Distinct gut microbiomes in Thai patients with colorectal polyps

BACKGROUND Colorectal polyps that develop via the conventional adenoma-carcinoma sequence[e.g.,tubular adenoma(TA)]often progress to malignancy and are closely associated with changes in the composition of the gut microbiome.There is limited research concerning the microbial functions and gut microbiomes associated with colorectal polyps that arise through the serrated polyp pathway,such as hyperplastic polyps(HP).Exploration of microbiome alterations asso-ciated with HP and TA would improve the understanding of mechanisms by which specific microbes and their metabolic pathways contribute to colorectal carcinogenesis.AIM To investigate gut microbiome signatures,microbial associations,and microbial functions in HP and TA patients.METHODS Full-length 16S rRNA sequencing was used to characterize the gut microbiome in stool samples from control participants without polyps[control group(CT),n=40],patients with HP(n=52),and patients with TA(n=60).Significant differences in gut microbiome composition and functional mechanisms were identified between the CT group and patients with HP or TA.Analytical techniques in this study included differential abundance analysis,co-occurrence network analysis,and differential pathway analysis.RESULTS Colorectal cancer(CRC)-associated bacteria,including Streptococcus gallolyticus(S.gallolyticus),Bacteroides fragilis,and Clostridium symbiosum,were identified as characteristic microbial species in TA patients.Mediterraneibacter gnavus,associated with dysbiosis and gastrointestinal diseases,was significantly differentially abundant in the HP and TA groups.Functional pathway analysis revealed that HP patients exhibited enrichment in the sulfur oxidation pathway exclusively,whereas TA patients showed dominance in pathways related to secondary metabolite biosynthesis(e.g.,mevalonate);S.gallolyticus was a major contributor.Co-occurrence network and dynamic network analyses revealed co-occurrence of dysbiosis-associated bacteria in HP patients,whereas TA patients exhibited co-occurrence of CRC-associated bacteria.Furthermore,the co-occurrence of SCFA-producing bacteria was lower in TA patients than HP patients.CONCLUSION This study revealed distinct gut microbiome signatures associated with pathways of colorectal polyp development,providing insights concerning the roles of microbial species,functional pathways,and microbial interactions in colorectal carcinogenesis.

Debaryomyces hansenii supplementation in low fish meal diets promotes growth,modulates microbiota and enhances intestinal condition in juvenile marine fish

Background The development of a sustainable business model with social acceptance,makes necessary to develop new strategies to guarantee the growth,health,and well-being of farmed animals.Debaryomyces hansenii is a yeast species that can be used as a probiotic in aquaculture due to its capacity to i)promote cell proliferation and differen-tiation,ii)have immunostimulatory effects,iii)modulate gut microbiota,and/or iv)enhance the digestive function.To provide inside into the effects of D.hansenii on juveniles of gilthead seabream(Sparus aurata)condition,we inte-grated the evaluation of the main key performance indicators coupled with the integrative analysis of the intestine condition,through histological and microbiota state,and its transcriptomic profiling.Results After 70 days of a nutritional trial in which a diet with low levels of fishmeal(7%)was supplemented with 1.1%of D.hansenii(17.2×10^(5) CFU),an increase of ca.12%in somatic growth was observed together with an improve-ment in feed conversion in fish fed a yeast-supplemented diet.In terms of intestinal condition,this probiotic modu-lated gut microbiota without affecting the intestine cell organization,whereas an increase in the staining intensity of mucins rich in carboxylated and weakly sulphated glycoconjugates coupled with changes in the affinity for certain lectins were noted in goblet cells.Changes in microbiota were characterized by the reduction in abundance of several groups of Proteobacteria,especially those characterized as opportunistic groups.The microarrays-based transcrip-tomic analysis found 232 differential expressed genes in the anterior-mid intestine of S.aurata,that were mostly related to metabolic,antioxidant,immune,and symbiotic processes.Conclusions Dietary administration of D.hansenii enhanced somatic growth and improved feed efficiency param-eters,results that were coupled to an improvement of intestinal condition as histochemical and transcriptomic tools indicated.This probiotic yeast stimulated host-microbiota interactions without altering the intestinal cell organization nor generating dysbiosis,which demonstrated its safety as a feed additive.At the transcriptomic level,D.hansenii pro-moted metabolic pathways,mainly protein-related,sphingolipid,and thymidylate pathways,in addition to enhance antioxidant-related intestinal mechanisms,and to regulate sentinel immune processes,potentiating the defensive capacity meanwhile maintaining the homeostatic status of the intestine.

