Biochemical, microbiological and technological characteristics of type II sourdoughs produced with lactic acid bacteria single-strains

The interplay between biochemical characteristics and the generation of volatile compounds in 11 type II sourdough fermented by single strains of lactic acid bacteria (LAB) was studied. Samples were collected at 0, 6, 9, 12, 15, 18 and 24h for analyses of microbial growth, pH, titratable acidity and CO2 production. During the first 12h, the LABs entered the stationary phase, and the formation of organic and carboxyl acids, alcohols, and esters were observed. Although acidity is an important characteristic of sourdough, in this work increasing the acetic acid content decreased yeast growth and the CO2 retention capacity of the doughs. The main carbohydrate consumed by autochthonous yeast was influenced by the LAB added (homo-or heterofermentative), as observed by correlation analysis. Maltose and glucose showed a strong and negative correlation with the yeast cell density in the dough fermented by homo and heterofermentative LAB, respectively. Moreover, LAB had an important effect on the aromatic profile, being the alcohols, aldehydes, alkanes, organics acids and esters mainly groups characterized. Altogether, 100 different volatile compounds were identified; however, each dough had a different volatile profile. This study shows, for the first time, the influence of a single strain of LAB on the characteristics of type II sourdough.

Natural Shifts in Endosymbionts' Occurrence and Relative Frequency in Their Ciliate Host Population

The role of bacterial endosymbionts harbored by heterotrophic Paramecium species is complex. Obligate intracellular bacteria supposedly always inflict costs as the host is the only possible provider of resources. However, several experimental studies have shown that paramecia carrying bacterial endosymbionts can benefit from their infection. Here, we address the question which endosymbionts occur in natural paramecia populations isolated from a small lake over a period of 5 years and which factors might explain observed shifts and persistence in the symbionts occurrence. One hundred and nineteen monoclonal strains were investigated and approximately two-third harbored intracellular bacteria. The majority of infected paramecia carried the obligate endosymbiotic “Candidatus Megaira polyxenophila”, followed by Caedimonas varicaedens, and Holospora undulata. The latter was only detected in a single strain. While “Ca. M. polyxenophila” was observed in seven out of 13 samplings, C. varicaedens presence was limited to a single sampling occasion. After the appearance of C. varicaedens, “Ca. M. polyxenophila” prevalence dramatically dropped with some delay but recovered to original levels at the end of our study. Potential mechanisms explaining these observations include differences in infectivity, host range, and impact on host fitness as well as host competitive capacities. Growth experiments revealed fitness advantages for infected paramecia harboring “Ca. M. polyxenophila” as well as C. varicaedens. Furthermore, we showed that cells carrying C. varicaedens gain a competitive advantage from the symbiosis-derived killer trait. Other characteristics like infectivity and overlapping host range were taken into consideration, but the observed temporal persistence of “Ca. M. polyxenophila” is most likely explained by the positive effect this symbiont provides to its host.

Isolation, characterization and S2−-oxidation metabolic pathway of a sulfur-oxidizing strain from a black-odor river in Beijing

A single strain capable of efficient S2−-oxidizing was isolated from a black-odor river in Beijing. The single strain was identified as Stenotrophomonas through the physiology and biochemical characteristics as well as the 16S rRNA sequencing experiment. This strain was named as Stenotrophomonas sp.sp3 (strain sp3). The experimental results showed that for the strain sp3 growth and S2− oxidization, the optimal conditions were as follows: 25 °C of temperature, initial pH 7, 2.5 g/L of initial glucose concentration and 1.00 g/L of initial cell concentration. It was found that there were 31 kinds of sulfur oxidation related genes in the strain sp3 through the whole genomic analysis. The results of the transcriptome analysis suggested that the main metabolic pathway of S2− to SO42− was the paracoccus sulfur oxidation process. The bioconversion processes of S2− to S0, S2− to SO32−, S2O32− to S0 and SO32−, and SO32− to SO42− were controlled by hdrA, cysIJ, tst and sox gene, respectively.

Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

Background Antibiotic growth promoters (AGPs) are commonly used within poultry production to improve feed conversion, bird growth, and reduce morbidity and mortality from clinical and subclinical diseases. Due to the association between AGP usage and rising antimicrobial resistance, the industry has explored new strategies including the use of probiotics and other microbial-based interventions to promote the development of a healthy microbiome in birds and mitigate against infections associated with food safety and food security. While previous studies have largely focused on the ability of probiotics to protect against Clostridium perfringens and Salmonella enterica, much less is known concerning their impact on Campylobacter jejuni, a near commensal of the chicken gut microbiome that nevertheless is a major cause of food poisoning in humans. Results Here we compare the efficacy of four microbial interventions (two single strain probiotics, the bacterium—Pediococcus acidilactici, and the yeast—Saccharomyces cerevisiae boulardii; and two complex, competitive exclusion, consortia—Aviguard and CEL) to bacitracin, a commonly used AGP, to modulate chicken gut microbiota and subsequently impact C. jejuni infection in poultry. Cecal samples were harvested at 30- and 39-days post hatch to assess Campylobacter burden and examine their impact on the gut microbiota. While the different treatments did not significantly decrease C. jejuni burden relative to the untreated controls, both complex consortia resulted in significant decreases relative to treatment with bacitracin. Analysis of 16S rDNA profiles revealed a distinct microbial signature associated with each microbial intervention. For example, treatment with Aviguard and CEL increased the relative abundance of Bacteroidaceae and Rikenellaceae respectively. Furthermore, Aviguard promoted a less complex microbial community compared to other treatments. Conclusions Depending upon the individual needs of the producer, our results illustrate the potential of each microbial interventions to serve flock-specific requirements.

First Detection of Rotavirus C in Asymptomatic Pigs from India with Unexpected Dominance and Characterization of the Structural and Nonstructural Genes

Epidemiological and molecular investigation was conducted on Rotavirus C (RVC), the viral agent documented with rising prevalence rate, disease severity and cross species transmission and large outbreak potential. Fecal specimens of pigs collected from two cities of Maharashtra state, India tested for RVC showed 20.1% detection rate with majority below 3 months of age. No significant difference in detection rates was observed in the specimens collected in 2009 from Northern and in 2013 from Western parts of Maharashtra. The phylogenetic analyses showed presence of the I7 and I10 genotypes of the VP6 gene and representative strains with G1 and E5 genotypes of the VP7 and NSP4 gene respectively. Full genome characterization of a single strain showed presence of G1, P1, I7, R1, C1, M3, A1, N5, T5, E5, H1 genotypes of the VP7, VP4, VP6, VP1, VP2, VP3, NSP1, NSP2, NSP3, NSP4 and NSP5 genes respectively. This is the first evidence of detection of porcine RVC in asymptomatic pigs in India as well as with highest detection rate reported in asymptomatic pigs till date globally. Identification of porcine RVC at two time intervals and two different parts of Maharashtra state indicates the possibility of continuous circulation of RVC in pig population through asymptomatic infections.

Construction of a potent pan-vaccine based on the evolutionary tendency of SARS-CoV-2 spike protein.

SARS-CoV-2 continued to spread globally along with different variants. Here, we systemically analyzed viral infectivity and immune-resistance of SARS-CoV-2 variants to explore the underlying rationale of viral mutagenesis. We found that the Beta variant harbors both high infectivity and strong immune resistance, while the Delta variant is the most infectious with only a mild immune-escape ability. Remarkably, the Omicron variant is even more immune-resistant than the Beta variant, but its infectivity increases only in Vero E6 cells implying a probable preference for the endocytic pathway. A comprehensive analysis revealed that SARS-CoV-2 spike protein evolved into distinct evolutionary paths of either high infectivity plus low immune resistance or low infectivity plus high immune resistance, resulting in a narrow spectrum of the current single-strain vaccine. In light of these findings and the phylogenetic analysis of 2674 SARS-CoV-2 S-protein sequences, we generated a consensus antigen (S6) taking the most frequent mutations as a pan-vaccine against heterogeneous variants. As compared to the ancestry SWT vaccine with significantly declined neutralizations to emerging variants, the S6 vaccine elicits broadly neutralizing antibodies and full protections to a wide range of variants. Our work highlights the importance and feasibility of a universal vaccine strategy to fight against antigen drift of SARS-CoV-2.

First Report of Penicillium digitatum causing Postharvest rot of Citron Fruit in Kunming, China

