Chicken is one of the economically important poultry species. Avian leucosis virus subgroup J (ALV-J) has emerged as a serious cause of mortality and suboptimal performance of domestic chickens. Changes in virome may contribute to pathogenesis. Thus, it is important to investigate the effects of ALV-J infection on the composition of the virome in chicken. In the study metagenomic sequencing was used to characterize the virome of feces collected from the AVL-J infected chickens and the controls. Our results indicated that the chicken gut virome contained a diverse range of viruses that can be found in mammal, reptile, fish, and frogs. Furthermore, at the order, family and genus levels, AVL-J infection significantly altered the chicken gut virome composition. The predominant order was Herpesvirales, accounting for more than 96% of the chicken gut virome. Furthermore, the relative abundance of Caudovirales in the controls was higher than that in the AVL-J-infected chickens. At the family level, the relative abundance of Herpesviridae, Myoviridae, Alloherpesviridae, and Genomoviridae was significantly altered in the AVL-J-infected chickens compared with that in the controls. Additionally, the relative abundance of 15 genera showed a significant difference between the AVL-J-infected chickens and controls. These results will increase our understanding of the viral diversity and changes in the virome of chicken gut, with implications in chicken health.

Nicastrese is an indigenous Italian goat breed reared in the Calabria region under semi-extensive practices. From January to June, the milk yield of 400 multiparous Nicastrese goats was evaluated. In addition, tank milk and ripened cheese samples were subjected to physico-chemical and microbiological analyses with the aim to assess the effect of the seasonality on quality parameters. The volatile organic compounds profile of the ripened Nicastrese cheese samples was evaluated. Results showed that the seasonality had a significant effect on milk fat, lactose, urea, citric acid contents and acidity. Microbiological analysis of tank milk samples revealed variability among the different microbial groups investigated except for Escherichia coli. In addition, faecal coliforms and Listeria spp. were never detected. Regarding 60 days ripened cheese samples, almost all microbial groups showed a significant decrease during the analysed period, with the exception of Enterobacteria. It is interesting to note that Escherichia coli and Listeria spp. were not detected in any cheese sample investigated, confirming the cheese safety. Overall, volatile organic compounds, detected on cheese samples, decreased trough the investigated period and this behavior could be related to the feeding quality and to the milk's goat nutritional components.

The first line of the Arthropods defense against infections is the hard-structured exoskeleton, a physical barrier, usually rich in insoluble chitin. For entomopathogenic fungi that actively penetrate the host body, an arsenal of hydrolytic enzymes (as chitinases and N-acetylglucosaminidases), that break down chitin, is essential. Notably, twenty-one putative chitinase genes have been identified in the genome of Metarhizium anisopliae, a generalist entomopathogenic fungus. As a multigenic family, with enzymes that, presumably, perform redundant functions, the main goal is to understand the singularity of each one of such genes and to discover their precise role in the fungal life cycle. Specially chitinases that can act as virulence determinants are of interest since these enzymes can lead to more efficient biocontrol agents. Here we explored a horizontally acquired chitinase from M. anisopliae, named chiMaD1. The deletion of this gene did not lead to phenotypic alterations or diminished supernatant's chitinolytic activity. Surprisingly, chiMaD1 deletion enhanced M. anisopliae virulence to the cattle tick (Rhipicephalus microplus) larvae and engorged females, while did not alter the virulence to the mealworm larvae (Tenebrio molitor). These results add up to recent reports of deleted genes that enhanced entomopathogenic virulence, showing the complexity of host-pathogen interactions.

Yeast is a suitable model system to analyze the mechanism of lifespan. In this study, to identify novel factors involved in chronological lifespan, we isolated a mutant with a long chronological lifespan and found a missense mutation in the sur2+ gene, which encodes a homolog of Saccharomyces cerevisiae sphingolipid C4-hydroxylase in fission yeast. Characterization of the mutant revealed that loss of sur2 function resulted in an extended chronological lifespan. The effect of caloric restriction, a well-known signal for extending lifespan, is thought to be dependent on the sur2+ gene.

