BACKGROUND: Many arthropods rely on their gut microbiome to digest plant material, which is often low in nitrogen but high in complex polysaccharides. Detritivores, such as millipedes, live on a particularly poor diet, but the identity and nutritional contribution of their microbiome are largely unknown. In this study, the hindgut microbiota of the tropical millipede Epibolus pulchripes (large, methane emitting) and the temperate millipede Glomeris connexa (small, non-methane emitting), fed on an identical diet, were studied using comparative metagenomics and metatranscriptomics. RESULTS: The results showed that the microbial load in E. pulchripes is much higher and more diverse than in G. connexa. The microbial communities of the two species differed significantly, with Bacteroidota dominating the hindguts of E. pulchripes and Proteobacteria (Pseudomonadota) in G. connexa. Despite equal sequencing effort, de novo assembly and binning recovered 282 metagenome-assembled genomes (MAGs) from E. pulchripes and 33 from G. connexa, including 90 novel bacterial taxa (81 in E. pulchripes and 9 in G. connexa). However, despite this taxonomic divergence, most of the functions, including carbohydrate hydrolysis, sulfate reduction, and nitrogen cycling, were common to the two species. Members of the Bacteroidota (Bacteroidetes) were the primary agents of complex carbon degradation in E. pulchripes, while members of Proteobacteria dominated in G. connexa. Members of Desulfobacterota were the potential sulfate-reducing bacteria in E. pulchripes. The capacity for dissimilatory nitrate reduction was found in Actinobacteriota (E. pulchripes) and Proteobacteria (both species), but only Proteobacteria possessed the capacity for denitrification (both species). In contrast, some functions were only found in E. pulchripes. These include reductive acetogenesis, found in members of Desulfobacterota and Firmicutes (Bacillota) in E. pulchripes. Also, diazotrophs were only found in E. pulchripes, with a few members of the Firmicutes and Proteobacteria expressing the nifH gene. Interestingly, fungal-cell-wall-degrading glycoside hydrolases (GHs) were among the most abundant carbohydrate-active enzymes (CAZymes) expressed in both millipede species, suggesting that fungal biomass plays an important role in the millipede diet. CONCLUSIONS: Overall, these results provide detailed insights into the genomic capabilities of the microbial community in the hindgut of millipedes and shed light on the ecophysiology of these essential detritivores. Video Abstract.

• Klíčová slova
• Acetogens, Ecosystem engineers, Glycoside hydrolases, Hindgut microbiota, Millipede holobiont, Nutrient cycling, Polysaccharide degradation, Symbiosis,
• MeSH
• Bacteria MeSH
• Bacteroidetes genetika   MeSH
• členovci * genetika   MeSH
• dusík metabolismus   MeSH
• fylogeneze MeSH
• metagenom MeSH
• metagenomika MeSH
• Proteobacteria genetika   MeSH
• sacharidy MeSH
• sírany metabolismus   MeSH
• střevní mikroflóra * genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• audiovizuální média MeSH
• časopisecké články MeSH
• Názvy látek
• dusík MeSH
• sacharidy MeSH
• sírany MeSH

