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Abstract Bacillus strains from the Moroccan Coordinated Collections of Microorganisms (CCMM) were characterised and tested for fibrolytic function and safety properties that would be beneficial for maintaining intestinal homeostasis, and recommend beneficial microbes in the field of health promotion research. Forty strains were investigated for their fibrolytic activities towards complex purified polysaccharides and natural fibres representative of dietary fibres (DFs) entering the colon for digestion. We demonstrated hemicellulolytic activities for nine strains of Bacillus aerius , re-identified as Bacillus paralicheniformis and Bacillus licheniformis , using xylan, xyloglucan or lichenan as purified polysaccharides, and orange, apple and carrot natural fibres, with strain- and substrate-dependent production of glycoside hydrolases (GHs). Our combined methods, based on enzymatic assays, secretome, and genome analyses, highlighted the hemicellulolytic activities of B. paralicheniformis and the secretion of specific glycoside hydrolases, in particular xylanases, compared to B. licheniformis . Genomic features of these strains revealed a complete set of GH genes dedicated to the degradation of various polysaccharides from DFs, including cellulose, hemicellulose and pectin, which may confer on the strains the ability to digest a variety of DFs. Preliminary experiments on the safety and immunomodulatory properties of B. paralicheniformis fibrolytic strains were evaluated in light of applications as beneficial microbes' candidates for health improvement. B. paralicheniformis CCMM B969 was therefore proposed as a new fibrolytic beneficial microbe candidate.

Drechmeria coniospora is an obligate fungal pathogen that infects nematodes via the adhesion of specialized spores to the host cuticle. D. coniospora is frequently found associated with Caenorhabditis elegans in environmental samples. It is used in the study of the nematode's response to fungal infection. Full understanding of this bi-partite interaction requires knowledge of the pathogen's genome, analysis of its gene expression program and a capacity for genetic engineering. The acquisition of all three is reported here. A phylogenetic analysis placed D. coniospora close to the truffle parasite Tolypocladium ophioglossoides, and Hirsutella minnesotensis, another nematophagous fungus. Ascomycete nematopathogenicity is polyphyletic; D. coniospora represents a branch that has not been molecularly characterized. A detailed in silico functional analysis, comparing D. coniospora to 11 fungal species, revealed genes and gene families potentially involved in virulence and showed it to be a highly specialized pathogen. A targeted comparison with nematophagous fungi highlighted D. coniospora-specific genes and a core set of genes associated with nematode parasitism. A comparative gene expression analysis of samples from fungal spores and mycelia, and infected C. elegans, gave a molecular view of the different stages of the D. coniospora lifecycle. Transformation of D. coniospora allowed targeted gene knock-out and the production of fungus that expresses fluorescent reporter genes. It also permitted the initial characterisation of a potential fungal counter-defensive strategy, involving interference with a host antimicrobial mechanism. This high-quality annotated genome for D. coniospora gives insights into the evolution and virulence of nematode-destroying fungi. Coupled with genetic transformation, it opens the way for molecular dissection of D. coniospora physiology, and will allow both sides of the interaction between D. coniospora and C. elegans, as well as the evolutionary arms race that exists between pathogen and host, to be studied.

Cadophora malorum Mo12 was isolated from the Rainbow hydrothermal site on the Mid-Atlantic Ridge. We present the draft genome sequence of this filamentous fungal strain, which has high biotechnological potentials as revealed by the presence of genes encoding biotechnologically important enzymes and genes involved in the synthesis of secondary metabolites.

Cryptococcus sp. strain Mo29 was isolated from the Rainbow hydrothermal site on the Mid-Atlantic Ridge. Here, we present the draft genome sequence of this basidiomycetous yeast strain, which has highlighted its biotechnological potential as revealed by the presence of genes involved in the synthesis of secondary metabolites and biotechnologically important enzymes.

Nowadays there is a growing trend towards carotenoids obtained from natural sources such as microalgae. Dunaliella salina is among the most significant natural sources of beta-carotene for commercial scale, which is used in many food industries. Enzymatic extraction of beta-carotene is one of the safe methods that ensure that the food product is not contaminated compared to ex-traction using solvents. In this study, beta-carotene was extracted using two methods: the organic solvent method by tetrahydrofuran and the enzymatic extraction using a bacterial lipase enzyme. The alga was exposed to different stress conditions (salinity/nitrogen) for increasing the beta-carotene production. The highest value of beta-carotene content was recorded in the extraction method using tetrahydrofuran (109.008 µg/mL at 2.5M NaCl/0.5 g/L KNO 3 ), compared to the extraction method using lipase enzyme (19.13 µg/mL at 1 mg/mL at 24 h exposure time). However, the beta-carotene yield slightly increased (21.4 µg/mL) in lipase enzyme extraction method for the algal samples exposed to more than 24 h under different conditions (3M NaCl/1g/L KNO 3 ). The results show that the enzymatic extraction method is less efficient in extracting beta-carotene compared to the tetrahydrofuran solvent extraction method, with the latter showing a higher content of extracted beta-carotene.

