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The gut microbiota (GM), which contains thousands of bacterial species, is a reservoir of antibiotic resistance genes (ARGs) called resistome. Early life exposure to antibiotics alters significantly the composition and function of the gut microbiota of children, which may trigger symptoms of autism spectrum disorder (ASD). This is because the GM plays an important role in the bidirectional communication between the gut and the brain and influences the brain normal functioning through multiple pathways. The goal of this article is to study the distribution of ARGs in the GM of 3- to 5-year-old healthy children and children with ASD living in Moscow, Russia. The metagenomic analysis of samples from both groups revealed differences in the signatures between them. The signatures consisted of the bacterial genera and aminoglycoside, β-lactam, macrolide, and tetracycline resistance genes that they harbored. Our results show an increase in ARGs in the resistome of the GM of children with ASD. These findings emphasize the negative influence of early-life antibiotic therapy. We found three ARGs, aac(6')-aph(2''), cepA-49, and tet(40), which could serve as markers of ASD. The additional functions carried out by the enzymes, encoded by these genes, are being discussed.

Two different approaches, real-time PCR and in silico analysis, were used to study the abundance of bacterial genes encoding the enzymes producing biomarker metabolites in metagenomes of gut microbiota of children with autism spectrum disorders (ASD) and healthy children. As a result of the analysis of the published data, the following biomarker metabolites of ASD were chosen for the research: p-cresol, indole, propionic acid, and D-lactic acid. For the real-time PCR and the transcriptomic analysis, primer sequences were used specifically developed for conservative regions of the genes involved in production of these bacterial metabolites. Nucleotide sequences of the conservative regions were also united into a catalog and were searched in metagenomic assemblies as part of in silico analysis. Comparison of the results revealed a decrease in abundance of the genes in the metagenomes of children with ASD during both PCR and bioinformatics analyses. In addition, real-time PCR made it possible to detect a significant increase in abundance of the genes encoding p-hydroxyphenylacetate decarboxylase and D-lactate dehydrogenase in Bacteroides fragilis and Alistipes finegoldii species and methylmalonyl-CoA decarboxylase in B. fragilis, Alistipes shahii, and Eubacterium rectali species. A low level of the transcripts in total RNA was found in microbiota of a child with severe form of ASD.

Plant cysteine-rich peptides (CRP) play a key role in protection of plants from pathogens and abiotic stress, in symbiosis with bacteria, and in plant development and reproduction. The composition and role of CRPs in tomato Solanum lycopersicum, one of the most important vegetable, has not been studied so far. In this paper, using two approaches, hidden Markov models and regular expressions, in silico identification of tomato CRP families was performed. A bioinformatic analysis of NCBI databases revealed 191 CRP precursors. The peptides found belong to the families of antimicrobial and signaling peptides. Among the antimicrobial peptides, defensins and defensin-like peptides, nonspecific lipid-transfer proteins, thionins, snakins, and hevein- and knottin-like peptides were found. Among signaling peptides, the peptides belonging to the RALF, Ole e 1, Ole e 6, and MEG families were discovered. In addition, peptides with new cysteine motifs were identified. All discovered CRPs are synthesized as pre- or preproproteins. The predicted mature peptides were characterized by cysteine motifs, antimicrobial activity, and domain structure. Thus, for the first time, using bioinformatic approaches, systemic data on the arsenal of CRPs in the tomato genome were obtained, which creates a basis for further functional studies of these peptides and their subsequent use in agriculture to develop new strategies for increasing tomato pathogen resistance, as well as in medicine to create next-generation drugs.