Cardinium bacteria are well known as endosymbionts that infect a wide range of arthropods and can manipulate host reproduction to promote their vertical transmission. As intracellular bacteria, Cardinium species undergo dramatic genome evolution, especially their chromosomal genome reduction. Although Cardinium plasmids have been reported to harbor important genes, the role of these plasmids in the genome evolution is yet to be fully understood. In this study, 2 genomes of Cardinium endosymbiont bacteria in astigmatic mites were de novo assembled, including the complete circular chromosomal genome of Cardinium sp. DF that was constructed in high quality using high-coverage long-read sequencing data. Intriguingly, 2 circular plasmids were assembled in Cardinium sp. DF and were identified to be endogenous for over 10 homologous genes shared with the chromosomal genome. Comparative genomics analysis illustrated an outline of the genome evolution of Cardinium bacteria, and the in-depth analysis of Cardinium sp. DF shed light on the multiple roles of endogenous plasmids in the molecular process of the chromosomal genome reduction. The endogenous plasmids of Cardinium sp. DF not only harbor massive homologous sequences that enable homologous recombination with the chromosome, but also can provide necessary functional proteins when the coding genes decayed in the chromosomal genome. IMPORTANCE As bacterial endosymbionts, Cardinium typically undergoes genome reduction, but the molecular process is still unclear, such as how plasmids get involved in chromosome reduction. Here, we de novo assembled 2 genomes of Cardinium in astigmatic mites, especially the chromosome of Cardinium sp. DF was assembled in a complete circular DNA using high-coverage long-read sequencing data. In the genome assembly of Cardinium sp. DF, 2 circular endogenous plasmids were identified to share at least 10 homologous genes with the chromosomal genome. In the comparative analysis, we identified a range of genes decayed in the chromosomal genome of Cardinium sp. DF but preserved in the 2 plasmids. Taken together with in-depth analyses, our results unveil that the endogenous plasmids harbor homologous sequences of chromosomal genome and can provide a structural basis of homologous recombination. Overall, this study reveals that endogenous plasmids participate in the ongoing chromosomal genome reduction of Cardinium sp. DF.

• Klíčová slova
• Cardinium endosymbiont, chromosomal genome reduction, endogenous plasmid, host-associated bacteria,
• MeSH
• Bacteria MeSH
• Bacteroidetes * genetika   MeSH
• chromozomy MeSH
• Dermatophagoides farinae * MeSH
• genom bakteriální MeSH
• plazmidy genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

An experimental group of one-day-old chicken from a commercial hatchery was given a defined mixture of 7 gut anaerobes. The next day the chicks were inoculated by an APEC strain O78:H4-ST117 resistant to ciprofloxacin, alongside with the control group and monitored for 4 wk after the inoculation for the presence of the colonizing strains and ciprofloxacin-resistant E. coli. Significant reduction of colonization rates in the first 2 wk was recorded in the experimental group for the numbers of ciprofloxacin-resistant E. coli. The results show that colonization of chicken by defined anaerobic mixtures may provide a decisive protection during the critical period of the chicken intestinal microflora development.

• Klíčová slova
• avian pathogenic Escherichia coli (APEC), chicken, colonization, competitive exclusion, probiotics,
• MeSH
• Bacteroides MeSH
• ciprofloxacin farmakologie   MeSH
• Escherichia coli MeSH
• infekce vyvolané Escherichia coli * prevence a kontrola   veterinární   MeSH
• kur domácí MeSH
• nemoci drůbeže * prevence a kontrola   MeSH
• probiotika * farmakologie   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• ciprofloxacin MeSH

Storage mites colonize a wide spectrum of food commodities and adaptations to diets have been suggested as mechanisms enabling successful colonization. We characterized the response of seven unique Tyrophagus putrescentiae cultures (5K, 5L, 5N, 5P, 5Pi, 5S, and 5Tk) with different baseline microbiomes to different diets. The offered diets included a rearing diet, protein-enriched diet, oat flakes, and sunflower seeds. Microbiome characterization was performed using 16S ribosomal RNA (rRNA) gene amplicon sequencing and 16S rRNA gene quantitative PCR. The mite culture microbiomes were classified into four groups: (i) Sodalis-dominated (5Pi), (ii) Wolbachia-dominated (5N and 5P), (iii) Cardinium-dominated (5L and 5S), and (iv) asymbiontic (5K and 5Tk) mites dominated by Bacillus and Bartonella. Mite growth rates were most strongly affected by nutrients in the diet, while respiration and microbial community profiles were largely influenced by mite culture. While growth rate was not directly explained by microbiome composition, microbiomes strongly influenced mite fitness as measured by respiration. While diet significantly influenced microbial profiles in all cultures, the effect of diet differed in impact between cultures (5Pi > 5S > 5N > 5K > 5Tk > 5L > 5P). Furthermore, no new bacterial taxa were acquired by mites after dietary changes. Bacteria from the taxa Bacillus, Bartonella-like, Solitalea-like, Kocuria, and Sodalis-like contributed most strongly to differentiating mite-associated microbiomes.