ABSTRACT Symbiotic interactions between humans and our communities of resident gut microbes (microbiota) play many roles in health and disease. Some gut bacteria utilize mucus as a nutrient source and can under certain conditions damage the protective barrier it forms, increasing disease susceptibility. We investigated how Ruminococcus torques— a known mucin degrader that has been implicated in inflammatory bowel diseases (IBDs)—degrades mucin glycoproteins or their component O -linked glycans to understand its effects on the availability of mucin-derived nutrients for other bacteria. We found that R. torques utilizes both mucin glycoproteins and released oligosaccharides from gastric and colonic mucins, degrading these substrates with a panoply of mostly constitutively expressed, secreted enzymes. Investigation of mucin oligosaccharide degradation by R. torques revealed strong α-L-fucosidase, sialidase and β1,4-galactosidase activities. There was a lack of detectable sulfatase and weak β1,3-galactosidase degradation, resulting in accumulation of glycans containing these structures on mucin polypeptides. While the Gram-negative symbiont, Bacteroides thetaiotaomicron grows poorly on mucin glycoproteins, we demonstrate a clear ability of R. torques to liberate products from mucins, making them accessible to B. thetaiotaomicron . This work underscores the diversity of mucin-degrading mechanisms in different bacterial species and the probability that some species are contingent on others for the ability to more fully access mucin-derived nutrients. The ability of R. torques to directly degrade a variety of mucin and mucin glycan structures and unlock released glycans for other species suggests that it is a keystone mucin degrader, which might contribute to its association with IBD. IMPORTANCE An important facet of maintaining healthy symbiosis between host and intestinal microbes is the mucus layer, the first defense protecting the epithelium from lumenal bacteria. Some gut bacteria degrade the various components of intestinal mucins, but detailed mechanisms used by different species are still emerging. It is imperative to understand these mechanisms as they likely dictate interspecies interactions and may illuminate species associated with bacterial mucus damage and subsequent disease susceptibility. Ruminococcus torques is positively associated with IBD in multiple studies. We identified mucin glycan-degrading enzymes in R. torques and found that it shares mucin degradation products with another species of gut bacteria, Bacteroides thetaiotaomicron . Our findings underscore the importance of understanding mucin degradation mechanisms in different gut bacteria and their consequences on interspecies interactions, which may identify keystone bacteria that disproportionately affect mucus damage and could therefore be key players in effects that result from reductions in mucus integrity.

Summary The ectomycorrhizal (ECM) symbiosis has independently evolved from diverse types of saprotrophic ancestors. In this study, we seek to identify genomic signatures of the transition to the ECM habit within the hyper-diverse Russulaceae. We present comparative analyses of the genomic architecture and the total and secreted gene repertoires of 18 species across the order Russulales of which 13 are newly sequenced, including a representative of a saprotrophic member of Russulaceae, Gloeopeniophorella convolvens. The genomes of ECM Russulaceae are characterized by a loss of genes for plant cell-wall degrading enzymes (PCWDEs), an expansion of genome size through increased transposable element (TE) content, a reduction in secondary metabolism clusters, and an association of small secreted proteins (SSPs) with TE “nests”, or dense aggregations of TEs. Some PCWDEs have been retained or even expanded, mostly in a species-specific manner. The genome of Gloeopeniophorella convolvens possesses some characteristics of ECM genomes (e.g., loss of some PCWDEs, TE expansion, reduction in secondary metabolism clusters). Functional specialization in ectomycorrhizal decomposition may drive diversification. Accelerated gene evolution predates the evolution of the ECM habit, indicating that changes in genome architecture and gene content may be necessary to prime the evolutionary switch.

Genome sequences of sponge bacterial endophytes will be useful for understanding the bioactive compound synthetic potential and molecular mechanisms of sponge-bacteria interactions. In this study, the complete genome of the bacterium E9 isolated from the Red Sea sponge species was sequenced and its antibiofilm activity was assessed through laboratory assay. Experiments indicated the strong antibacterial and antibiofilm activity of the extracts of bacterium E9. Complete genome sequencing reveals that genome assembly generated a single chromosome of 2123451 base pairs with a guanine-cytosine (GC) content of 32.9% with 2420 protein coding sequences and a gene/genome ratio of 83.7%. The bacterial strain was identified as Staphylococcus epidermidis based on phylogenetic analysis. A total of 9 biosynthetic gene clusters were identified in the genome using the open-source platform AntiSMASH. The observed antibacterial and antibiofilm activity of the strain E9 may be due the presence of gene clusters such as nonribosomal peptides, lasso peptides and terpenes. Overall, the whole genome analysis indicated the bacterium’s capability to adapt in diverse environments including invertebrate hosts, and bioactive compound synthesis.

International audience

Most people in Matrouh Governorate consume camel milk as a treatment for many diseases in a raw state to obtain nutritive value. Raw dromedary camel milk can be contaminated by through fecal matter at any point of milk handling; therefore, it may lose its value and safety specifications. This survey aimed to estimate the incidence of in fresh camel milk. 100 fresh camel milk samples (50 from markets and 50 from farms) were randomly collected from different districts in Matrouh Governorate, Egypt, over 4 months for the detection of incidence through conventional bacterial isolation, molecular investigation, and gene sequencing. The prevalence rates of in the examined market and farm raw camel milk based on conventional methods were 24% and 8%, respectively, while those by molecular identification using as an determinate gene were 4% and 6%, respectively. Moreover, gene phylogenetic analysis revealed high sequence similarity to strain CP033158.1 in India and strain CP047594.1 in China. Antibiotic sensitivity of isolates showed high susceptibility to norfloxacin (10 µg) and cefoperazone (75 µg). On the other hand, high resistance was found in rifamycin (30 µg) and cefoxitin (30 µg). The results indicate that market camel milk is more contaminated than the farms' own. Additionally, antibiotic resistance is increasing due to antibiotic abuse.