Embryonic and Larval Development of Reciprocal Crosses between Clarias gariepinus (Burchell, 1822) and Clarias jaensis (Boulenger, 1909) in West Cameroon

Establishing intraspecific breeding and hybridization programs and determining genetic variability are two important issues for aquaculture. However, interspecific hybridization to improve growth and feeding efficiency is limited. For this purpose, the embryonic and larval development of reciprocal crosses of Clarias gariepinus (Burchell, 1822) and Clarias jaensis (Boulenger, 1909) were studied under laboratory conditions. The fertilization rate varied from 63.33% to 92%, while the hatching rate ranged from 55.68% to 76% with the highest value in hybrids ♀Cg × ♂Cj. Crosses between ♀Cj × ♂Cj, ♀Cg × ♂Cj and ♀Cj × ♂Cg had embryonic stages similar to those of the pure sib ♀Cg x ♂Cg. All crosses, however, had different timing for the various embryological stages. Hatching occurred at 32 h 15 min and 38 h for ♀Cj × ♂Cj and ♀Cj × ♂Cg, and 23 h and 23 h 30 min, respectively, for ♀Cg × ♂Cg and ♀Cg × ♂Cj. However, both crosses produced viable larvae until the first external feeding. The external morphological features of the larvae were completely formed by the 10th day after hatching. The body forms of the crosses at this time were indistinguishable from the pure sib. This study thus laid the groundwork for further comparative studies on hybrid performance and characterization.

Differential molecular profiles and associated functionalities characterize connective tissue grafts obtained at different locations and depths in the human palate

The present study aimed to assess the molecular profiles of subepithelial connective tissue grafts(CTGs)obtained at different locations and depths in the human palate.Sixty-four CTGs belonging to anterior deep(AD),anterior superficial(AS),posterior deep(PD),and posterior superficial(PS)groups were subjected to RNA-Sequencing and their transcriptomes were analyzed computationally.Functional correlations characterizing the CTG groups were validated by cell biological experiments using primary human palatal fibroblasts(HPFs)extracted from the CTGs.A clearly more pronounced location-dependent than depth-dependent difference between the grafts,with a minimal number of genes(4)showing no dependence on the location,was revealed.Epithelial,endothelial,and monocytic cell migration was strongly(P<0.001)potentiated by AD-and PS-HPFs.Moreover,significantly increased expression of genes encoding C-C and C-X-C motif chemokine ligands as well as significantly(P<0.01)activated p38 signaling suggested immunomodulatory phenotype for AD-and PS-HPFs.Increased growth factor gene expression and significantly activated(P<0.001)Erk and Akt signaling in HPFs originating from A-CTGs implied their involvement in cell survival,proliferation,and motility.Prominent collagen-rich expression profile contributing to high mechanical stability,increased osteogenesis-related gene expression,and strongly activated(P<0.001)Smad1/5/8 signaling characterized HPFs originating from P-CTGs.The present data indicate that in humans,differences between palatal CTGs harvested from different locations and depths appear to be location-rather than depth-dependent.Our findings provide the basis for future personalization of the therapeutic strategy by selecting an optimal graft type depending on the clinical indications.

Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea(Hydrangea macrophylla)and insights into Asterid evolution

The Hydrangea genus belongs to the Hydrangeaceae family,in the Cornales order of flowering plants,which early diverged among the Asterids,and includes several species that are commonly used ornamental plants.Of them,Hydrangea macrophylla is one of the most valuable species in the nursery trade,yet few genomic resources are available for this crop or closely related Asterid species.Two high-quality haplotype-resolved reference genomes of hydrangea cultivars‘Veitchii’and‘Endless Summer’[highest quality at 2.22 gigabase pairs(Gb),396 contigs,N5022.8 megabase pairs(Mb)]were assembled and scaffolded into the expected 18 pseudochromosomes.Utilizing the newly developed high-quality reference genomes along with high-quality genomes of other related flowering plants,nuclear data were found to support a single divergence point in the Asterids clade where both the Cornales and Ericales diverged from the euasterids.Genetic mapping with an F1 hybrid population demonstrated the power of linkage mapping combined with the new genomic resources to identify the gene for inflorescence shape,CYP78A5 located on chromosome 4,and a novel gene,BAM3 located on chromosome 17,for causing double flower.Resources developed in this study will not only help to accelerate hydrangea genetic improvement but also contribute to understanding the largest group of flowering plants,the Asterids.

Farming Features of African Bonytongue Fish Heterotis niloticus in Cameroon, Central Africa

The characterization of African bonytongue Heterotis niloticus fish farming was conducted in the Bi-modal agro-ecological zone of Cameroon from January to May 2021, Thirty-two fish farmers were interviewed and SPSS 6.2 Version was used to analyse the data. The results showed that the majority of fish farmers (81%) are men above 51 years, all of whom are Christians with more than fifty percent of them married. About 43% of them have university level education, and more than 6% of them considered the farming of Heterotis niloticus as their main income-earning activity. The main objective of Heterotis niloticus farming is sales (50%) and the uses (56%) of waged labour. A majority of the farmers produced reared African bonytongue in a polyculture system and 65% of them raised Heterotis niloticus in derivation ponds.

Molecular Identification of Isolated Bacteria from Soils in Likouala Peat Bog Area, Republic of Congo

This study aimed to the molecular identification of isolated bacteria from the soils of Likouala (Congo-Brazzaville) peat bog area. Counting and isolation were carried out on Mossel and TSB media enriched with petroleum and vegetable oil;the amplification and sequencing of 16S RNA genes by PCR and Artic Oxford Nanopore Technology. The results showed bacterial loads of (5.81 ± 1.08) × 104;(6.64 ± 1.94) × 104 et (8.56 ± 1.19) × 103 CFU/g on Mossel respectively for samples 1, 2 and 3 against (2.12 ± 4.1) × 108 et (8.15 ± 10.1) × 107 CFU/g respectively on TSB enriched with petroleum and vegetable oil exclusively with sample 2. The analysis of the 16S rRNA of the isolates gene made it possible, after PCR, agarose gel electrophoresis, sequencing and bioinformatics analysis, to identify eight (08) strains with similarities of 99 to 100% whose sequences genes placed in GenBank have made it possible to obtain accession numbers corresponding to: Bacillus thuringiensis strain (ON303633);Bacillus cereus strain (ON350770);Bacillus thuringiensis strain (ON350771);Bacillus thuringiensis strain (ON738723);Priestia megaterium strain (ON738719);Bacillus anthracis strain (ON738720);Bacillus subtilis (ON738721);Enterobacter sp (ON738722). The phylogenetic classification of strains was done and revealed two genuses which are Bacillus and Enterobacteriaceae.

Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map

Genetic improvement for drought stress tolerance in rice involves the quantitative nature of the trait, which reflects the additive effects of several genetic loci throughout the genome. Yield components and related traits under stressed and well-water conditions were assayed in mapping populations derived from crosses of Azucena×IR64 and Azucena×Bala. To find the candidate rice genes underlying Quantitative Trait Loci (QTL) in these populations, we conducted in silico analysis of a candidate region flanked by the genetic markers RM212 and RM319 on chromosome 1, proximal to the semi-dwarf (sd1) locus. A total of 175 annotated genes were identified from this region. These included 48 genes annotated by functional homology to known genes, 23 pseudogenes, 24 ab initio predicted genes supported by an alignment match to an EST (Expressed sequence tag) of unknown function, and 80 hypothetical genes predicted solely by ab initio means. Among these, 16 candidate genes could potentially be involved in drought stress response.

