Comparative genomics of Vibrio toranzoniae strains.

Vibrio toranzoniae is a marine bacterium belonging to the Splendidus clade that was originally isolated from healthy clams in Galicia (NW Spain). Its isolation from different hosts and seawater indicated two lifestyles and wide geographical distribution. The aim of the present study was to determine the differences at the genomic level among six strains (4 isolated from clam and 2 from seawater) and to determine their phylogeny. For this purpose, whole genomes of the six strains were sequenced by different technologies including Illumina and PacBio, and the resulting sequences were corrected. Genomes were annotated and compared using different online tools. Furthermore, the study of core- and pan-genomes were examined, and the phylogeny was inferred. The content of the core genome ranged from 2953 to 2766 genes and that of the pangenome ranged from 6278 to 6132, depending on the tool used. Although the strains shared certain homology, with DDH values ranging from 77.10 to 82.30 and values of OrthoANI values higher than 97%, some differences were found related to motility, capsule synthesis, iron acquisition systems or mobile genetic elements. Phylogenetic analysis of the core genome did not reveal a differentiation of the strains according to their lifestyle (commensal or free-living), but that of the pangenome indicated certain geographical isolation in the same growing area. This study led to the reclassification of some isolates formerly described as V. toranzoniae and demonstrated the importance of cured deposited sequences to proper phylogenetic assignment.

Comparison of gene targets and sampling regimes for SARS-CoV-2 quantification for wastewater epidemiology in UK prisons.

Prisons are high-risk settings for infectious disease transmission, due to their enclosed and semi-enclosed environments. The proximity between prisoners and staff, and the diversity of prisons reduces the effectiveness of non-pharmaceutical interventions, such as social distancing. Therefore, alternative health monitoring methods, such as wastewater-based epidemiology (WBE), are needed to track pathogens, including SARS-CoV-2. This pilot study assessed WBE to quantify SARS-CoV-2 prevalence in prison wastewater to determine its utility within a health protection system for residents. The study analysed 266 samples from six prisons in England over a 12-week period for nucleoprotein 1 (N1 gene) and envelope protein (E gene) using quantitative reverse transcriptase-polymerase chain reaction. Both gene assays successfully detected SARS-CoV-2 fragments in wastewater samples, with both genes significantly correlating with COVID-19 case numbers across the prisons (p < 0.01). However, in 25% of the SARS-positive samples, only one gene target was detected, suggesting that both genes be used to reduce false-negative results. No significant differences were observed between 14- and 2-h composite samples, although 2-h samples showed greater signal variance. Population normalisation did not improve correlations between the N1 and E genes and COVID-19 case data. Overall, WBE shows considerable promise for health protection in prison settings.

Analysis of Varroa Mite Colony Infestation Level Using New Open Software Based on Deep Learning Techniques.

Varroa mites, scientifically identified as Varroa destructor, pose a significant threat to beekeeping and cause one of the most destructive diseases affecting honey bee populations. These parasites attach to bees, feeding on their fat tissue, weakening their immune systems, reducing their lifespans, and even causing colony collapse. They also feed during the pre-imaginal stages of the honey bee in brood cells. Given the critical role of honey bees in pollination and the global food supply, controlling Varroa mites is imperative. One of the most common methods used to evaluate the level of Varroa mite infestation in a bee colony is to count all the mites that fall onto sticky boards placed at the bottom of a colony. However, this is usually a manual process that takes a considerable amount of time. This work proposes a deep learning approach for locating and counting Varroa mites using images of the sticky boards taken by smartphone cameras. To this end, a new realistic dataset has been built: it includes images containing numerous artifacts and blurred parts, which makes the task challenging. After testing various architectures (mainly based on two-stage detectors with feature pyramid networks), combination of hyperparameters and some image enhancement techniques, we have obtained a system that achieves a mean average precision (mAP) metric of 0.9073 on the validation set.

Bull Sperm SWATH-MS-Based Proteomics Reveals Link between High Fertility and Energy Production, Motility Structures, and Sperm-Oocyte Interaction.