Kinetics of thiosulfate oxidation, product and intermediate formation, and 34S fractionation, were studied for the members of Alphaproteobacteria Paracoccus sp. SMMA5 and Mesorhizobium thiogangeticum SJTT, the Betaproteobacteria member Pusillimonas ginsengisoli SBO3, and the Acidithiobacillia member Thermithiobacillus sp. SMMA2, during chemolithoautotrophic growth in minimal salts media supplemented with 20 mM thiosulfate. The two Alphaproteobacteria oxidized thiosulfate directly to sulfate, progressively enriching the end-product with 34S; Δ34Sthiosulfate-sulfate values recorded at the end of the two processes (when no thiosulfate was oxidized any further) were -2.9‰ and -3.5‰, respectively. Pusillimonas ginsengisoli SBO3 and Thermithiobacillus sp. SMMA2, on the other hand, oxidized thiosulfate to sulfate via tetrathionate intermediate formation, with progressive 34S enrichment in the end-product sulfate throughout the incubation period; Δ34Sthiosulfate-sulfate, at the end of the two processes (when no further oxidation took place), reached -3.5‰ and -3.8‰, respectively. Based on similar 34S fractionation patterns recorded previously during thiosulfate oxidation by strains of Paracoccus pantotrophus, Advenella kashmirensis and Hydrogenovibrio crunogenus, it was concluded that progressive reverse fractionation, enriching the end-product sulfate with 34S, could be a characteristic signature of bacterial thiosulfate oxidation.

The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life.

One of the major parameters that characterizes the kinetics of microbial processes is the maximum specific growth rate. The maximum specific growth rate for a single microorganism (${\mu _{max}}$) is fairly constant. However, a certain microbial process is typically catalyzed by a group of microorganisms (guild) that have various ${\mu _{max}}$ values. In many occasions, it is not feasible to breakdown a guild into its constituent microorganisms. Therefore, it is a common practice to assume a constant maximum specific growth rate for the guild ($\acute{\mu}_{max}$) and determine its value by fitting experimental data. This assumption is valid for natural environments, where microbial guilds are stabilized and dominated by microorganisms that grow optimally in those environments' conditions. However, a change in an environment's conditions will trigger a community shift by favoring some of the microorganisms. This shift leads to a variable ${\acute{\mu}_{max}}$ as long as substrate availability is significantly higher than substrate affinity constant. In this work, it is illustrated that the assumption of constant ${\acute{\mu}_{max}}$ may underestimate or overestimate microbial growth. To circumvent this, a novel relationship that characterizes changes in ${\acute{\mu}_{max}}$ under abundant nutrient availability is proposed. The proposed relationship is evaluated for various random microbial guilds in batch experiments.

During Bad Bugs Bookclub meetings, scientists and non-scientists discuss novels in which infectious disease forms part of the plot in order to encourage public understanding of, and engagement with, microbiology. The website presents meeting reports and reading guides for over 70 novels. The aim of this work was to raise awareness of the bookclub and increase website engagement. In 2019, events designed to reach new audiences maintained an increase in page views from the end of 2018 (around 200 per month). In 2020, the coronavirus pandemic forced bookclub meetings online (Zoom). These, with podcasts and some Twitter discussion, increased page views with a peak of 400 per month. Membership increased, and global 'attendance' was facilitated. Feelings and observations related to each book and the pandemic were noted in meeting reports. A survey of current and previous bookclub members carried out early in lockdown with the aim of determining the future direction of the bookclub revealed the continuing value of both literary and scientific experiences to members. The bookclub has engaged scientists and non-scientists in meaningful discussion about infectious disease. Reach is modest, but the resource is significant, with potential impact in education and engagement.

Environmental DNA is made-up of intracellular (iDNA) and extracellular (eDNA) pools. In soils, eDNA can be present up to 40% and could distort the assessment of living microorganisms. Distribution of microbial community is inconsistent among different size-aggregates, and the persistence and turnover of eDNA are thus uneven. Uneven persistence and distribution of eDNA could lead to heterogeneity in community analysis biases that arise due to eDNA sequences at micro-scale distribution. Here, we investigated the diversity and structure of eDNA and iDNA bacterial communities in bulk soil and different size-aggregates. Significant differences were observed between eDNA and iDNA bacterial diversity and composition. Changes in community composition are more important than the amount of eDNA to assess the biases caused by eDNA in community analysis. Furthermore, variations were also observed in aggregates-levels for eDNA and iDNA community which indicates that colonization pattern of iDNA community and protection of eDNA through absorbance on particle surface within soil-matrix is heterogeneous. Our work provides empirical evidence that eDNA presence could mask the detection of aggregates-level spatial dynamics in soil microbial community and have potential to qualitatively baffle observed live effects of given treatment by adequately muting the actual response dynamics of the soil microbiome.

Microalgae are rapidly evolving alternative ingredients in food and feed. Desirable nutritional and functional qualities make them high potential sources of feed ingredients. Certain microalgae species are known to accumulate large amounts of protein, containing all essential amino acids while some species contain essential fatty acids and bioactive compounds hence offering several possible health benefits. However, successful inclusion of microalgae-based products in feed requires a clear understanding of physiological responses and microbiota of animals receiving microalgae diets. In this review, key microalgae-based feed ingredients and their effect on gut microbiome and immunomodulatory responses of microalgae fed animals, with a focus on aquatic species will be discussed.

