Comparative 16S rRNA Sequence Research Articles

Molecular characterization of ‘Candidatus Phytoplasma australasiaticum’ associated with ornamentals, amaranthus, French bean and sunhemp crops and development of rapid LAMP assay for detection

Phytoplasma is one of the most economically important pathogens, causing significant yield losses in many crops worldwide. During a survey in Bengaluru rural and Chikkabalpura areas of Karnataka, India, a total of 33 symptomatic plant samples including ornamentals, amaranthus, french bean, and sunhemp displaying phytoplasma symptoms were collected and confirmed as infected with phytoplasma through PCR targeting the 16S rRNA and secY genes. Pairwise sequence comparison and phylogenetic analysis of 16S rRNA and secY gene sequences confirmed the presence of ‘Candidatus Phytoplasma australasiaticum’ in antirrhinum, chrysanthemum, china aster, dianthus, amaranthus, french bean, and sunhemp. In-silico restriction fragment length polymorphism (RFLP) analysis indicated that phytoplasma strains infecting Antirrhinum, China aster, Dianthus, French bean, and Sunhemp represented distinct variants within the 16SrII phytoplasma group, with a threshold similarity coefficient of less than 0.98. A loop-mediated isothermal amplification (LAMP) assay was developed for detecting phytoplasma strains infecting the four ornamentals and other studied crops, targeting the phytoplasma 16S rRNA gene sequence with detection in 60 min. The comparative testing of LAMP products using various nucleic acid dyes and a colorimetric dye (hydroxy naphthol blue) confirmed the presence of phytoplasmas in symptomatic samples. This LAMP assay offers superior ease of use, cost-effectiveness, and rapid results for detecting phytoplasmas in symptomatic plants.

Analysis of Human Milk Microbiota in Northern Greece by Comparative 16S rRNA Sequencing vs. Local Dairy Animals.

Milk is a biological fluid with a dynamic composition of micronutrients and bioactive molecules that serves as a vital nutrient source for infants. Milk composition is affected by multiple factors, including genetics, geographical location, environmental conditions, lactation phase, and maternal nutrition, and plays a key role in dictating its microbiome. This study addresses a less-explored aspect, comparing the microbial communities in human breast milk with those in mature milk from species that are used for milk consumption. Since mature animal milk is used as a supplement for both the infant (formula) and the child/adolescent, our main aim was to identify shared microbial communities in colostrum and mature human milk. Using 16S rRNA metagenomic sequencing, we focused on characterizing the milk microbiota in the Northern Greek population by identifying shared microbial communities across samples and comparing the relative abundance of prevalent genera. We analyzed ten human milk samples (from five mothers), with five collected three days postpartum (colostrum) and five collected thirty to forty days postpartum (mature milk) from corresponding mothers. To perform an interspecies comparison of human milk microbiota, we analyzed five goat and five bovine milk samples from a local dairy industry, collected fifty to seventy days after birth. Alpha diversity analysis indicated moderate diversity and stability in bovine milk, high richness in goat milk, and constrained diversity in breast milk. Beta diversity analysis revealed significant distinctions among mammalian species, emphasizing both presence/absence and abundance-based clustering. Despite noticeable differences, shared microbial components underscore fundamental aspects across all mammalian species, highlighting the presence of a core microbiota predominantly comprising the Proteobacteria, Firmicutes, and Actinobacteriota phyla. At the genus level, Acinetobacter, Gemella, and Sphingobium exhibit significant higher abundance in human milk compared to bovine and goat milk, while Pseudomonas and Atopostipes are more prevalent in animal milk. Our comparative analysis revealed differences and commonalities in the microbial communities of various mammalian milks and unraveled the existence of a common fundamental milk core microbiome. We thus revealed both species-specific and conserved microbial communities in human, bovine, and goat milk. The existence of a common core microbiome with conserved differences between colostrum and mature human milk underscores fundamental similarities in the microbiota of milk across mammalian species, which could offer valuable implications for optimizing the nutritional quality and safety of dairy products as well as supplements for infant health.

Porphyromonas levii – A Boon for Periodontists?

