The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Campylobacter jejuni infection is one of the most widespread infectious diseases of the last century. The incidence and prevalence of campylobacteriosis have increased in both developed and developing countries over the last 10 years. The dramatic increase in North America, Europe, and Australia is alarming, and data from parts of Africa, Asia, and the Middle East indicate that campylobacteriosis is endemic in these areas, especially in children. In addition to C. jejuni, there is increasing recognition of the clinical importance of emerging Campylobacter species, including Campylobacter concisus and Campylobacter ureolyticus. Poultry is a major reservoir and source of transmission of campylobacteriosis to humans. Other risk factors include consumption of animal products and water, contact with animals, and international travel. Strategic implementation of multifaceted biocontrol measures to reduce the transmission of this group of pathogens is paramount for public health. Overall, campylobacteriosis is still one of the most important infectious diseases that is likely to challenge global health in the years to come. This review provides a comprehensive overview of the global epidemiology, transmission, and clinical relevance of Campylobacter infection.

Global Epidemiology of Campylobacter Infection

The symbiotic microbiota profoundly affect many aspects of host physiology; however, the molecular mechanisms underlying host-microbe cross-talk are largely unknown. Here, we show that the pyrroloquinoline quinone–dependent alcohol dehydrogenase (PQQ-ADH) activity of a commensal bacterium, Acetobacter pomorum, modulates insulin/insulin-like growth factor signaling (IIS) in Drosophila to regulate host homeostatic programs controlling developmental rate, body size, energy metabolism, and intestinal stem cell activity. Germ-free animals monoassociated with PQQ-ADH mutant bacteria displayed severe deregulation of developmental and metabolic homeostasis. Importantly, these defects were reversed by enhancing host IIS or by supplementing the diet with acetic acid, the metabolic product of PQQ-ADH.

https://ir.ymlib.yonsei.ac.kr/bitstream/22282913/94449/1/T201103709.pdf

Drosophila microbiome modulates host developmental and metabolic homeostasis via insulin signaling

http://sgpwe.izt.uam.mx/files/users/uami/acym/articulo_1.pdf

Food fermentations: Microorganisms with technological beneficial use

Isolated from a wide range of sources, the genus Paenibacillus comprises bacterial species relevant to humans, animals, plants, and the environment. Many Paenibacillus species can promote crop growth directly via biological nitrogen fixation, phosphate solubilization, production of the phytohormone indole-3-acetic acid (IAA), and release of siderophores that enable iron acquisition. They can also offer protection against insect herbivores and phytopathogens, including bacteria, fungi, nematodes, and viruses. This is accomplished by the production of a variety of antimicrobials and insecticides, and by triggering a hypersensitive defensive response of the plant, known as induced systemic resistance (ISR). Paenibacillus-derived antimicrobials also have applications in medicine, including polymyxins and fusaricidins, which are nonribosomal lipopeptides first isolated from strains of Paenibacillus polymyxa. Other useful molecules include exo-polysaccharides (EPS) and enzymes such as amylases, cellulases, hemicellulases, lipases, pectinases, oxygenases, dehydrogenases, lignin-modifying enzymes, and mutanases, which may have applications for detergents, food and feed, textiles, paper, biofuel, and healthcare. On the negative side, Paenibacillus larvae is the causative agent of American Foulbrood, a lethal disease of honeybees, while a variety of species are opportunistic infectors of humans, and others cause spoilage of pasteurized dairy products. This broad review summarizes the major positive and negative impacts of Paenibacillus: its realised and prospective contributions to agriculture, medicine, process manufacturing, and bioremediation, as well as its impacts due to pathogenicity and food spoilage. This review also includes detailed information in Additional files 1, 2, 3 for major known Paenibacillus species with their locations of isolation, genome sequencing projects, patents, and industrially significant compounds and enzymes. Paenibacillus will, over time, play increasingly important roles in sustainable agriculture and industrial biotechnology.

https://link.springer.com/content/pdf/10.1186%2Fs12934-016-0603-7.pdf

Current knowledge and perspectives of Paenibacillus : a review

Treated wastewater as irrigation source: a microbiological and chemical evaluation in apple and nectarine trees