The Hok/Gef family consists of structurally similar, single-span membrane peptides that all contain a positively charged N-terminal domain, an α-helix and a periplasmic C-terminal domain. Hok/Gef peptides have previously been described to play distinct physiological roles. Indeed, while HokB has been implicated in bacterial persistence, other members of the Hok/Gef family are known to induce cell lysis. However, the generalizability of previously published studies is problematic, as they have all used different expression systems. Therefore, we conducted a systematic study of the nine Hok/Gef peptides of Escherichia coli. We observed rapid cell death following expression of hokA, hokC, hokD, hokE, pndA1, hok or srnB, while expression of hokB or pndA2 does not result in cell lysis. A remarkable feature of Hok/Gef peptides is the presence of conserved periplasmic tyrosine and/or cysteine residues. For the HokB peptide, one of these residues has previously been implicated in intermolecular dimerization, which is essential for HokB to exert its role in persistence. To assess the role of the periplasmic cysteine and tyrosine residues in other Hok/Gef peptides and to decipher whether these residues determine peptide toxicity, an array of substitution mutants were constructed. We found that these residues are important activators of toxicity for Hok, HokA and HokE peptides. Despite the loss of the cell killing phenotype in HokS31_Y48, HokAS29_S46 and HokES29_Y46, these peptides do not exert a persister phenotype. More research is needed to fully comprehend why HokB is the sole peptide of the Hok/Gef family that mediates persistence.

Gram-negative pathogens are a rapidly increasing threat to human health worldwide due to high rates of antibiotic resistance and the lack of development of novel antibiotics. The protective cell envelope of gram-negative bacteria is a major permeability barrier that contributes to the problem by restricting the uptake of antibiotics. On the other hand, its unique architecture also makes it a suitable target for antibiotic interference. In particular, essential multiprotein machines that are required for biogenesis of the outer membrane have attracted attention in antibacterial design strategies. Recently, significant progress has been made in the development of inhibitors of the β-barrel assembly machine (BAM) complex. Here, we summarize the current state of drug development efforts targeting the BAM complex in pursuit of new antibiotics.

Increasing antimicrobial resistance of nosocomial pathogens is becoming a serious threat to public health. To control the spread of this resistance, it is necessary to detect β-lactamase-producing organisms in the clinical setting. The aims of the study were to design a PCR assay for rapid detection of clinically encountered β-lactamase genes described in Enterobacteriaceae and Gram-negative non-fermenting bacteria. The functionality of proposed primers was verified using eight reference strains and 17 strains from our collection, which contained 29 different β-lactamase genes. PCR products of the test strains were confirmed by Sanger sequencing. Sequence analysis was performed using bioinformatics software Geneious. Overall, 67 pairs of primers for detecting 12 members of the class C β-lactamase family, 15 members of class A β-lactamases, six gene families of subclass B1, one member each of subclasses B2, B3 and class D β-lactamases were designed, of which 43 pairs were experimentally tested in vitro. All 29 β-lactamase genes, including 10 oxacillinase subgroups, were correctly identified by PCR. The proposed set of primers should be able to specifically detect 99.7% of analyzed β-lactamase subtypes and more than 79.8% of all described β-lactamase genes.

Artisanal products support the conservation of the indigenous biodiversity of food microbiomes, although they do not always comply to quality and hygienic requirements for the dairy industry. This study describes the development of an autochthonous starter culture to produce Matsoni, a traditional Georgian fermented milk. To this end, strains of lactic acid bacteria isolated from artisanal Matsoni samples were used to design a starter formulation reproducing the dominant microbial diversity, also preserving quality characteristics and ensuring the safety of the product. As a result, strains that represent the acidifying portion of the starter (Lactobacillus delbrueckii subsp. lactis, L. delbrueckii subsp. bulgaricus and Streptococcus thermophilus) were combined in different ratios and strain combinations, together with cultures of Lactobacillus rhamnosus that were chosen for their potential beneficial traits. The strain association acting better in milk cultures at laboratory scale was selected as starter culture for the production of Matsoni in pilot-scale industrial trials.