ABSTRACT The majority of species previously categorized as Bacteroides have been reassigned into new genera. Bacteroides levii (Holdeman, Cato, and Mooretaxonomic)’s status has remained uncertain. This species shares a high degree of similarity with members of the genus Porphyromonas based on biochemical, chemical, and comparative 16s rRNA sequence analysis. As a result, Bacteroides levii (Holdeman, Cato, and Moore) was reclassified as Porphyromonas levii comb. now under the genus Porphyromonas.

Identification of safe putative probiotics from various food products.

The objective of this study was to isolate, identify, and assess the safety and functionality in vitro of putative probiotic bacterial strains. Isolation procedures were based on standard methods using elective and selective media. The isolates were identified by comparative 16S rRNA sequencing analysis while their safety was determined according to the safety tests recommended by the FAO/WHO such as antibiotic resistance, hemolysin, and biogenic amine production. Most of the isolates did not pass the in vitro safety tests; therefore, only Lactiplantibacillus plantarum (from ant intestine and cheese), Lacticaseibacillus paracasei (from goat milk and kimchi), Enterococcus faecium (from chili doenjang and vegetables with kimchi ingredients), Limosilactobacillus fermentum (from saliva), and Companilactobacillus alimentarius (from kimchi) were identified and selected for further studies. The isolates were further differentiated by rep-PCR and identified to the strain level by genotypic (16S rRNA) and phenotypic (Gen III) approaches. Subsequently, the strain tolerance to acid and bile was evaluated resulting in good viability after simulated gastrointestinal tract passage. Adhesion to mucin in vitro and the presence of mub, mapA, and ef-tu genes confirmed the adhesive potential of the strains and the results of features associated with adhesion such as hydrophobicity and zeta potential extended the insights. This study reflects the importance of fermented and non-fermented food products as a promising source of lactic acid bacteria with potential probiotic properties. Additionally, it aims to highlight the challenges associated with the selection of safe strains, which often fail in the in vitro tests, thus hindering the possibilities of "uncovering" novel and safe probiotic strains.

Spirochaete genome identified in red abalone sample represents a novel genus Candidatus Haliotispira gen. nov. within the order Spirochaetales.

A fully assembled spirochaete genome was identified as a contaminating scaffold in our red abalone (Haliotis rufescens) genome assembly. In this paper, we describe the analysis of this bacterial genome. The assembled spirochaete genome is 3.25 Mb in size with 48.5 mol% G+C content. The proteomes of 38 species were compared with the spirochaete genome and it was discovered to form an independent branch within the family Spirochaetaceae on the phylogenetic tree. The comparison of 16S rRNA sequences and average nucleotide identity scores between the spirochaete genome with known species of different families in Spirochaetia indicate that it is an unknown species. Further, the percentage of conserved proteins compared to neighbouring taxa confirm that it does not belong to a known genus within Spirochaetaceae. We propose the name Candidatus Haliotispira prima gen. nov., sp. nov. based on its taxonomic placement and origin. We also tested for the presence of this species in different species of abalone and found that it is also present in white abalone (Haliotis sorenseni). In addition, we highlight the need for better classification of taxa within the class Spirochaetia.

Arcanobacterium buesumense sp. nov., isolated from an anal swab of a male harbour seal (Phoca vitulina).

A polyphasic taxonomic study was performed on an unidentified previously described Arcanobacterium-like Gram-positive strain 2701T isolated from an anal swab of a dead male harbour seal. Comparative 16S rRNA sequencing showed that the bacterium belonged to the genus Arcanobacterium in the family Arcanobacteriaceae. The genome sequence of the strain was obtained by Borowiak et al. [1]. The genome had a G+C content of 49 mol% and a total length of 1.94 Mb. The presence of the major menaquinone MK-9(H4) supported the affiliation of the isolate with the genus Arcanobacterium. The polar lipid profile consisted of diphosphatidylglycerol and an unidentified phospholipid as major components and two unidentified lipids, a further unidentified phospholipid, two unidentified phosphoglycolipids as well as phosphatidylglycerol. The major fatty acids were C16 : 0, C18 : 1 and C18 : 0. Biochemical and phylogenetic analyses clearly distinguished the isolate from other members of the genus Arcanobacterium and closely related other species. Based on these results, it is proposed that the unknown Arcanobacterium sp. strain 2701T should be classified as representing a novel species with the name Arcanobacterium buesumense sp. nov. The type strain is 2701T (=DSM 112952T=LMG 32446T).