Several studies have outlined that a balanced gut microbiota offers metabolic and protective functions supporting honeybee health and performance. The present work contributes to increasing knowledge on the impact on the honeybee gut microbiota of the three most common veterinary drugs (oxytetracycline, sulfonamides, and tylosin). The study was designed with a semi-field approach in micro-hives containing about 500 honeybees. Micro-hives were located in an incubator during the day and moved outdoors in the late afternoon, considering the restrictions on the use of antibiotics in the open field but allowing a certain freedom to honeybees; 6 replicates were considered for each treatment. The absolute abundance of the major gut microbial taxa in newly eclosed individuals was studied with qPCR and next-generation sequencing. Antimicrobial resistance genes for the target antibiotics were also monitored using a qPCR approach. The results showed that the total amount of gut bacteria was not altered by antibiotic treatment, but qualitative variations were observed. Tylosin treatment determined a significant decrease of α- and β-diversity indices and a strong depletion of the rectum population (lactobacilli and bifidobacteria) while favoring the ileum microorganisms (Gilliamella, Snodgrassella, and Frischella spp.). Major changes were also observed in honeybees treated with sulfonamides, with a decrease in Bartonella and Frischella core taxa and an increase of Bombilactobacillus spp. and Snodgrassella spp. The present study also shows an important effect of tetracycline that is focused on specific taxa with minor impact on alfa and beta diversity. Monitoring of antibiotic resistance genes confirmed that honeybees represent a great reservoir of tetracycline resistance genes. Tetracycline and sulfonamides resistance genes tended to increase in the gut microbiota population upon antibiotic administration. IMPORTANCE This study investigates the impact of the three most widely used antibiotics in the beekeeping sector (oxytetracycline, tylosin, and sulfonamides) on the honeybee gut microbiota and on the spread of antibiotic resistance genes. The research represents an advance to the present literature, considering that the tylosin and sulfonamides effects on the gut microbiota have never been studied. Another original aspect lies in the experimental approach used, as the study looks at the impact of veterinary drugs and feed supplements 24 days after the beginning of the administration, in order to explore perturbations in newly eclosed honeybees, instead of the same treated honeybee generation. Moreover, the study was not performed with cage tests but in micro-hives, thus achieving conditions closer to real hives. The study reaches the conclusion that the most common veterinary drugs determine changes in some core microbiota members and that incidence of resistance genes for tetracycline and sulfonamides increases following antibiotic treatment.

Honeybee Exposure to Veterinary Drugs: How Is the Gut Microbiota Affected?

Identification of Bifidobacterium spp. using hsp60 PCR-RFLP analysis: an update.

The study aimed to investigate the antibacterial activity of Melia azedarach fruit extracts in plant shoot culture. Unripe fruits were collected in different periods and the extracts were obtained through homogenization in an ethanol (EtOH) solution (40 g fresh weight in 100 ml 50 % EtOH) followed by EtOH evaporation. Their activity was tested against isolates of several bacterial species (Bacillus spp., Pseudomonas spp.) of agronomic interest, and on shoots of ‘MRS 2/5’ (Prunus cerasifera x Prunus spinosa) and calla lily (Zantedeschia aethiopica) inoculated (bacterized) with Microbacterium oleivorans (Mo), Bacillus subtilis (A17), Sphingomonas meloni (Sm) and Bacillus nealsonii (Bn). Shoot number and fresh weight of explants of ‘MRS 2/5’ on the proliferation medium and shoot length on the rooting medium were reduced in cultures derived from shoots bacterized with Mo and A17. Moreover, rooting frequency and root number decreased in A17-bacterized shoots. In calla lily, the number of rooted shoots was strongly reduced also by Sm. The extracts had a bactericidal activity against Mo, A17, Bn and most other Bacillus spp. isolates within 2-year trials. This activity remained unchanged against most of the tested bacterial strains after autoclave-sterilization (20 min at 120 °C). The filter-sterilized (0.22-μm Millipore membrane) extract generally reduced shoot elongation, and caused the death of some ‘MRS 2/5’shoots at a 20 % level in the proliferation medium, while all calla lily shoots survived the treatment. It strongly reduced Mo and Bn spread in both plant genotypes, and was even bactericidal against Mo in’MRS 2/5’, without showing any negative effect on growth of survived shoots already at the second subculture on standard medium. The HPTLC analysis revealed the prevalence of polyphenols in the extracts from fruits collected in two successive periods; this was consistent with their antimicrobial activity.

Antimicrobial activity of Melia azedarach fruit extracts for control of bacteria in inoculated in-vitro shoots of ‘MRS 2/5’ plum hybrid and calla lily and extract influence on the shoot cultures

The role of a balanced gut microbiota to maintain health and prevent diseases is largely established in humans and livestock. Conversely, in honeybees, studies on gut microbiota perturbations by external factors have started only recently. Natural methods alternative to chemical products to preserve honeybee health have been proposed, but their effect on the gut microbiota has not been examined in detail. This study aims to investigate the effect of the administration of a bacterial mixture of bifidobacteria and Lactobacillaceae and a commercial product HiveAliveTM on honeybee gut microbiota. The study was developed in 18 hives of about 2500 bees, with six replicates for each experimental condition for a total of three experimental groups. The absolute abundance of main microbial taxa was studied using qPCR and NGS. The results showed that the majority of the administered strains were detected in the gut. On the whole, great perturbations upon the administration of the bacterial mixture and the plant-based commercial product were not observed in the gut microbiota. Significant variations with respect to the untreated control were only observed for Snodgrassella sp. for the bacterial mixture, Bartonella sp. in HiveAliveTM and Bombilactobacillus sp. for both. Therefore, the studied approaches are respectful of the honeybee microbiota composition, conceivably without compromising the bee nutritional, social and ecological functions.

https://www.mdpi.com/2076-2607/9/5/1009/pdf

Loredana Baffoni

Papers

Treated wastewater as irrigation source: a microbiological and chemical evaluation in apple and nectarine trees

Honeybee Exposure to Veterinary Drugs: How Is the Gut Microbiota Affected?

Identification of Bifidobacterium spp. using hsp60 PCR-RFLP analysis: an update.

Antimicrobial activity of Melia azedarach fruit extracts for control of bacteria in inoculated in-vitro shoots of ‘MRS 2/5’ plum hybrid and calla lily and extract influence on the shoot cultures

Honeybees Exposure to Natural Feed Additives: How Is the Gut Microbiota Affected?