Quasispecies dynamics in main core epitopes of hepatitis B virus by ultra-deep-pyrosequencing

AIM:To investigate the variability of the main immunodominant motifs of hepatitis B virus(HBV) core gene by ultra-deep-pyrosequencing(UDPS).METHODS:Four samples(2 genotype A and 2 genotype D) from 4 treatment-na ve patients were assessed for baseline variability.Two additional samples from one patient(patient 4,genotype D) were selected for analysis:one sample corresponded to a 36-mo treatment-free period from baseline and the other to the time of viral breakthrough after 18 mo of lamivudine treatment.The HBV region analyzed covered amino acids 40 to 95 of the core gene,and included the two main epitopic regions,Th50-69 and B74-84.UDPS was carried out in the Genome Sequencer FLX system(454 Life Sciences,Roche).After computer filtering of UDPS data based on a Poisson statistical model,122 813 sequences were analyzed.The most conserved position detected by UDPS was analyzed by site-directed mutagenesis and evaluated in cell culture.RESULTS:Positions with highest variability rates were mainly located in the main core epitopes,confirming their role as immune-stimulating regions.In addition,the distribution of variability showed a relationship with HBV genotype.Patient 1(genotype A) presented the lowest variability rates and patient 2(genotype A) had 3 codons with variability higher than 1%.Patient 3 and 4(both genotype D) presented 5 and 8 codons with variability higher than 1%,respectively.The median baseline frequencies showed that genotype A samples had higher variability in epitopic positions than in the other positions analyzed,approaching significance(P = 0.07,sample 1 and P = 0.05,sample 2).In contrast,there were no significant differences in variability between the epitopic and other positions in genotype D cases.Interestingly,patient 1 presented a completely mutated motif from amino acid 64 to 67(E 64 LMT 67),which is commonly recognized by T helper cells.Additionally,the variability observed in all 4 patients was particularly associated with the E 64 LMT 67 motif.Codons 78 and 79 were highly conserved in all samples,in keeping with their involvement in the interaction between the HBV virion capsid and the surface antigens(HBsAg).Of note,codon 76 was even more conserved than codons 78 and 79,suggesting a possible role in HBsAg interactions or even in hepatitis B e antigen conformation.Sequential analysis of samples from patient 4(genotype D) illustrated the dynamism of the HBV quasispecies,with strong selection of one minor baseline variant coinciding with a decrease in core variability during the treatment-free and lamivudinetreated period.The drop in variability seemed to result from a "steady state" situation of the HBV quasispecies after selection of the variant with greatest fitness.CONCLUSION:Host immune pressure seems to be the main cause of HBV core evolution.UDPS analysis is a useful technique for studying viral quasispecies.

Microglia activation,classification and microglia-mediated neuroinflammatory modulators in subarachnoid hemorrhage

Subarachnoid hemorrhage is a devastating disease with significant mortality and morbidity,despite advances in treating cerebral aneurysms.There has been recent progress in the intensive care management and monitoring of patients with subarachnoid hemorrhage,but the results remain unsatisfactory.Microglia,the resident immune cells of the brain,are increasingly recognized as playing a significant role in neurological diseases,including subarachnoid hemorrhage.In early brain injury following subarachnoid hemorrhage,microglial activation and neuroinflammation have been implicated in the development of disease complications and recovery.To understand the disease processes following subarachnoid hemorrhage,it is important to focus on the modulators of microglial activation and the pro-inflammatory/anti-inflammatory cytokines and chemokines.In this review,we summarize research on the modulators of microglia-mediated inflammation in subarachnoid hemorrhage,including transcriptome changes and the neuroinflammatory signaling pathways.We also describe the latest developments in single-cell transcriptomics for microglia and summarize advances that have been made in the transcriptome-based classification of microglia and the implications for microglial activation and neuroinflammation.

Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library

Linked-Read sequencing technology has recently been employed successfully for de novo assembly of human genomes,however,the utility of this technology for complex plant genomes is unproven.We evaluated the technology for this purpose by sequencing the 3.5-gigabase(Gb)diploid pepper(Capsicum annuum)genome with a single Linked-Read library.Plant genomes,including pepper,are characterized by long,highly similar repetitive sequences.Accordingly,significant effort is used to ensure that the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus.With a phased assembly approach,we targeted a heterozygous F1 derived from a wide cross to assess the ability to derive both haplotypes and characterize a pungency gene with a large insertion/deletion.The Supernova software generated a highly ordered,more contiguous sequence assembly than all currently available C.annuum reference genomes.Over 83%of the final assembly was anchored and oriented using four publicly available de novo linkage maps.A comparison of the annotation of conserved eukaryotic genes indicated the completeness of assembly.The validity of the phased assembly is further demonstrated with the complete recovery of both 2.5-Kb insertion/deletion haplotypes of the PUN1 locus in the F1 sample that represents pungent and nonpungent peppers,as well as nearly full recovery of the BUSCO2 gene set within each of the two haplotypes.The most contiguous pepper genome assembly to date has been generated which demonstrates that Linked-Read library technology provides a tool to de novo assemble complex highly repetitive heterozygous plant genomes.This technology can provide an opportunity to cost-effectively develop high-quality genome assemblies for other complex plants and compare structural and gene differences through accurate haplotype reconstruction.

Long-term survival of patients with stage Ⅱ and Ⅲgastric cancer who underwent gastrectomy with inadequate nodal assessment

BACKGROUND Gastric cancer is an aggressive disease with frequent lymph node(LN)involvement.The NCCN recommends a D2 lymphadenectomy and the harvesting of at least 16 LNs.This threshold has been the subject of great debate,not only for the extent of surgery but also for more appropriate staging.The reclassification of stage IIB through IIIC based on N3b nodal staging in the eighth edition of the American Joint Committee on Cancer(AJCC)staging system highlights the efforts to more accurately discriminate survival expectancy based on nodal number.Furthermore,studies have suggested that pathologic assessment of 30 or more LNs improve prognostic accuracy and is required for proper staging of gastriccancer.AIM To evaluate the long-term survival of advanced gastric cancer patients who deviated from expected survival curves because of inadequate nodal evaluation.METHODS Eligible patients were identified from the Surveillance,Epidemiology,and End Results database.Those with stage II-III gastric cancer were considered for inclusion.Three groups were compared based on the number of analyzed LNs.They were inadequate LN assessment(ILA,<16 LNs),adequate LN assessment(ALA,16-29 LNs),and optimal LN assessment(OLA,≥30 LNs).The main outcomes were overall survival(OS)and cancer-specific survival.Data were analyzed by the Kaplan-Meier product-limit method,log-rank test,hazard risk,and Cox proportional univariate and multivariate models.Propensity score matching(PSM)was used to compare the ALA and OLA groups.RESULTS The analysis included 11607 patients.Most had advanced T stages(T3=48%;T4=42%).The pathological AJCC stage distribution was IIA=22%,IIB=18%,IIIA=26%,IIIB=22%,and IIIC=12%.The overall sample divided by the study objective included ILA(50%),ALA(35%),and OLA(15%).Median OS was 24 mo for the ILA group,29 mo for the ALA group,and 34 mo for the OLA group(P<0.001).Univariate analysis showed that the ALA and OLA groups had better OS than the ILA group[ALA hazard ratio(HR)=0.84,95%confidence interval(CI):0.79-0.88,P<0.001 and OLA HR=0.73,95%CI:0.68-0.79,P<0.001].The OS outcome was confirmed by multivariate analysis(ALA HR=0.68,95%CI:0.64-0.71,P<0.001 and OLA:HR=0.48,95%CI:0.44-0.52,P<0.001).A 1:1 PSM analysis in 3428 patients found that the OLA group had better survival than the ALA group(OS:OLA median=34 mo vs ALA median=26 mo,P<0.001,which was confirmed by univariate analysis(HR=0.81,95%CI:0.75-0.89,P<0.001)and multivariate analysis:(HR=0.71,95%CI:0.65-0.78,P<0.001).CONCLUSION Proper nodal staging is a critical issue in gastric cancer.Assessment of an inadequate number of LNs places patients at high risk of adverse long-term survival outcomes.