Introduction. The human gut microbiota is currently seen as an important factor that can promote autism spectrum disorder (ASD) development in children. Aim. This study aimed to detect differences in the taxonomic composition and content of bacterial genes encoding key enzymes involved in the metabolism of neuroactive biomarker compounds in the metagenomes of gut microbiota of children with ASD and neurotypical children. Methodology. A whole metagenome sequencing approach was used to obtain metagenomic data on faecal specimens of 36 children with ASD and 21 healthy neurotypical children of 3–5 years old. Taxonomic analysis was conducted using MetaPhlAn2. The developed bioinformatics algorithm and created catalogue of the orthologues were applied to identify bacterial genes of neuroactive compounds in the metagenomes. For the identification of metagenomic signatures of children with ASD, Wilcoxon's test and adjustment for multiple comparisons were used. Results. Statistically significant differences with decreases in average abundance in the microbiota of ASD children were found for the genera Barnesiella and Parabacteroides and species Alistipes putredinis , B. caccae , Bacteroides intestinihominis, Eubacterium rectale , Parabacteroides distasonis and Ruminococcus lactaris . Average relative abundances of the detected genes and neurometabolic signature approach did not reveal many significant differences in the metagenomes of the groups that were compared. We noted decreases in the abundance of genes linked to production of GABA, melatonine and butyric acid in the ASD metagenomes. Conclusion. For the first time, the neurometabolic signature of the gut microbiota of young children with ASD is presented. The data can help to provide a comparative assessment of the transcriptional and metabolomic activity of the identified genes.

A great amount of attention has been paid to the study of the microbiota–gut–brain axis in recent years. Gut microbiota can affect development and functioning of the brain through synthesis of various neuroactive metabolites, such as neurotransmitters, hormones, and other compounds. In the present study, the presence and distribution are analyzed for the genes controlling the synthesis of enzymes involved in production of neuroactive compounds in 147 gut metagenomes of healthy people from Human Microbiome Project database and synthetic metagenome artificially assembled from 508 bacterial genomes. The analysis is conducted using the collected catalog of orthologs for 17 key enzymes and an algorithm developed for their search. As a result of analyses of genomic and metagenomic data of healthy people, seven bacterial genera containing the greatest number of enzyme genes and 8 enzymes out of 17 that are observed the most frequently are chosen. It is assumed that the selected “core” genera and enzymes form a metagenomic signature reflecting the neurometabolic potential of the human intestinal microbiota in the norm.

Antimicrobial peptides (AMPs) are the main components of the plant innate immune system. Defensins represent the most important AMP family involved in defense and non-defense functions. In this work, global RNA sequencing and de novo transcriptome assembly were performed to explore the diversity of defensin-like (DEFL) genes in the wheat Triticum kiharae and to study their role in induced resistance (IR) mediated by the elicitor metabolites of a non-pathogenic strain FS-94 of Fusarium sambucinum. Using a combination of two pipelines for DEFL mining in transcriptome data sets, as many as 143 DEFL genes were identified in T. kiharae, the vast majority of them represent novel genes. According to the number of cysteine residues and the cysteine motif, wheat DEFLs were classified into ten groups. Classical defensins with a characteristic 8-Cys motif assigned to group 1 DEFLs represent the most abundant group comprising 52 family members. DEFLs with a characteristic 4-Cys motif CX{3,5}CX{8,17}CX{4,6}C named group 4 DEFLs previously found only in legumes were discovered in wheat. Within DEFL groups, subgroups of similar sequences originated by duplication events were isolated. Variation among DEFLs within subgroups is due to amino acid substitutions and insertions/deletions of amino acid sequences. To identify IR-related DEFL genes, transcriptional changes in DEFL gene expression during elicitor-mediated IR were monitored. Transcriptional diversity of DEFL genes in wheat seedlings in response to the fungus Fusarium oxysporum, FS-94 elicitors, and the combination of both (elicitors + fungus) was demonstrated, with specific sets of up- and down-regulated DEFL genes. DEFL expression profiling allowed us to gain insight into the mode of action of the elicitors from F. sambucinum. We discovered that the elicitors up-regulated a set of 24 DEFL genes. After challenge inoculation with F. oxysporum, another set of 22 DEFLs showed enhanced expression in IR-displaying seedlings. These DEFLs, in concert with other defense molecules, are suggested to determine enhanced resistance of elicitor-pretreated wheat seedlings. In addition to providing a better understanding of the mode of action of the elicitors from FS-94 in controlling diseases, up-regulated IR-specific DEFL genes represent novel candidates for genetic transformation of plants and development of pathogen-resistant crops.

The draft genome sequences of Bifidobacterium angulatum GT102 and Bifidobacterium adolescentis 150 strains isolated from the human intestinal microbiota are reported. Both strains are able to produce gamma-aminobutyric acid (GABA). Detailed genomes analysis will help to understand the role of GABA in the functioning of gut-brain axis.