Citron (Citrus medica L.) is a perennial evergreen woody tree of Rutaceae family and Genus of Citrus. The citron is cultivated for its economic, medicinal and ornamental values in the south of China. (Yang et al., 2015). The shapes range from spherical to ovate and the sizes range from 3 to 5 kg (Klein et al., 2016). In June 2021, some postharvest citron fruits (Citrus medica var. medica) were found to have decay with a green or greyish mycelium on part or whole citron in 2 farmer’s markets in Kunming city, Yunnan Province (N 25°02′; E 102°42′), southwest China. Initial symptoms appeared as white, brown, and irregular necrotic spots in the pericarp. The lesions enlarged gradually and developed into green, water-soaked areas which extend rapidly. Eventually, the diseased fruits were rotten, soften, and the green spore masses confined to the surface (Fig. 1A). The incidence of this disease in postharvest citron fruits ranges from 15 % to 35 %, which is extremely destructive to the fruit of Rutaceae family plants (Chen et al., 2019). Small pieces (5 mm2) of symptomatic citron fruits were surface disinfected in 75 % ethanol and 0.3 % NaClO for 30 s and 2 min respectively, rinsed with distilled water for three times, blotted dry, placed onto potato dextrose agar (PDA) medium aseptically and incubated in a growth chamber at 25 ± 1 ℃, after 7 days, different colonies grew on PDA plates that were isolated and purified on new PDA medium at 25 ± 1 ℃ for 7 days. Inoculating repeatedly until six single-strain (XY01 to XY06) were obtained, and these isolates were stored in 15 % glycerol at –80 ℃ in a refrigerator in the State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan Agricultural University. The selected pathogens (XY01 to XY06) were inoculated on PDA medium, incubated at 25 ± 1 ℃. After 7 days, colonies of the isolate obverse are olive green, the white margin and greyish-green spores on the surface, and the reverse colorless to cream yellow or pale dull brown. Colonies texture was velutinous, with a special fragrance. The conidia structure was very fragile and break up easily into many cellular elements. Conidiophores were terverticillate, produced by subsurface or aerial hyphae, irregularly branched and composed of short stipes with few metulae and branches that terminate in whorls of three to six phialides, which are often solitary, cylindrical with a short neck. Conidia are hyaline to pale green, smooth-walled, without septate, partially ellipsoidal, or obovate (4.9 to11.9× 4.3 to 8.9 μm). Partial cylindrical (8.2 to 10.5× 2.7 to 5.3 μm), there are some small conidia, which were ellipsoidal or spherical (3.9 to 5.2× 2.7 to 5.2 μm). According to morphological characteristics, the fungus was identified as Penicillium digitatum (Pers.) Sacc. Isolate XY01 and XY02 were used for molecular identification and genomic DNA was extracted using the CTAB method (Aboul-Maaty & Oraby, 2019). The universal primers ITS1 and ITS4 were used to amplify and sequence the ITS1, 5.8S, and ITS2 rDNA region. Using NCBI’s BLASTn tools, the nucleotide sequences of XY01 and XY02 (Gen-Bank accessions MZ976843 and OK513274) show 100 % identity to MK450692 (P. digitatum strain CMV010G4). Pathogenicity tests have used the fruits (Citrus medica), which maturity was more than 80%. The pathogens (XY01, XY02) were cultured for 7 days on PDA medium, washed with sterilized water the resulting spore suspensions diluted to 1.0 × 106 spores/ml. Wounds (0.5 × 0.5 cm) were made on the surface of citron fruits by scraping with a sterile scalpel and then treated with 200 µl of spore suspension (Wild, 1994). Control citron fruits were treated with sterile water. citron fruits were incubated at 24-26 °C. Each treatment was performed in triplicate with 6 citron fruits. After 3 days, all fruits had developed lesions, in a water-stained, pale brown, and rapidly formed white hyphae, white mold layer was observed with a length of 1.5-2.5 cm and a width of 1-2 cm (Fig.1C), but control did induce infection. After 7 days, decay developed more quickly, the hyphae rapidly expanded on the surface of the pericarp, with vague and irregular edges, then a green mold layer was formed, the whole fruit was observed to rot and soften, When the citron was cut, the white flesh inside turned black and rotted (Fig.1B). P. digitatum was consistently reisolated from the inoculated plants but not from the controls. No symptoms developed on the control (Fig.1D). According to Koch’s postulates, the inoculated strains of XY01 and XY02 were the isolates causing citron decay disease. Based on symptoms, morphological characteristics, rDNA-ITS sequence analysis, and pathogenicity, this fungus was identified as P. digitatum. To our knowledge, this is the first report of the distribution of P. digitatum on Citron (Citrus medica) in China.

Genotypic and phenotypic portrait of Candida albicans clinical isolates colonizing the airways of patients with cystic fibrosis