• Klíčová slova
• diets, feeding, fitness, microorganisms, mite, transmission,
• MeSH
• Acaridae * genetika   mikrobiologie   MeSH
• Bacteria genetika   MeSH
• Bacteroidetes genetika   MeSH
• dieta MeSH
• Enterobacteriaceae genetika   MeSH
• mikrobiota * MeSH
• RNA ribozomální 16S genetika   MeSH
• roztoči * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• 5-(4'-(N-piperidinyl)phenylazo)indazole MeSH Prohlížeč
• RNA ribozomální 16S MeSH

BACKGROUND: The contribution of the microbiome to pesticide breakdown in agricultural pests remains unclear. We analyzed the effect of pirimiphos-methyl (PM) on four geographically different cultures of the stored product pest mite Acarus siro (6 L, 6Tu, 6Tk and 6Z) under laboratory experiments. The effect of PM on mite mortality in the impregnated filter paper test was compared. RESULTS: The mite sensitivity to PM decreased in the order of 6 L, 6Tu, 6Tk, and 6Z. Then, the mites were cultured on PM residues (0.0125 and 1.25 µg·g-1), and population growth was compared to the control after 21 days of exposure. The comparison showed two situations: (i) increasing population growth for the most sensitive cultures (6 L and 6Tu), and (ii) no effect on mite population growth for tolerant cultures (6Z and 6Tk). The microbiome of mites was analyzed by quantification of 16S DNA copies based on quantitative polymerase chain reaction (qPCR) and by barcode sequencing of the V4 fragment of 16S DNA on samples of 30 individuals from the control and PM residues. The microbiome comprised primarily Solitalea-like organisms in all cultures, except for 6Z, followed by Bacillus, Staphylococcus, and Lactobacillus. The microbiomes of mite cultures did not change with increasing population density. The microbiome of cultures without any differences in population density showed differences in the microbiome composition. A Sodalis-like symbiont replaced Solitalea in the 1.25 µg·g-1 PM in the 6Tk culture. Sodalis and Bacillus prevailed in the microbiomes of PM-treated mites of 6Z culture, while Solitalea was almost absent. CONCLUSION: The results showed that the microbiome of A. siro differs in composition and in response to PM residues in the diet. The results indicate that Sodalis-like symbionts can help recover mites from pesticide-induced stress.

• Klíčová slova
• Pesticide; Storage; Interaction; Tolerance; Symbionts,
• MeSH
• Acaridae * MeSH
• Bacteroidetes MeSH
• lidé MeSH
• mikrobiota * MeSH
• rezidua pesticidů * MeSH
• roztoči * MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• pirimiphos methyl MeSH Prohlížeč
• rezidua pesticidů * MeSH

Understanding disease aetiology and pathologic mechanisms is essential for fish health evaluation. Carp edema virus (CEV) is the causative agent of a disease (CEVD) responsible for high mortality rates in both wild and cultured common carp Cyprinus carpio. Inspection of two carp specimens from a pond with high fish mortality revealed CEV infection in both the host and its ectoparasite (Argulus foliaceus). In addition to flavobacteria, well known to be associated with gill lesions, we found that free-living eukaryotes (amoebae and ciliates) and a temporary parasite (Ichthyobodo spp.) colonizing the gills may also contribute to alterations in gill structure and/or function, either directly, through firm (Ichthyobodo) or weak (amoebae) attachment of trophozoites to the gill epithelium, or indirectly, through carriage of pathogenic bacteria. Bacterial assemblages rich in families and genera, with predominance of Cetobacterium spp. in low-intensity alteration of the gill tissue and of Flavobacterium spp. in gills with extensive necrotic lesions, were detected in gills and within the cytoplasm of associated amoebae using high-throughput sequencing. Quantitative PCR indicated F. swingsii as the prevailing flavobacterial species within amoebae from less affected gills and F. psychrophilum within amoebae from extensively affected gills. This case study suggests that eukaryotic organisms as part of the gill pathobiome may also contribute to irreversible gill lesions seen in CEVD. Emphasizing the complexity of mutual relationships between bacterial assemblages and eukaryotic co-pathogens, further studies regarding factors that trigger pathology and influence severity in the CEV-positive carp are needed.