The prediction of male or semen fertility potential remains a persistent challenge that has yet to be fully resolved. This work analyzed several in vitro parameters and proteome of spermatozoa in bulls cataloged as high- (HF; n = 5) and low-field (LF; n = 5) fertility after more than a thousand artificial inseminations. Sperm motility was evaluated by computer-assisted sperm analysis. Sperm viability, mitochondrial membrane potential (MMP) and reactive oxygen species (mROS) of spermatozoa were assessed by flow cytometry. Proteome was evaluated by the SWATH-MS procedure. Spermatozoa of HF bulls showed significantly higher total motility than the LF group (41.4% vs 29.7%). Rates of healthy sperm (live, high MMP, and low mROS) for HF and LF bull groups were 49% and 43%, respectively (p > 0.05). Spermatozoa of HF bulls showed a higher presence of differentially abundant proteins (DAPs) related to both energy production (COX7C), mainly the OXPHOS pathway, and the development of structures linked with the motility process (TPPP2, SSMEM1, and SPAG16). Furthermore, we observed that equatorin (EQTN), together with other DAPs related to the interaction with the oocyte, was overrepresented in HF bull spermatozoa. The biological processes related to protein processing, catabolism, and protein folding were found to be overrepresented in LF bull sperm in which the HSP90AA1 chaperone was identified as the most DAP. Data are available via ProteomeXchange with identifier PXD042286.

Environmental vibrio phage-bacteria interaction networks reflect the genetic structure of host populations.

Phages depend on their bacterial hosts to replicate. The habitat, density and genetic diversity of host populations are therefore key factors in phage ecology, but our ability to explore their biology depends on the isolation of a diverse and representative collection of phages from different sources. Here, we compared two populations of marine bacterial hosts and their phages collected during a time series sampling program in an oyster farm. The population of Vibrio crassostreae, a species associated specifically to oysters, was genetically structured into clades of near clonal strains, leading to the isolation of closely related phages forming large modules in phage-bacterial infection networks. For Vibrio chagasii, which blooms in the water column, a lower number of closely related hosts and a higher diversity of isolated phages resulted in small modules in the phage-bacterial infection network. Over time, phage load was correlated with V. chagasii abundance, indicating a role of host blooms in driving phage abundance. Genetic experiments further demonstrated that these phage blooms can generate epigenetic and genetic variability that can counteract host defence systems. These results highlight the importance of considering both the environmental dynamics and the genetic structure of the host when interpreting phage-bacteria networks.

Scientific evidence on the origin of SARS-CoV-2.

Even reaching the end of the year 2022, there is still a controversy on the origin of the SARS-CoV-2 virus. This Virtual Special Issue (VSI), focused on the "Scientific evidence on the origin of SARS-CoV-2", was launched some months ago with the aim of stimulating the submission of new high quality scientific research papers on the matter, to shed light on it. As indicated in the call for papers, the Editors involved in the VSI were aware of the difficulties of presenting concluding facts on that issue, however, bearing in mind that some teams of researchers had started investigations regarding this subject, a VSI like this (searching for stimulating the scientific controversy while requiring scientific evidence), could help to elucidate complicated aspects, going a step ahead in this way. The Editors made a call encouraging interested teams of researchers having solid results to submit high quality manuscripts dealing with this crucial theme. We thought -and we still think-that it is of maximum interest for the scientific community, as well as for the whole society, now and probably for the future. The VSI have received 50 submissions, which could be considered a limited number highlighting the difficulties of elaborating new high-quality manuscripts providing solid evidence on the matter. After a careful peer-review, those manuscripts considered to reach the highest scientific value were accepted for publication. The Editors think that the set of papers included in this VSI constitute interesting and high-quality contributions, providing further scientific knowledge on this issue. In this editorial piece, the Editors make some comments on the papers published, including some additional reflections.

A review of bacterial disease outbreaks in rainbow trout (Oncorhynchus mykiss) reported from 2010 to 2022.