Ready to migrate?Reading cellular signs of migration in an epithelial to mesenchymal transition model

The epithelial to mesenchymal transition(EMT)is a cellular program that drives de-differentiation of cells in both physiological and pathological processes.One of the characteristics of cells describing an EMT is the(re)acquisition of a motility capacity that allows them to migrate through the original tissue as well as to other sites in the organism.The molecular mechanisms that control the EMT are rapidly emerging and here we add to the idea that the adaptation required for cells to commit to the EMT includes adjustments of the translation machinery and metabolic pathways to cope with a high demand of extracellular components.

Susceptibility Testing of <i>Mycobacterium frederiksbergense</i>Strains Isolated from Alfalfa Plants against Antibacterial Compounds

Mycobacteria constitute vast population of bacteria that are found in animals, plants and outer environments. Tuberculosis mycobacteria are a group that causes very dangerous diseases for human and animals. Nontuberculous mycobacteria are mainly environmental and are pathogenic in certain circumstances. There are reports of finding mycobacteria in plant tissues, which can be effective to survey in case of different infectious disease issues. In a previous study, we found mycobacteria strains in alfalfa vascular tissues and identified them to species level using 16S rRNA gene sequence analysis, causing some symptoms in plant tissues and aerial parts. As these rapidly growing mycobacteria (RGM) have the potential to cause opportunistic infections in human tissues, one of the most important issues for dealing with these agents is to find the best and most effective drug to treat them. Here, we conducted some assays to investigate the MIC of 7 antibiotics and two antibacterial agents against eight Mycobacterium frederiksbergense alfalfa isolated strains, in order to find the susceptible and resistant ones. We performed susceptibility testing based on broth microdilution method using Mueller hinton broth as the medium used. Results were different among the strains and different resistant and susceptible reactions were observed among different strains against each drug tested, but ethambutol resulted in similar high MIC for all of them. This variability could be attributed to many factors, such as plant tissue composition and developmental stage from which the strains have been isolated, existence and nature of drug targets and other factors such as test conditions and environmental causes. These results can bring us some insights into design and develop new drugs for treating these kinds of organisms, based on the variations in susceptibility reactions and the plant composition effect on them.

Transcriptome response of wheat Norin 10 to long-term elevated CO_2 under high yield field condition

The increasing atmospheric carbon dioxide concentration, caused by fossil fuel combustion and deforestation, plays an important role in plant growth and development. Wheat, as a major staple crop, adapts to climate change by tuning its inherent molecular mechanism, which is not well understood. The present study employed the RNA-Seq method to generate transcriptome profiles of the wheat Norin 10 in response to elevated CO_2 in comparison with ambient CO_2. The 10 895 787 high-quality clean reads of Norin 10 were assembled de novo using Trinity（without a reference genome） resulting in a total of 18 206 candidate transcripts with significant BLAST matches. GO enrichment analysis of Norin 10 at different CO_2 concentrations showed that some functional genes related to plastids, precursor metabolites, and energy, thylakoid and photosynthesis were apparently enriched at elevated CO_2（550 μmol mol^–1） in contrast to that at ambient CO_2（400 μmol mol^–1）; these findings were further confirmed by RT-PCR analysis. The findings demonstrated the specific effects of elevated CO_2 during long-term period in free air CO_2 enrichment（FACE） on transcriptome response of the high yielding wheat variety, Norin 10, which has a large spike.