Dysbiosis in the Rhizosphere Microbiome of Standing Dead Korean Fir (Abies koreana).

The Korean fir (Abies koreana), a native coniferous tree species mainly found on Mt. Halla in Jeju, South Korea, is suffering from continuous population decline and has been declared an endangered species. Research efforts have focused on the possible abiotic causes behind this worrying decline. However, the potential link between tree vitality and the rhizosphere microbiome remains unclear. In this study, a comparative metagenomic 16S rRNA sequence analysis was used to investigate the composition of the rhizosphere microbiota of samples collected from healthy and die-back-affected trees on Mt. Halla. The results indicated a significant reduction in the richness and diversity of microbiota in the rhizosphere of die-back-affected trees. Moreover, the relative abundance of Proteobacteria, Actinobacteria, and Bacteroidetes were significantly higher in healthy trees than in standing dead trees. Many bacterial genera were significantly more abundant in the rhizosphere of healthy trees, including those known for promoting plant growth and tolerance to biotic and abiotic stresses (e.g., Bradyrhizobium, Rhizomicrobium, Caulobacter, Nitrosospira, Rhizobacter, Paraburkholderia, Rhizobium, Devosia, Caballeronia, Niveispirillum, Dyella, Herbaspirillum, Frankia, Streptomyces, Actinoallomurus, Lysobacter, Luteibacter, Mucilaginibacter, and Variovorax). To our knowledge, this is the first report on rhizosphere bacterial microbiome dysbiosis in die-back-affected Korean fir trees, suggesting that the influence of rhizosphere microbiota should be considered to save this endangered species by investigating possible intervention strategies in future work.

Antibiotic Resistance Patterns of Coagulase-Negative Staphylococcus (CoNS) Isolates from a Major Teaching Hospital in Kuala Lumpur, Malaysia

Coagulase-negative Staphylococcus (CoNS) species is a leading cause of nosocomial infection in patients with indwelling medical devices and immunocompromised patients. This study was conducted to determine the antibiotic resistance pattern of CoNS isolated from a major teaching hospital in Malaysia. A total of 43 CoNS isolates were collected from August to October 2018 at Hospital Canselor Tuanku Muhriz, Kuala Lumpur, Malaysia. Speciation of CoNS species was conducted by 16S rRNA sequencing. Antibiotic susceptibility test was performed using a standard procedure, and detection of staphylococcal cassette chromosome mec (SCCmec) elements and antibiotic resistance genes were conducted via multiplex polymerase chain reaction (PCR). Comparison of 16S rRNA sequences showed that 67.44% of the isolates were identified as S. epidermidis, followed by S. haemolyticus (11.63%), S. hominis (9.3%), S. capitis (4.65%), and other Staphylococcus sp. (6.98%). All the CoNS isolates were susceptible to linezolid and tedizolid, while most of them were resistant towards penicillin (86.05%), cefoxitin (69.77%), erythromycin (72.02%), and 88.37% of them were resistant to at least 3 antibiotics. The majority of CoNS harboured nontypeable SCCmec elements. AacA-D (95.5%) and ermC (78.6%) were the most commonly detected antibiotic resistance genes while no detection of tetK, tetM and ermA genes were observed. This study showed a high prevalence of multidrug-resistant CoNS in HCTM healthcare settings. Understanding CoNS resistance mechanism is warranted for intervention strategy.

Isolation and Molecular Characterization of Camel (Camelus dromedarius) Urine Microbiota and its Response to Different Grazing

Background: Camels' urine has been utilized for therapeutic purposes and anecdotally hailed as a treatment for a variety of ailments for millennia. The purported medicinal effects of camel urine, on the other hand, have yet to be thoroughly investigated and it has not been verified whether it is free of bacteria dangerous to human health. The common practice of using camel urine as a therapeutic agent in the Taif region of Saudi Arabia may pose health risks. This study examines the distribution of urine microbiota in camels and effect of the type of nutrition on microbiota. Material and methods: Therefore, 80 camel urine samples were collected from 6 different stations in this region. Urine was collected from healthy male and female (pregnant ,mother ) camels aged 1–8 years .The camels were divided into two groups with a different natural feeding pattern G1:which grazes naturally on wild plants ( wild feeding)&G2: which grazes naturally on wild plants, fodder and barley(mixed feeding). The 16S rRNA gene of the bacteria will be sequenced to the identify of bacteria isolated from camel urine. Finding a relationship between the urine microbiota and the mode of nutrition by profiling the bacterial species in both groups. Results: 16S rRNA gene sequence analysis showed that most of the isolates were Bacillus velezensis and Bacillus tropicus, constituting 42 % and 15 % of the samples, respectively. Surprisingly, these bacterial species have an antimicrobial effect. This may explain the role of camel urine as an antimicrobial. The comparative 16SrRNA Sequencing revealed significant differences in the urine microbiota between the two groups. This indicates the effect of the camel's diet on the microbiota of camel urine.