Outbreaks of bacterial infections in aquaculture have emerged as significant threats to the sustainable production of rainbow trout (Oncorhynchus mykiss) worldwide. Understanding the dynamics of these outbreaks and the bacteria involved is crucial for implementing effective management strategies. This comprehensive review presents an update on outbreaks of bacteria isolated from rainbow trout reported between 2010 and 2022. A systematic literature survey was conducted to identify relevant studies reporting bacterial outbreaks in rainbow trout during the specified time frame. More than 150 published studies in PubMed, Web of Science, Scopus, Google Scholar and relevant databases met the inclusion criteria, encompassing diverse geographical regions and aquaculture systems. The main bacterial pathogens implicated in the outbreaks belong to both gram-negative, namely Chryseobacterium, Citrobacter, Deefgea Flavobacterium, Janthinobacterium, Plesiomonas, Pseudomonas, Shewanella, and gram-positive genera, including Lactococcus and Weissella, and comprise 36 new emerging species that are presented by means of pathogenicity and disturbance worldwide. We highlight the main characteristics of species to shed light on potential challenges in treatment strategies. Moreover, we investigate the role of various risk factors in the outbreaks, such as environmental conditions, fish density, water quality, and stressors that potentially cause outbreaks of these species. Insights into the temporal and spatial patterns of bacterial outbreaks in rainbow trout aquaculture are provided. Furthermore, the implications of these findings for developing sustainable and targeted disease prevention and control measures are discussed. The presented study serves as a comprehensive update on the state of bacterial outbreaks in rainbow trout aquaculture, emphasizing the importance of continued surveillance and research to sustain the health and productivity of this economically valuable species.

Co-existence of two Yersinia ruckeri biotypes and serotype O1a retrieved from rainbow trout (Oncorhynchus mykiss) farmed in Puno, Peru.

Yersinia ruckeri causes important economic losses for rainbow trout (Oncorhynchus mykiss) farms worldwide. This bacterial disease is likely the most common among trout in Peru; however, no commercial vaccine is available nationally, which is, in part, due to a lack of information on the bacterium. The aim of the current study was to characterize 29 Y. ruckeri isolates sampled from seven cage-reared farms in the Puno Region, the focal point for aquaculture activities in Peru. For this, samples were taken from fish with clinical signs (i.e. haemorrhages, uni- or bilateral exophthalmia, hyphaemia and/or melanosis). Notable among our findings was the existence of both Y. ruckeri biotype 1 (9 isolates) and biotype 2 (20 isolates; negative for sorbitol and Tween 80). The isolates further differed in API profiles 5307100 (21 isolates), 1307100 (4 isolates), 1305100 (2 isolates), 1307120 (1 isolate) and 5305100 (1 isolate), with the main differences being in the tests for lysine decarboxylase, gelatine hydrolysis and D-saccharose fermentation. Despite these differences, all isolates shared identical ERIC-PCR and REP-PCR profiles and belonged to the O1a serotype. Fingerprints were identical to the reference strain CECT 955 (serotype O1a). The information obtained will be used for epidemiological purposes by health authorities and for the development of a vaccine against Y. ruckeri, a prominent request made by fish farmers in Peru.

Novel Bayesian Inference-Based Approach for the Uncertainty Characterization of Zhang's Camera Calibration Method.

Camera calibration is necessary for many machine vision applications. The calibration methods are based on linear or non-linear optimization techniques that aim to find the best estimate of the camera parameters. One of the most commonly used methods in computer vision for the calibration of intrinsic camera parameters and lens distortion (interior orientation) is Zhang's method. Additionally, the uncertainty of the camera parameters is normally estimated by assuming that their variability can be explained by the images of the different poses of a checkerboard. However, the degree of reliability for both the best parameter values and their associated uncertainties has not yet been verified. Inaccurate estimates of intrinsic and extrinsic parameters during camera calibration may introduce additional biases in post-processing. This is why we propose a novel Bayesian inference-based approach that has allowed us to evaluate the degree of certainty of Zhang's camera calibration procedure. For this purpose, the a prioriprobability was assumed to be the one estimated by Zhang, and the intrinsic parameters were recalibrated by Bayesian inversion. The uncertainty of the intrinsic parameters was found to differ from the ones estimated with Zhang's method. However, the major source of inaccuracy is caused by the procedure for calculating the extrinsic parameters. The procedure used in the novel Bayesian inference-based approach significantly improves the reliability of the predictions of the image points, as it optimizes the extrinsic parameters.