Multi-omic study to unmask genes involved in prostate cancer development in amulti-case family

Dear Editor,Hereditary prostate cancer(PC)comprises 5%-10%of all PC cases.The increased risk of PC in menwith a family his-tory of the disease is well known and is commonly caused by germline mutations,leading to clinical guidelines men-tioning various genes for identifying high-risk individuals.However,the complex inheritance patterns involvingmul-tiple single nucleotide polymorphisms(SNPs)make it a genetically heterogeneous disease,with genetic testing still in its early stages.

Corrigendum to“Antibiotic Treatment Drives the Diversification of the Human Gut Resistome”[Genomics Proteomics Bioinformatics 17(1)(2019)39-51]

The editors regret there was an error in“Shotgun metagenome library construction and sequencing”section.“The raw sequences can be found in BGID(CRA000815)”should be corrected to“The raw metagenome sequencing data have been deposited in the Genome Sequence Archive at Beijing Institute of Genomics,Chinese Academy of Sciences(GSA:CRA000815),and are publicly accessible at https://bigd.big.ac.cn/gsa/”.The correct section is shown below.The editors would like to apologize for any inconvenience caused.

Transcriptome and Metabolic Profiling Provides Insigh into Betalain Biosynthesis and Evolution in Mirabilis jalapa

Betalains are tyrosine-derived pigments that occur solely in one plant order, the Caryophyllales, where they largely replace the anthocyanins in a mutually exclusive manner. In this study, we conducted multi-species transcriptome and metabolic profiling in Mirabilisjalapa and additional betalain-producing species to identify candidate genes possibly involved in betalain biosynthesis. Among the candidates identified, betalainrelated ytochrome P450 and glucosyltransferase-type genes, which catalyze tyrosine hydroxylation or （hydroxy）cinnamoyl-glucose formation, respectively, were further functionally characterized. We detected the expression of genes in the flavonoid/anthocyanin biosynthetic pathways as well as their metabolite intermediates in betalain-accumulating M. jalapa flowers, and found that the anthocyanin-related gene ANTHOCYANIDIN SYNTHASE （MjANS） is highly expressed in the betalain-accumulating petals. However, it appears that MjANS contains a significant deletion in a region spanning the corresponding enzyme active site. These findings provide novel insights into betalain biosynthesis and a possible explanation for how anthocyanins have been lost in this plant species. Our study also implies a complex, non-uniform history for the loss of anthocyanin production across betalain producers, previously assumed to be strictly due to diminished expression of anthocyanin-related genes.

Antibiotic Treatment Drives the Diversification of the Human Gut Resistome

Despite the documented antibiotic-induced disruption of the gut microbiota, the impact of antibiotic intake on strain-level dynamics, evolution of resistance genes, and factors influencing resistance dissemination potential remains poorly understood. To address this gap we analyzed public metagenomic datasets from 24 antibiotic treated subjects and controls, combined with an in-depth prospective functional study with two subjects investigating the bacterial community dynamics based on cultivation-dependent and independent methods. We observed that shortterm antibiotic treatment shifted and diversified the resistome composition, increased the average copy number of antibiotic resistance genes, and altered the dominant strain genotypes in an individual-specific manner. More than 30% of the resistance genes underwent strong differentiation at the single nucleotide level during antibiotic treatment. We found that the increased potential for horizontal gene transfer, due to antibiotic administration, was ～3-fold stronger in the differentiated resistance genes than the non-differentiated ones. This study highlights how antibiotic treatment has individualized impacts on the resistome and strain level composition, and drives the adaptive evolution of the gut microbiota.

Recent advances in diabetes and microbiota

Diabetes mellitus is a global public health problem that causes great economic and social burdens.Its pathogenesis is complex and unclear.Recently,with considerable attention paid to the interaction between gut microbiota and host,gut microbiota has been found to play an important role in several chronic diseases,including diabetes.