Seawater dilution desalination with hybrid FO-RO and UF-RO: Characterisation and assessment of pathogen removal efficacy

This study investigated the feasibility of embedding two low-energy dilution desalination processes, namely osmotic dilution desalination (ODD; the FO-RO membrane configuration) and mixing dilution desalination (MDD; the UF-RO membrane configuration), in a conventional seawater desalination approach (i.e., seawater reverse osmosis) using real seawater and recycled wastewater. The removal efficacy of bacterial indicators (Clostridium perfringens and Escherichia coli), coliphage genera Microviradae, and Human adenovirus (HAdV) was assessed in influent/effluent samples collected from each membrane configuration. Mixing dilution of the influent feed waters reduced the number of all pathogenic contaminants as well as organic/inorganic compounds. The rejection rate of total suspended solids was 35.7% in FO to 63.6% in UF respectively, whereas that of total organic carbon was 53.8% and 56.9% in FO and UF, respectively. The FO membrane in the ODD process more efficiently removed viruses (5.0 LRV) and bacterial indicators (4.2 LRV) than the UF membrane (3.7 and 3.6 LRV, respectively). Nevertheless, the different methods of detection used in our study, such as culture-based and qPCR, were found to have significant influences on the LRVs. Comparative 16S rRNA sequencing indicated that the vast majority of bacterial indicators in RO permeating from the FO-RO and UF-RO configurations were nonpathogenic strains.

Proteolytic Processing, Maturation, and Unique Synteny of Streptomyces Hemagglutinin, SHA

Blood-type B specific hemagglutinin (L-rham/D-gal-specific lectin) secreted by Streptomyces sp. 27S5 (SHA) was purified over 40 years ago. Despite the loss of the original strain and the lack of genomic information, the amino acid sequence of its SHA was recently determined based on peptides matching to a hypothetical protein of S. lavendulae, differing only by a single amino acid, A108E (J Biol Chem 293:368, 2018). Recombinant SHA (rSHA A108E) exhibited binding to L-rham on Lactobacillus casei (Shirota) and blood type B-specificity, supporting the notion that rSHA A108E is equivalent to the authentic SHA. To address questions how SHA was biosynthesized and secreted by the lost strain as well as what biological roles SHA may have, we needed to identify SHA-secreting S. strains that are identical to or at least comparable to the lost strain. We took advantage of the IMC's collection of over 40,000 actinomycete strains. Out of 5,000 strains with available 16S rRNA gene signatures, 67 strains shared significant 16S rRNA sequence homology with S. lavendulae, and were examined. We found that 17 S. lavendulae-related strains secreted SHA homologues in cultures. Seven SHA homologues were purified to homogeneity by gum arabic affinity chromatography. All homologues were secreted as pro-SHA proteins having larger masses than archived SHA. Proteolytic processing of the pro-SHAs occurred during and after purification, which indicated that associated proteases apparently converted pro-SHAs into mature SHAs with molecular masses similar to that of the archived SHA. Pro-SHAs did not exhibit hemagglutination (HA) activity, but bound to gum arabic gels, suggesting that pro-SHAs have one active glycan binding site. The processed SHA proteins appear to possess specific HA activities equivalent to that of the archived SHA. Comparison of strain-specific 16S rRNA and SHA sequences revealed phylogenetic inconsistencies, which cannot be explained by the deletion and horizontal transmission repeated in this phylogenic group alone. Genome analysis of 1,234 Streptomyces strains from the database resulted in the discovery of 18 strains encoding SHA genes. Of those, 15 strains were newly identified and 16 strains revealed a unique syntenic region which encodes the SHA gene, supporting limited propagation of SHA in the course of evolution. In short, we succeeded in purifying SHA homologues from seven strains. The lost strain Streptomyces sp. 27S5, however, was exceptional, because it expressed and secreted a processed form of SHA protein at levels that were at least 4 times higher than those of the two best-SHA homologue-producing strains. Apart from structural and functional studies on homologous SHA proteins, this study led to an intriguing discovery, i.e., the identification of SHA gene in syntenic regions. It is plausible that SHA would play a role in the unknown function achieved by the ensemble of accompanying genes in synteny.