The pan-genome of Splendidus clade species in the family Vibrionaceae: Insights into evolution, adaptation, and pathogenicity.

The Splendidus clade is the largest clade in Vibrionaceae, and its members are often related to mortality of marine animals with huge economic losses. The molecular bases of their pathogenicity and virulence, however, remain largely unknown. In particular, the complete genome sequences of the Splendidus clade species are rarely registered, which is one of the obstacles to predict core and/or unique genes responsible for their adaptation and pathogenicity, and to perform a fine scale meta-transcriptome during bacterial infection to their hosts. In this study, we obtained the complete genomes of all type strains in the Splendidus clade and revealed that (1) different genome sizes (4.4-5.9 Mb) with V. lentus the biggest and most of them had several big plasmids, likely because of the different features on mobilome elements; (2) the Splendidus clade consists of 19 species except V. cortegadensis, and 3 sub-clades (SC) were defined with the 15 most closely related members as SC1; (3) different carbohydrate degradation preferences may be the result of environmental adaptation; and (4) a broad prediction of virulence factors (VFs) revealed core and species unique VF genes.

Women survivors of intimate partner violence talk about using e-health during pregnancy: a focus group study.

BACKGROUND: Pregnancy is a period of particular vulnerability to experience intimate partner violence against women (IPVAW). eHealth strategies have been implemented to identify women exposed to IPVAW and to combat the abuse and empower them, but there is a lack of evidence on the use of these strategies among pregnant women. This work aims to identify the needs, concerns and preferences of survivors about the use of eHealth strategies to counsel and empower pregnant victims of IPVAW in antenatal care. METHODS: A focus group of six IPVAW survivors who had been pregnant was conducted and open questions about the use of eHealth strategies were asked. The session was recorded, transcribed and thematically analyzed. We identified three main themes: needs and worries of pregnant women experiencing IPVAW, key aspects of video counseling sessions and usefulness of safety planning apps. RESULTS: Women highlighted the relevant role of healthcare professionals-especially midwives-in the identification of IPVAW and the wellbeing of their children as one of the main concerns. They perceived video counseling and safety planning apps as valuable resources. The preferred contents for a video counseling intervention were awareness-raising of the situation, self-esteem and legal advice. They also proposed safety and pregnant-related aspects that should be taken into account in the design of the video counseling sessions and the safety planning app. CONCLUSIONS: Video counseling sessions and safety planning apps are potentially useful tools to counsel and empower women who experience IPVAW during pregnancy. Midwives play a key role in this endeavor.

Screening for intimate partner violence during pregnancy: a test accuracy study.

BACKGROUND: Intimate partner violence (IPV) against women is a serious health problem that affects pregnancy more frequently than other obstetric complications usually evaluated in antenatal visits. We aimed to estimate the accuracy of the Women Abuse Screening Tool-Short (WAST-Short) and the Abuse Assessment Screen (AAS) for the detection of IPV during and before pregnancy. METHODS: Consecutive eligible mothers in 21 public primary health antenatal care centres in Andalusia (Spain) who received antenatal care and gave birth during January 2017-March 2019, had IPV data gathered by trained midwives in the first and third pregnancy trimesters. The index tests were WAST-Short (score range 0-2; cut-off 2) and AAS (score range 0-1; cut-off 1). The reference standard was World Health Organization (WHO) IPV questionnaire. Area under receiver operating characteristics curve (AUC), sensitivity and specificity with 95% confidence intervals (CI) were estimated for test performance to capture IPV during and before pregnancy, and compared using paired samples analysis. RESULTS: According to the reference standard, 9.5% (47/495) and 19.4% (111/571) women suffered IPV during and before pregnancy, respectively. For capturing IPV during pregnancy in the third trimester, the WAST-Short (AUC 0.73, 95% CI 0.63, 0.81), performed better than AAS (AUC 0.57, 95% CI 0.47, 0.66, P = 0.0001). For capturing IPV before pregnancy in the first trimester, there was no significant difference between the WAST-Short (AUC 0.69, 95% CI 0.62, 0.74) and the AAS (AUC 0.69, 95% CI 0.62, 0.74, P = 0.99). CONCLUSIONS: The WAST-Short could be useful to screen IPV during pregnancy in antenatal visits.