• Klíčová slova
• Cyprinus carpio, CEV, fish, pathogenic assemblage, virus diseases,
• MeSH
• edém MeSH
• Flavobacterium MeSH
• infekce vyvolané poxviry * veterinární   MeSH
• kapři * MeSH
• nemoci ryb * mikrobiologie   MeSH
• Poxviridae * MeSH
• žábry patologie   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• kazuistiky MeSH

Invertebrate-microbial associations are widespread in the biosphere and are often related to the function of novel genes, fitness advantages, and even speciation events. Despite ~ 13,000 species of millipedes identified across the world, millipedes and their gut microbiota are markedly understudied compared to other arthropods. Exploring the contribution of individual host-associated microbes is often challenging as many are uncultivable. In this study, we conducted metatranscriptomic profiling of different body segments of a millipede at the holobiont level. This is the first reported transcriptome assembly of a tropical millipede Telodeinopus aoutii (Demange, 1971), as well as the first study on any Myriapoda holobiont. High-throughput RNA sequencing revealed that Telodeinopus aoutii contained > 90% of the core Arthropoda genes. Proteobacteria, Bacteroidetes, Firmicutes, and Euryarchaeota represented dominant and functionally active phyla in the millipede gut, among which 97% of Bacteroidetes and 98% of Firmicutes were present exclusively in the hindgut. A total of 37,831 predicted protein-coding genes of millipede holobiont belonged to six enzyme classes. Around 35% of these proteins were produced by microbiota in the hindgut and 21% by the host in the midgut. Our results indicated that although major metabolic pathways operate at the holobiont level, the involvement of some host and microbial genes are mutually exclusive and microbes predominantly contribute to essential amino acid biosynthesis, short-chain fatty acid metabolism, and fermentation.

• MeSH
• Bacteroidetes MeSH
• členovci * genetika   MeSH
• esenciální aminokyseliny MeSH
• kyseliny mastné těkavé MeSH
• střevní mikroflóra * genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• esenciální aminokyseliny MeSH
• kyseliny mastné těkavé MeSH

Western lowland gorillas (Gorilla gorilla gorilla) are Critically Endangered and show continued population decline. Consequently, pressure is mounting to better understand their conservation threats and ecology. Gastrointestinal symbionts, such as bacterial and eukaryotic communities, are believed to play vital roles in the physiological landscape of the host. Gorillas host a broad spectrum of eucaryotes, so called parasites, with strongylid nematodes being particularly prevalent. While these communities are partially consistent, they are also shaped by various ecological factors, such as diet or habitat type. To investigate gastrointestinal symbionts of wild western lowland gorillas, we analysed 215 faecal samples from individuals in five distinct localities across the Congo Basin, using high-throughput sequencing techniques. We describe the gut bacterial microbiome and genetic diversity of strongylid communities, including strain-level identification of amplicon sequence variants (ASVs). We identified strongylid ASVs from eight genera and bacterial ASVs from 20 phyla. We compared these communities across localities, with reference to varying environmental factors among populations, finding differences in alpha diversity and community compositions of both gastrointestinal components. Moreover, we also investigated covariation between strongylid nematodes and the bacterial microbiome, finding correlations between strongylid taxa and Prevotellaceae and Rikenellaceae ASVs that were consistent across multiple localities. Our research highlights the complexity of the bacterial microbiome and strongylid communities in several gorilla populations and emphasizes potential interactions between these two symbiont communities. This study provides a framework for ongoing research into strongylid nematode diversity, and their interactions with the bacterial microbiome, among great apes.