Prevotella hominis sp. nov., isolated from human faeces.

A strictly anaerobic predominant bacterium, designated as strain gm001T, was isolated from a freshly voided faecal sample collected from a healthy Taiwanese adult. Cells were Gram-stain-negative rods, non-motile and non-spore-forming. Strain gm001T was identified as a member of the genus Prevotella, and a comparison of 16S rRNA and hsp60 gene sequences revealed sequence similarities of 98.5 and 93.3 %, respectively, demonstrating that it was most closely related to the type strain of Prevotella copri. Phylogenomic tree analysis indicated that the gm001T cluster is an independent lineage of P. copri DSM 18205T. The average nucleotide identity, digital DNA‒DNA hybridization and average amino acid identity values between strain gm001T and P. copri DSM 18205T were 80.9, 28.6 and 83.8 %, respectively, which were clearly lower than the species delineation thresholds. The species-specific genes of this novel species were also identified on the basis of pan-genomic analysis. The predominant menaquinones were MK-11 and MK-12, and the predominant fatty acids were anteiso-C15 : 0, C15 : 0 and iso-C15 : 0. Acetate and succinate were produced from glucose as metabolic end products. Taken together, the results indicate that strain gm001T represents a novel species of the genus Prevotella, for which the name Prevotella hominis sp. nov. is proposed. The type strain is gm001T (=BCRC 81118T=JCM 33280T).

Identification of phytoplasmas in 16SrI-D subgroup in mango with malformation and witches’ broom disease in Punjab, India

Symptoms of mango malformation and witches’ broom were observed in mango orchards at Ludhiana, Punjab, India during 2020. Phytoplasmas were detected in the symptomatic mango samples by polymerase chain reaction with specific primer pairs amplifying 16S rRNA and secA genes. Pair wise sequence comparison and phylogenetic analysis of 16S rRNA and secA gene sequences of mango phytoplasma strains indicate their relatedness with phytoplasmas in the aster yellows group. In silico RFLP analyses using the iPhy Classifier of the 16S rDNA sequence of the mango phytoplasma allowed its classification into the 16SrI-D subgroup. This is first report of this phytoplasma in mango plants showing a malformation and witches’ broom disease.

A new species of Zhangixalus (Anura: Rhacophoridae), previously confused with Zhangixalus smaragdinus (Blyth, 1852).

We describe a new species of Zhangixalus from southern Yunnan of China, Vietnam, and Thailand based on morphological and molecular evidence. The new species had been confused with Zhangixalus smaragdinus (Blyth, 1852) in the past. Zhangixalus pachyproctus sp. nov. can be distinguished from Z. smaragdinus morphologically by the protruding vent in adult males, large thick grey reticular mottles below the white stripe on flank, more oblique snout in profile and wider head, longer snout, greater internarial distance, larger tympanum and longer hindlimb. The new species can be distinguished from other species of Zhangixalus with green dorsum by the following combination of characters: body size larger (SVL of adult males: 74.2-83.3 mm; SVL of adult female: 102.4 mm); dorsum smooth; narrow white stripes along edge of the lower jaw, body sides, outer side of limbs and above the vent; absence of brown bands on canthus rostralis, upper eyelid and supratympanic fold; webbing between fingers and toes complete except between the first two fingers; and internal single subgular vocal sac. Phylogeny based on comparison of 16S rRNA sequences suggests that the new species is the sister taxon to Z. smaragdinus and the two species differ by 7.63% in the uncorrected pairwise distance of 16S sequences.