A deep-sea bacterium related to coastal marine pathogens.

Evolution of virulence traits from adaptation to environmental niches other than the host is probably a common feature of marine microbial pathogens, whose knowledge might be crucial to understand their emergence and pathogenetic potential. Here, we report genome sequence analysis of a novel marine bacterial species, Vibrio bathopelagicus sp. nov., isolated from warm bathypelagic waters (3309 m depth) of the Mediterranean Sea. Interestingly, V. bathopelagicus sp. nov. is closely related to coastal Vibrio strains pathogenic to marine bivalves. V. bathopelagicus sp. nov. genome encodes genes involved in environmental adaptation to the deep-sea but also in virulence, such as the R5.7 element, MARTX toxin cluster, Type VI secretion system and zinc-metalloprotease, previously associated with Vibrio infections in farmed oysters. The results of functional in vitro assays on immunocytes (haemocytes) of the Mediterranean mussel Mytilus galloprovincialis and the Pacific oyster Crassostrea gigas, and of the early larval development assay in Mytilus support strong toxicity of V. bathopelagicus sp. nov. towards bivalves. V. bathopelagicus sp. nov., isolated from a remote Mediterranean bathypelagic site, is an example of a planktonic marine bacterium with genotypic and phenotypic traits associated with animal pathogenicity, which might have played an evolutionary role in the origin of coastal marine pathogens.

Metataxonomic analysis of tissue-associated microbiota in grooved carpet-shell (Ruditapes decussatus) and Manila (Ruditapes philippinarum) clams.

Culture-dependent techniques only permit the study of a low percentage of the microbiota diversity in the environment. The introduction of next generation sequencing (NGS) technologies shed light into this hidden microbial world, providing a better knowledge on the general microbiota and, specifically, on the microbial populations of clams. Tissue-associated microbiota of Ruditapes decussatus and Ruditapes philippinarum (mantle, gills, gonad and hepatopancreas) was analysed in two different locations of Galicia (northwest of Spain) during Spring (April) and Autumn (October), employing a metataxonomic approach. High bacterial diversity and richness were found in all samples where a total of 22,044 OTUs were obtained. In most samples, phylum Proteobacteria was most frequently retrieved, although other phyla as Actinobacteria, Bacteroidetes, Tenericutes, Firmicutes or Chlamydiae also appeared at high relative abundances in the samples. At genus level, great variation was found across tissues and sampling periods. A Nonmetric Multidimensional Scaling (NMDS) and a hierarchical clustering analysis allowed to further analyse the factors responsible for the differences among groups of samples in the different sites. Results showed sample ordination based on tissue origin and sampling periods, pointing out that the microbiota was influenced by these factors. Indeed, predominance of certain genera was observed, such as Endozoicomonas or Methylobacterium in gills and gonads, respectively, suggesting that selection of specific bacterial taxa is likely to occur. So far, this study provided a general picture of the tissue associated microbial population structure in R. decussatus and R. philippinarum clams, which, ultimately, allowed the identification of specific tissue-related taxa.

Sterility assurance of technetium-99m radiopharmaceuticals: no specific air conditions are required for their preparation, storage and dispensation.