• Klíčová slova
• Strongylida, bacterial microbiome, gorilla, helminth, non-human primates,
• MeSH
• Bacteria genetika   MeSH
• Bacteroidetes MeSH
• feces mikrobiologie   MeSH
• Gorilla gorilla genetika   MeSH
• lidé MeSH
• mikrobiota * MeSH
• střevní mikroflóra * genetika   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Research in the field of human microbiota and its impact on human health has opened new possibilities for the diagnosis, prevention or treatment of certain pathological conditions. A negative change in the composition of the intestinal microbiota, dysbiosis, is associated with diseases such as inflammatory bowel diseases, obesity, diabetes mellitus, or Clostridium difficile infections. For the use of human microbiota or its biologically active products in clinical practice, it is necessary to thoroughly identify and characterize properties that may be beneficial to human health. The use of the latest technology enables such research to be carried out, and we are already aware of several potential candidates for the so-called probiotics of the next generation. The aim of this article is to summarize available information on the bacteria Akkermansia muciniphila, Bacteroides fragilis, and Faecalibacterium prausnitzii, which are among the most promising and studied candidates.

• Klíčová slova
• Akkermansia muciniphila, Bacteroides fragilis, Faecalibacterium prausnitzii, gut microbiota, intestinal microbiota, next generation probiotics,
• MeSH
• Bacteria MeSH
• Bacteroides fragilis MeSH
• lidé MeSH
• obezita MeSH
• probiotika * terapeutické užití   MeSH
• střevní mikroflóra * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

Flavobacterium columnare is the causative agent of columnaris disease in freshwater fish and four discrete genetic groups exist within the species, suggesting that the species designation requires revision. The present study determined the taxonomic status of the four genetic groups of F. columnare using polyphasic and phylogenomic approaches and included five representative isolates from each genetic group (including type strain ATCC 23463T; genetic group 1). 16S rRNA gene sequence analysis revealed genetic group 2 isolate AL-02-36T, genetic group 3 isolate 90-106T, and genetic group 4 isolate Costa Rica 04-02-TNT shared less than <98.8 % sequence identity to F. columnare ATCC 23463T. Phylogenetic analyses of 16S rRNA and gyrB genes using different methodologies demonstrated the four genetic groups formed well-supported and distinct clades within the genus Flavobacterium. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (GGDC) values between F. columnare ATCC 23463T, genetic group 2 isolate AL-02-36T, genetic group 3 isolate 90-106T, and genetic group 4 isolate Costa Rica 04-02-TNT were less than 90.84% and 42.7%, respectively. Biochemical and physiological characteristics were similar among the four genetic groups; however, quantitative differences in fatty acid profiles were detected and MALDI-TOF analyses demonstrated numerous distinguishing peaks unique to each genetic group. Chemotaxonomic, MALDI-TOF characterization and ANI/GGDC calculations afforded differentiation between the genetic groups, indicating each group is a discrete species. Herein, the names F. covae sp. nov. (AL-02-36T), F. davisii sp. nov. (90-106T), and F. oreochromis sp. nov. (Costa Rica 04-02-TNT) are proposed to represent genetic groups 2, 3, and 4, respectively.

• Klíčová slova
• Columnaris disease, Genetic groups, MALDI-TOF, Polyphasic, Taxonomy,
• MeSH
• DNA bakterií genetika   MeSH
• Flavobacterium * MeSH
• fylogeneze MeSH
• hybridizace nukleových kyselin MeSH
• mastné kyseliny * analýza   MeSH
• RNA ribozomální 16S genetika   MeSH
• sekvenční analýza DNA MeSH
• techniky typizace bakterií MeSH
• zastoupení bazí MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA bakterií MeSH
• mastné kyseliny * MeSH
• RNA ribozomální 16S MeSH