Characterization of rhizosphere and endophytic bacteria from roots of maize (Zea mays L.) plant irrigated with wastewater with biotechnological potential in agriculture

The aim of this study was to characterize culturable rhizosphere and endophytic bacterial isolates isolated from rhizosphere soil and roots of maize plant irrigated with industrial and municipal wastewater in terms of resistance to heavy metals and salinity and plant growth promoting (PGP) traits. Results illustrated that both rhizosphere isolates and endophytic ones had various PGP characteristics in terms of both the number and the production amount of these characteristics. A substantial number of the bacterial isolates (both endophytic isolates and rhizosphere isolates) were tolerant to heavy metals (multi-metal resistant bacteria). Compared to endophytic isolates, rhizosphere isolates had greater resistance to heavy metals. Both endophytic isolates and rhizosphere ones showed remarkable resistance to salinity (7% NaCl). Based on comparison of 16S rRNA sequences and biochemical tests, the effective isolates, based on having multiple PGP characteristics and higher resistance to heavy metals and salinity, were identified. Isolates N5 and R7 were closely related to Bacillus cereus and Enterobacter cloacae, respectively. In addition, the ability of rhizosphere strain R7, as a multi-metal resistant bacterium, in the removal of cadmium (Cd) and lead (Pb) by its biomass and colonization of maize roots in the presence of these metals was evaluated. This strain could remove these metals from the solution (46.5–88.95%) and colonize both root surface and inside root of maize (4–7 Log10 CFU (colony–forming unit) g−1 fresh root weight) under heavy metal stress. Therefore, it can be concluded that maize plant irrigated with industrial and municipal wastewater harbors salinity and heavy metals–resistant bacteria and may be potential reservoirs for isolating bacteria effective at alleviating heavy metal stress in the plant, reducing accumulation of heavy metals in crops such as maize, and removing heavy metals in aqueous media (bioremediation of heavy metal-contaminated wastewater system).

Whole Genome Sequence of Marinobacter salarius Strain SMR5, Shown to Promote Growth in its Diatom Host.

Attempts to obtain axenic cultures of the marine diatom Skeletonema marinoi often result in poor growth, indicating the importance of the microbiome to the growth of its host. In order to identify the precise roles played by these associated bacteria, individual strains were isolated, cultured and sequenced. We report the genome of one such strain - SMR5, isolated from a culture of S. marinoi strain R05AC sampled from top layer sediments of the Swedish west coast. Its genome of 4,630,160 bp consists of a circular chromosome and one circular plasmid, and 4,263 CDSs were inferred in the annotation. Comparison of 16S rRNA sequences and other markers, along with phylotaxonomic analysis, leads us to place strain SMR5 in the taxon Marinobacter salarius. Pathway analysis and previous experimental work suggest that this strain may produce a growth factor, as well as improve iron availability for its host via siderophores.

Streptococcus gallolyticus conspires myeloid cells to promote tumorigenesis of inflammatory bowel disease

Metagenomic analyses indicate that streptococcus gallolyticus is enriched at carcinoma in colitis associated colorectal cancer compared with sporadic colorectal cancer. But the particular mechanism of streptococcus gallolyticus in Inflammatory Bowel Disease malignant progression remains undefined yet. We aim to explore the biological carcinogenesis efficacy of streptococcus gallolyticus and its potential mechanism in azoxymethane and dextran sodium sulphate-induced colitis associated colorectal cancer in mice. Oral pretreatment of streptococcus gallolyticus was adopted to evaluate its detrimental effect. The colorectums of experimental C57BL/6 mice were collected and examined for the degree of tumorigenesis. Comparative 16S rRNA sequencing was carried out to observe streptococcus gallolyticus alterations in abundance. We found that streptococcus gallolyticus are enriched in colonic carcinoma compared to adenoma and healthy mice. Pretreatment of Streptococcus gallolyticus aggravated tumor formation, with more colonic obstruction, larger number and diameter of tumor node. Furthermore, Streptococcus gallolyticus selectively recruits tumor-infiltrating myeloid cells but not mast cells, including marrow-derived suppressor cells, tumor-associated macrophages and dendritic cells, which can inhibit competence of T cells. Moreover, several myeloid-cell-derived proinflammatory cytokines (IL-6, IL-1β, IL-8, CCL2, COX-2, TNF-α) were increased with the formation of carcinoma in IBD. Collectively, these data suggest that, through recruitment of tumor-infiltrating immune cells, Streptococcus gallolyticus generate an immune suppressive microenvironment that is conducive for neoplasia progression of Inflammatory Bowel Disease.