BACKGROUND: The aim of this study was to ascertain whether the extemporaneous technetium-99m radiopharmaceuticals - prepared by closed procedures - maintain or not sterility throughout their lifespan regardless the quality of the environmental air where they are prepared, stored and dispensed, provided that the basic aseptic rules for closed procedures are followed. METHODS: Three different types of assays were performed in this study: 1) sterility tests of each and every one of the vials with the remains of technetium-99m radiopharmaceuticals, which have been prepared in our hospital radiopharmacy during three years without any special environmental air conditions; 2) integrity tests of punctured rubber plug closures using both microbial challenge testing and dye ingress testing; and 3) simulation of the dispensing process using a liquid growth medium. RESULTS: Sterility tests of more than 6,000 vials with the remains of technetium-99m radiopharmaceuticals - prepared without any special ambient air conditions - were performed, all of them with a negative result (no growth of microorganisms occurs). The integrity of punctured rubber plugs closure was sufficiently proven under extreme conditions by two different methods. The maintenance of sterility during the dispensing process of technetium-99m radiopharmaceuticals was also proven by simulation of the dispensing process using a liquid growth medium. CONCLUSIONS: This study strongly supports that it is not necessary any special ambient air conditions to prepare, store and dispense extemporaneous technetium-99m radiopharmaceuticals in order to preserve their sterility when the basic aseptic rules for closed procedures are followed.

Effects of dietary fibre intake in chemotherapy-induced mucositis in murine model.

Mucositis is an inflammation of the gastrointestinal mucosa resulting from high doses of radio/chemotherapy treatment and may lead to interruption of antineoplasic therapy. Soluble fibres, like pectin, increase SCFA production, which play a role in gut homoeostasis and inflammation suppression. Due to the properties of pectin, the aim of the present study was to evaluate the effect of a high-fibre (HF) diet on chemotherapy-induced mucositis in a murine model. C57/BL6 mice received control (AIN93M), HF, low/zero fibre (LF) diets for 10 d prior to mucositis challenging with irinotecan (75 mg/kg), or they were treated with acetate added to drinking water 5 d prior to and during the mucositis induction. Mice that received the HF diet showed decreased immune cells influx and improved histopathological parameters in the intestine, compared with mice that received the normal diet. Furthermore, the HF diet decreased intestinal permeability induced in the mucositis model when compared with the control group. This effect was not observed for acetate alone, which did not improve gut permeability. For instance, mice that received the LF diet had worsened gut permeability, compared with mice that received the normal diet and mucositis. The effects of the HF and LF diets were shown to modulate the intestinal microbiota, in which the LF diet increased the levels of Enterobacteriaceae, a group associated with gut inflammation, whereas the HF diet decreased this group and increased Lactobacillus and Bifidobacterium (SCFA producers) levels. In conclusion, the results demonstrated the importance of dietary fibre intake in the modulation of gut microbiota composition and homoeostasis maintenance during mucositis in this model.

Extended-Spectrum ß-Lactamase and Carbapenemase Genes are Substantially and Sequentially Reduced during Conveyance and Treatment of Urban Sewage.

Urban wastewater systems (UWSs) are a main receptacle of excreted antibiotic resistance genes (ARGs) and their host microorganisms. However, we lack integrated and quantitative observations of the occurrence of ARGs in the UWS to characterize the sources and identify processes that contribute to their fate. We sampled the UWSs from three medium-size cities in Denmark, Spain, and the United Kingdom and quantified 70 clinically important extended-spectrum ß-lactamase and carbapenemase genes along with the mobile genetic elements and microbial communities. Results from all three countries showed that sewage-especially from hospitals-carried substantial loads of ARGs (106-107 copies per person equivalent), but these loads progressively declined along sewers and through sewage treatment plants, resulting in minimal emissions (101-104 copies per person equivalent). Removal was primarily during sewage conveyance (65 ± 36%) rather than within sewage treatment (34 ± 23%). The extended-spectrum ß-lactamase and carbapenemase genes were clustered in groups based on their persistence in the UWS compartments. The less-persistent groups were associated to putative host taxa (especially Enterobacteriaceae and Moraxellaceae), while the more persistent groups appeared horizontally transferred and correlated significantly with total cell numbers and mobile genetic elements. This documentation of a substantial ARG reduction during sewage conveyance provides opportunities for antibiotic resistance management and a caution for sewage-based antibiotic resistance surveillance.

Monitoring Emergence of the SARS-CoV-2 B.1.1.7 Variant through the Spanish National SARS-CoV-2 Wastewater Surveillance System (VATar COVID-19).