Host-directed therapies (HDTs) could enhance the activity of traditional antibiotics. AR-12 is a promising HDT against intracellular pathogens including Salmonella enterica serovar Typhimurium, and has been shown to act through modulation of autophagy and the Akt kinase pathway. Since AR-12 does not inhibit the growth of planktonic bacteria but only works in conjunction with the infected host-cell, we hypothesized that AR-12 could enhance the activity of antibiotics in less-susceptible strains in the intracellular host environment. We found that repetitive passaging of S. typhimurium in macrophages in the absence of antibiotics led to a 4-fold reduction in their intracellular susceptibility to streptomycin (STR), but had no effect on the bacteria's sensitivity to AR-12. Moreover, when the host-passaged strains were treated with a combined therapy of AR-12 and STR, there was a significant reduction of intracellular bacterial burden compared to STR monotherapy. Additionally, co-treatment of macrophages infected with multi-drug resistant S. typhimurium with AR-12 and STR or ampicillin showed enhanced clearance of the intracellular bacteria. The drug combination did not elicit this effect on planktonic bacteria. Overall, AR-12 enhanced the clearance of less susceptible S. typhimurium in an intracellular environment.

A freshwater dwelling cyanobacterium (strain MKW3) was isolated from a sample collected from a water logged sugarcane field located in Malkapur, Karad, Maharashtra, India, and was characterized using a polyphasic approach. In the 16S rRNA gene phylogenetic analysis, strain MKW3 clustered with two misidentified strains-Nostoc sp. CENA239 and Calothrix sp. NIES2100. The phylogenetically related members included strains identified as Nostoc, Aulosira, Calothrix, Tolypothrix, Camptylonemopsis and Microchaete. The phylogenetic and the morphological analysis of the strain MKW3 indicated that it does not belong to any of the above mentioned genera. Furthermore, the 16S-23S ITS secondary structure analysis provided clear evidence indicating that strain MKW3 is different from Nostoc sp. CENA239 and Calothrix sp. NIES2100. Based on the morphological, phylogenetic and 16S-23S ITS secondary structure analysis we describe our strain as Constrictifilum karadense gen. et sp. nov. in accordance with the International Code of Nomenclature for algae, fungi and plants.

Their biochemical versatility and biotechnological importance make actinomycete bacteria attractive targets for ambitious genetic engineering using the toolkit of synthetic biology. But their complex biology also poses unique challenges. This mini review discusses some of the recent advances in synthetic biology approaches from an actinomycete perspective and presents examples of their application to the rational improvement of industrially relevant strains.

Intestinal flora structure and function change with age and have been associated with a variety of aging-related diseases. Until now, how age affects the functions of gut bacteria has not been fully understood. We used 16S-rRNA-sequencing technology and PICRUSt2 analysis to predict the functions encoded by intestinal flora in male Wistar rats across lifespan. We found that the abundance of gut microbiota genes encoding the L-tryptophan, L-histidine, L-leucine, inositol and catechol degradation pathways as well as L-arginine, ectoine, flavin and ubiquinol synthesis pathways increased with age. Differential analysis of the associated genera revealed that Rhodococcus spp. were significantly abundant during middle-old aged stage. This genus contributed greatly to the L-tryptophan, catechol and inositol degradation pathways as well as ectoine and L-arginine biosynthesis pathways. We concluded that gut bacteria-encoded functions such as amino acid metabolism, B vitamin metabolism, aromatic compound metabolism and energy metabolism varied in an age-dependent manner, and Rhodococcus spp. were the most associated functional bacteria in middle-old aged rats. These may be closely associated with the physiological phenotype of the aging process, which offers new insights for evaluating the relationship between intestinal flora and aging.

Obesity, which is often caused by adipocyte metabolism dysfunction, is rapidly becoming a serious global health issue. Studies in the literature have shown that camellia oil (Camellia oleifera Abel) exerted potential lipid regulation and other multiple biological activities. Here, we aimed to investigate the effects of camellia oil on obese mice induced by a high-fat diet and to explore gut microbiota alterations after camellia oil intervention. The results showed that oral administration of camellia oil dramatically attenuated the fat deposits, serum levels of the total cholesterol, triacylglycerol, low-density lipoprotein cholesterol, fasting plasma glucose, the atherosclerosis index, the hepatic steatosis and inflammation in high-fat diet-induced obese mice. Meanwhile, the high-density lipoprotein cholesterol level in obese mice was enhanced after the camellia oil treatment. Furthermore, 16S rRNA analysis showed that certain aspects of the gut microbiota, especially the gut microbiota diversity and the relative abundance of Actinobacteria, Coriobacteriaceae, Lactobacillus and Anoxybacillus, were significantly increased by camellia oil treatment while the ratio of Firmicutes to Bacteroidetes was decreased. Taken together, our finding suggested that camellia oil was a potential dietary supplement and functional food for ameliorating fat deposits, hyperglycemia and fatty liver, probably by modifying the gut microbiota composition.