Pretreatment with probiotic Bifico ameliorates colitis-associated cancer in mice: Transcriptome and gut flora profiling.

Individuals with inflammatory bowel disease are at high risk of developing colitis‐associated cancer (CAC). Strategies to block the process from inflammatory bowel disease to CAC should be considered. In the experiment, we aim to explore the chemopreventive efficacy of the probiotic cocktail Bifico and its potential mechanism in azoxymethane and dextran sodium sulphate‐induced CAC in mice. Oral pretreatment of Bifico was adopted to evaluate its protective effect. The colorectums of 35 C57BL/6 mice were collected and examined for the degree of inflammation and tumorigenesis. Comparative 16S rRNA sequencing was carried out to observe Bifico‐target alterations in gene expression and microbiota structure. We found that pretreatment of Bifico alleviated intestinal inflammation and reduced tumor formation. Furthermore, we identified a subset of genes as potential targets of Bifico treatment, including CXCL1,CXCL2,CXCL3, and CXCL5, which are all ligands of C‐X‐C motif receptor 2 (CXCR2). The 16S rRNA sequencing showed that Bifico decreased the abundance of genera Desulfovibrio, Mucispirillum, and Odoribacter, and a bloom of genus Lactobacillus was detected. Notably, we found that an abundance of these Bifico‐target taxa was significantly associated with the expression of CXCR2 ligand genes. Our studies indicate that Bifico, given orally, can ameliorate CAC in mice through intervening with the possible link between Desulfovibrio, Mucispirillum, Odoribacter, Lactobacillus, and CXCR2 signaling.

The potential contribution of siderophore producing bacteria on growth and Fe ion concentration of sunflower (Helianthus annuus L.) under water stress

ABSTRACTIn the present study, 100 bacterial strains were isolated from the soil and tested for siderophore producing ability. Among siderophore producing bacteria, three superior isolates with the highest level of siderophore (F13, F58 and F66) selected for further study. Production of lecithinase, arginine dehydrolase, catalase, oxidase, hydrogen cyanide, indole acetic acid, solubilization of phosphate, gelatin hydrolysis, oxidative/fermentative, motility and gram staining by these strains was evaluated. In greenhouse experiment, the ability of selected isolates in solubilizing insoluble iron-containing compounds was examined at three moisture levels (0.45–0.6, 0.6–0.7 and 0.7–0.85 field capacity). Results showed that isolates F13 and F66 have greatest effects on chlorophyll amount and shoot dry weight compared to isolate F58. On average, iron concentration of sunflower in the presence of bacteria was 2.85-fold more than control, while it was 1.88-fold for roots. In addition, bacterial treatments enhanced resistance to water stress in sunflower. Based on biochemical tests and by comparison of 16S rRNA sequences, the F13, F58 and F66 isolates were closely related to Pseudomonas spp., Enterobacter spp. and Bacillus Sporothernodurans, respectively.

Isolation and Identification of Halophilic and Halotolerant Bacteria From Badab-e Surt Travertine Spring, Kiasar, Iran, and Investigation of Calcite Biomineralization Induction

ABSTRACTBadab-e Surt spring is a travertine spring that has low to moderate levels of salt, so it is a good model for isolating moderately halophilic bacteria and investigating the relationship between microbe and environment. For isolating bacterial strains, water and sediment samples were collected from different springheads of the Badab-e Surt spring. Among the 171 bacterial isolates, 110 strains were halophiles. According to comparative partial 16S rRNA sequence analysis, the selected halophilic gram-positive and gram-negative strains were identified as members of the genera: Roseovarius, Labrenzia, Erythrobacter, Erythromicrobium, Massilia, Marinobacter, Halomonas, Shewanella, Pseudomonas, Flavobacterium, Bacillus, Brevibacterium, Staphylococcus, Microbacterium, Kocuria, and Streptomyces. To investigate mineralization, potential strains were screened by the culturing method, and then analyzed with a polarizing and scanning microscope. Five strains, Bss-11a, Bss-3, Bsw-1c1, Bsw-28d, and Bsw-39b, had potential for the mineralization of calcite that very closely resembled species Bacillus cohenii DSM 6307T, Labrenzia aggregate IAM 12614T, Bacillus safensis FO-036bT, Marinobacter flavimaris SW-145T, and Marinobater adhaerens HP15T, respectively.