Since its first identification in the United Kingdom in late 2020, the highly transmissible B.1.1.7 variant of SARS-CoV-2 has become dominant in several countries raising great concern. We developed a duplex real-time RT-qPCR assay to detect, discriminate, and quantitate SARS-CoV-2 variants containing one of its mutation signatures, the ΔHV69/70 deletion, and used it to trace the community circulation of the B.1.1.7 variant in Spain through the Spanish National SARS-CoV-2 Wastewater Surveillance System (VATar COVID-19). The B.1.1.7 variant was detected earlier than clinical epidemiological reporting by the local authorities, first in the southern city of Málaga (Andalucía) in week 20_52 (year_week), and multiple introductions during Christmas holidays were inferred in different parts of the country. Wastewater-based B.1.1.7 tracking showed a good correlation with clinical data and provided information at the local level. Data from wastewater treatment plants, which reached B.1.1.7 prevalences higher than 90% for ≥2 consecutive weeks showed that 8.1 ± 2.0 weeks were required for B.1.1.7 to become dominant. The study highlights the applicability of RT-qPCR-based strategies to track specific mutations of variants of concern as soon as they are identified by clinical sequencing and their integration into existing wastewater surveillance programs, as a cost-effective approach to complement clinical testing during the COVID-19 pandemic.

Production of ß-galactosidase by Trichoderma sp. through solid-state fermentation targeting the recovery of galactooligosaccharides from whey cheese.

AIMS: Optimization of ß-galactosidase production by Trichoderma sp. under solid-state fermentation using wheat bran as solid substrate through an experimental design and its application targeting the recovery of galactooligosaccharides (GOS) from whey cheese. METHODS AND RESULTS: The ß-galactosidase production by Trichoderma sp. increased 2·3-fold (2·67 U g-1 of substrate) culturing the fungus at 30°C for 187 h, at an inoculum of 105 spores per ml, and a 1 : 1·65 (w/v) ratio of wheat bran to tap water. The best enzyme activity was obtained at 55°C and pH 4·5. The catalytic activity was maintained for up to 180 min incubating at 35-45°C, and above 50% at acidic or alkaline pH for up to 24 h. It also presented resistance to chemical compounds. ß-galactosidase catalysed the hydrolysis of the lactose and the transgalactosylation reaction leading to the production of GOS. CONCLUSION: Trichoderma sp. produced ß-galactosidase with transgalactosylation activity that may be used to recover GOS, products with high added value, from whey cheese. SIGNIFICANCE AND IMPACT OF THE STUDY: ß-galactosidases are used in different industrial sectors. Therefore, the Trichoderma ß-galactosidase is a promising alternative for the production of GOS as prebiotic from the dairy effluents, contributing to the reduction in the environmental impact.

Vibrio Clade 3.0: New Vibrionaceae Evolutionary Units Using Genome-Based Approach.

Currently, over 190 species in family Vibrionaceae, including not-yet-cultured taxa, have been described and classified into over nine genera, in which the number of species has doubled compared to the previous vibrio evolutionary update (Vibrio Clade 2.0) (Sawabe et al. 2014). In this study, "Vibrio Clade 3.0," the second update of the molecular phylogenetic analysis was performed based on nucleotide sequences of eight housekeeping genes (8-HKGs) retrieved from genome sequences, including 22 newly determined genomes. A total of 51 distinct clades were observed, of which 21 clades are newly described. We further evaluated the delineation powers of the clade classification based on nucleotide sequences of 34 single-copy genes and 11 ribosomal protein genes (11-RPGs) retrieved from core-genome sequences; however, the delineation power of 8-HKGs is still high and that gene set can be reliably used for the classification and identification of Vibrionaceae. Furthermore, the 11-RPGs set proved to be useful in identifying uncultured species among metagenome-assembled genome (MAG) and/or single-cell genome-assembled genome (SAG) pools. This study expands the awareness of the diversity and evolutionary history of the family Vibrionaceae and accelerates the taxonomic applications in classifying as not-yet-cultured taxa among MAGs and SAGs.