Candida albicans colonizes the respiratory tract of patients with Cystic Fibrosis (CF). It competes with CF-associated pathogens, such as Pseudomonas aeruginosa and Staphylococcus aureus, and contributes to disease severity. We serially recovered 160 C. albicans clinical isolates over a period of 30 months from the sputum of 23 pediatric and 2 adult antifungal-naive CF patients at Children’s Hospital Tunis and characterized the genotype and phenotype of a subset of strains using multilocus sequence typing (MLST) and growth assays on multiple stress-, filamentous growth- and biofilm-inducing media. Out of 16 patients regularly sampled for at least 9 months, 8 and 4 were chronically and transiently colonized with C. albicans, respectively. MLST analyses of 56 strains originating from 15 patients indicated that each patient was colonized with a single strain, while 8 patients (53%) carried isolates from clade 4 known to be enriched with strains from Middle East-Africa. A subset of these isolates with the same sequence type and colonizing 3 unrelated patients displayed altered susceptibility to cell wall-perturbing agents, suggesting changes in cell wall structure/function during growth in the CF lung. We also observed differential ability to filament and/or form biofilms in a set of identical isolates from clade 10 sampled over a period of 9 months in a pediatric CF patient, suggesting alterations in phenotypes associated with virulence. Our findings will rely on future whole-genome sequencing analyses to identify polymorphisms that could explain the emergence of new traits in C. albicans strains thriving in the CF host environment.

Acidovorax pan-genome reveals specific functional traits for plant beneficial and pathogenic plant-associations

Beta-proteobacteria belonging to the genus Acidovorax have been described from various environments. Many strains can interact with a range of hosts, including humans and plants, forming neutral, beneficial or detrimental associations. In the frame of this study, we investigated the genomic properties of 52 bacterial strains of the genus Acidovorax , isolated from healthy roots of Lotus japonicus, with the intent of identifying traits important for effective plant-growth promotion. Based on single-strain inoculation bioassays with L. japonicus, performed in a gnotobiotic system, we distinguished seven robust plant-growth promoting strains from strains with no significant effects on plant-growth. We showed that the genomes of the two groups differed prominently in protein families linked to sensing and transport of organic acids, production of phytohormones, as well as resistance and production of compounds with antimicrobial properties. In a second step, we compared the genomes of the tested isolates with those of plant pathogens and free-living strains of the genus Acidovorax sourced from public repositories. Our pan-genomics comparison revealed features correlated with commensal and pathogenic lifestyle. We showed that commensals and pathogens differ mostly in their ability to use plant-derived lipids and in the type of secretion-systems being present. Most free-living Acidovorax strains did not harbour any secretion-systems. Overall, our data indicate that Acidovorax strains undergo extensive adaptations to their particular lifestyle by horizontal uptake of novel genetic information and loss of unnecessary genes.

Dietary Probiotic Pediococcus acidilactici MA18/5M Improves the Growth, Feed Performance and Antioxidant Status of Penaeid Shrimp Litopenaeus stylirostris: A Growth-Ration-Size Approach

Probiotics are increasingly documented to confer health and performance benefits across farmed animals. The aim of this study was to assess the effect of a constant daily intake of the single-strain probiotic Pedicococcus acidilactici MA18/5M (4 × 108 CFU.day−1.kg−1 shrimp) fed over fixed, restricted ration sizes (1% to 6% biomass.day−1) on the nutritional performance and metabolism of adult penaeid shrimp Litopenaeus stylirostris (initial body-weight, BWi = 10.9 ± 1.8 g). The probiotic significantly increased the relative daily growth rate (RGR) across all ration size s tested (Mean-RGR of 0.45 ± 0.08 and 0.61 ± 0.07% BWi.day−1 for the control and probiotic groups, respectively) and decreased the maintenance ration (Rm) and the optimal ration (Ropt) by 18.6% and 11.3%, respectively. Accordingly, the probiotic group exhibited a significantly higher gross (K1) and net (K2) feed conversion efficiency with average improvement of 35% and 30%, respectively. Enhanced nutritional performances in shrimps that were fed the probiotic P. acidilactici was associated with, in particular, significantly higher α-amylase specific activity (+24.8 ± 5.5% across ration sizes) and a concentration of free-glucose and glycogen in the digestive gland at fixed ration sizes of 3% and below. This suggests that the probiotic effect might reside in a better use of dietary carbohydrates. Interestingly, P. acidilactici intake was also associated with a statistically enhanced total antioxidant status of the digestive gland and haemolymph (+24.4 ± 7.8% and +21.9 ± 8.5%, respectively; p < 0.05). As supported by knowledge in other species, enhanced carbohydrate utilization as a result of P. acidilactici intake may fuel the pentose-phosphate pathway, generating NADPH or directly enhancing OH-radicals scavenging by free glucose, in turn resulting in a decreased level of cellular oxidative stress. In conclusion, the growth-ration method documented a clear contribution of P. acidilactici MA18/5M on growth and feed efficiency of on-growing L. stylirostris that were fed fixed restricted rations under ideal laboratory conditions. The effect of the probiotic on α-amylase activity and carbohydrate metabolism and its link to the shrimp’s antioxidant status raises interesting prospects to optimize dietary formulations and helping to sustain the biological and economic efficiency of the penaeid shrimp-farming industry.