
• příprava pacienta k transplantaci škodlivé účinky   MeSH
• RNA ribozomální 16S genetika   MeSH
• senioři MeSH
• stomatitida etiologie   mikrobiologie   patologie   patofyziologie   MeSH
• transplantace hematopoetických kmenových buněk škodlivé účinky   MeSH
• ústní sliznice mikrobiologie   MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• srovnávací studie MeSH
• Názvy látek
• antibakteriální látky MeSH
• beta-laktamy MeSH
• chinolony MeSH
• DNA bakterií MeSH
• glykopeptidy MeSH
• RNA ribozomální 16S MeSH

Relationships between gastrointestinal parasites (GIPs) and the gastrointestinal microbiome (GIM) are widely discussed topics across mammalian species due to their possible impact on the host's health. GIPs may change the environment determining alterations in GIM composition. We evaluated the associations between GIP infections and fecal microbiome composition in two habituated and two unhabituated groups of wild western lowland gorillas (Gorilla g. gorilla) from Dzanga Sangha Protected Areas, Central African Republic. We examined 43 fecal samples for GIPs and quantified strongylid nematodes. We characterized fecal microbiome composition through 454 pyrosequencing of the V1-V3 region of the bacterial 16S rRNA gene. Entamoeba spp. infections were associated with significant differences in abundances of bacterial taxa that likely play important roles in nutrition and metabolism for the host, besides being characteristic members of the gorilla gut microbiome. We did not observe any relationships between relative abundances of several bacterial taxa and strongylid egg counts. Based on our findings, we suggest that there is a significant relationship between fecal microbiome and Entamoeba infection in wild gorillas. This study contributes to the overall knowledge about factors involved in modulating GIM communities in great apes.

• Klíčová slova
• Entamoeba, bacteria, fecal microbiome, lowland gorilla, parasite infection, strongylid nematodes,
• Publikační typ
• časopisecké články MeSH

The worldwide prevalence of obesity more than doubled between 1980 and 2014. The obesity pandemic is tightly linked to an increase in energy availability, sedentariness and greater control of ambient temperature that have paralleled the socioeconomic development of the past decades. The most frequent cause which leads to the obesity development is a dysbalance between energy intake and energy expenditure. The gut microbiota as an environmental factor which influence whole-body metabolism by affecting energy balance but also inflammation and gut barrier function, integrate peripheral and central food intake regulatory signals and thereby increase body weight. Probiotics have physiologic functions that contribute to the health of gut microbiota, can affect food intake and appetite, body weight and composition and metabolic functions through gastrointestinal pathways and modulation of the gut bacterial community.

• Klíčová slova
• Gut microbiota, Intestinal microflora, Obesity, Prevention, Probiotics, Treatment,
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

Methane production by intestinal methanogenic Archaea and their community structure were compared among phylogenetic lineages of millipedes. Tropical and temperate millipedes of 35 species and 17 families were investigated. Species that emitted methane were mostly in the juliform orders Julida, Spirobolida, and Spirostreptida. The irregular phylogenetic distribution of methane production correlated with the presence of the methanogen-specific mcrA gene. The study brings the first detailed survey of methanogens' diversity in the digestive tract of millipedes. Sequences related to Methanosarcinales, Methanobacteriales, Methanomicrobiales and some unclassified Archaea were detected using molecular profiling (DGGE). The differences in substrate preferences of the main lineages of methanogenic Archaea found in different millipede orders indicate that the composition of methanogen communities may reflect the differences in available substrates for methanogenesis or the presence of symbiotic protozoa in the digestive tract. We conclude that differences in methane production in the millipede gut reflect differences in the activity and proliferation of intestinal methanogens rather than an absolute inability of some millipede taxa to host methanogens. This inference was supported by the general presence of methanogenic activity in millipede faecal pellets and the presence of the 16S rRNA gene of methanogens in all tested taxa in the two main groups of millipedes, the Helminthophora and the Pentazonia.

• MeSH
• biodiverzita * MeSH
• členovci mikrobiologie   MeSH
• denaturační gradientová gelová elektroforéza MeSH
• Euryarchaeota genetika   metabolismus   fyziologie   MeSH
• feces chemie   MeSH
• fylogeneze MeSH
• gastrointestinální trakt mikrobiologie   MeSH
• methan biosyntéza   metabolismus   MeSH
• molekulární sekvence - údaje MeSH
• RNA ribozomální 16S genetika   MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH
• Rumunsko MeSH
• Slovenská republika MeSH
• Názvy látek
• methan MeSH
• RNA ribozomální 16S MeSH

BACKGROUND: A set of 1181 E. coli strains of human fecal origin isolated in the South Moravia region of the Czech Republic was collected during the years 2007-2010. Altogether, 17 virulence determinants and 31 bacteriocin-encoding genes were tested in each of them. RESULTS: The occurrence of bacteriocin-encoding genes was found to be positively correlated with the occurrence of E. coli virulence factors. Based on the presence of virulence factors and their combinations, E. coli strains were classified as non-pathogenic E. coli (n = 399), diarrhea-associated E. coli (n = 179) and ExPEC strains (n = 603). Non-pathogenic and diarrhea-associated E. coli strains had a low frequency of bacteriocinogeny (32.6% and 36.9%, respectively). ExPEC strains encoding S-fimbriae (sfa), P-fimbriae (pap) and having genes for aerobactin biosynthesis (aer, iucC), α-hemolysis (α-hly) and cytotoxic necrosis factor (cnf1) were often bacteriocinogenic (73.8%), had a high prevalence of bacteriocin multi-producers and showed a higher frequency of genes encoding microcins H47, M, V, B17 and colicins E1, Ia and S4. CONCLUSIONS: The occurrence of bacteriocin-encoding genes and ExPEC virulence determinants correlate positively in E. coli strains of human fecal origin. Bacteriocin synthesis appears to modulate the ability of E. coli strains to reside in the human intestine and/or the virulence of the corresponding strains.

• MeSH
• bakteriální geny * MeSH
• bakteriociny genetika   MeSH
• DNA bakterií chemie   genetika   MeSH
• Escherichia coli genetika   izolace a purifikace   MeSH
• faktory virulence genetika   MeSH
• feces mikrobiologie   MeSH
• genotyp MeSH
• lidé MeSH
• molekulární sekvence - údaje MeSH
• sekvenční analýza DNA MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH
• Názvy látek
• bakteriociny MeSH
• DNA bakterií MeSH
• faktory virulence MeSH