TY - JOUR AB - In recent years, microbiomes and their potential applications for human, animal or plant health, food production and environmental management came into the spotlight of major national and international policies and strategies. This has been accompanied by substantial R&D investments in both public and private sectors, with an increasing number of products entering the market. Despite widespread agreement on the potential of microbiomes and their uses across disciplines, stakeholders and countries, there is no consensus on what defines a microbiome application. This often results in non-comprehensive communication or insufficient documentation making commercialisation and acceptance of the novel products challenging. To showcase the complexity of this issue we discuss two selected, well-established applications and propose criteria defining a microbiome application and their conditions of use for clear communication, facilitating suitable regulatory frameworks and building trust among stakeholders. AU - Kostic, T.* AU - Schloter, M. AU - Arruda, P.* AU - Berg, G.* AU - Charles, T.C.* AU - Cotter, P.D.* AU - Kiran, G.S.* AU - Lange, L.* AU - Maguin, E.* AU - Meisner, A.* AU - van Overbeek, L.* AU - Sanz, Y.* AU - Sarand, I.* AU - Selvin, J.* AU - Tsakalidou, E.* AU - Smidt, H.* AU - Wagner, M.* AU - Sessitsch, A.* C1 - 71630 C2 - 56321 CY - 111 River St, Hoboken 07030-5774, Nj Usa TI - Concepts and criteria defining emerging microbiome applications. JO - Microb. Biotechnol. VL - 17 IS - 9 PB - Wiley PY - 2024 SN - 1751-7907 ER - TY - JOUR AB - We are surrounded by microbes, mostly bacteria and their viruses or phages, on the inside and outside of our bodies. These bacteria in constant interactions with phages are regulating multiple functions critical to our health. Luckily, they are amenable, but we need precise tools for their safe manipulation and improving human health. Here, we argue that recent advances in single-cell technologies, culturomics and synthetic biology offer exciting opportunities to create these tools as well as revealing specific phages-bacteria interactions in the body. AU - Khan Mirzaei, M. AU - Deng, L. C1 - 60595 C2 - 49407 CY - 111 River St, Hoboken 07030-5774, Nj Usa SP - 45-50 TI - Sustainable microbiome: A symphony orchestrated by synthetic phages. JO - Microb. Biotechnol. VL - 14 IS - 1 PB - Wiley PY - 2021 SN - 1751-7907 ER - TY - JOUR AB - Polymeric substances produced by microbes play a key role for the development of soil aggregates. Here, we investigated the dynamics of bacterial families contributing to the formation of exopolysaccharides and lipopolysaccharides, major constituents of polymeric substances, at a managed land reclamation site of a post-mining area. We collected soil samples from the initial and the agricultural management phase and expected a peak in the abundance of bacteria capable for exopolysaccharide and lipopolysaccharide production at the points of the biggest disturbances. We used shotgun metagenomic sequencing in combination with measurements of exopolysaccharide concentrations. Our results underline the importance of exopolysaccharide and lipopolysaccharide-producing bacteria after nutrient input combined with structural disturbance events, caused here by the initial planting of alfalfa and the introduction of a tillage regime together with organic fertilization in the agricultural management phase. Moreover, the changes in management caused a shift in the exopolysaccharide/lipopolysaccharide-producing community. The initial phase was dominated by typical colonizers of oligotrophic environments, specifically nitrogen fixers (Rhizobiaceae, Comamonadaceae, Hyphomicrobiaceae), while bacteria common in agricultural soils, such as Sphingomonadaceae, Oxalobacteraceae and Nitrospiraceae, prevailed in the agricultural management phase. AU - Vuko, M. AU - Cania, B. AU - Vogel, C.* AU - Kublik, S. AU - Schloter, M. AU - Schulz, S. C1 - 57803 C2 - 48108 CY - 111 River St, Hoboken 07030-5774, Nj Usa SP - 584-598 TI - Shifts in reclamation management strategies shape the role of exopolysaccharide and lipopolysaccharide-producing bacteria during soil formation. JO - Microb. Biotechnol. VL - 13 IS - 2 PB - Wiley PY - 2020 SN - 1751-7907 ER - TY - JOUR AB - The absence of suitable terminal electron acceptors (TEA) in soil might limit the oxidative metabolism of environmental microbial populations. Bioelectroventing is a bioelectrochemical strategy that aims to enhance the biodegradation of a pollutant in the environment by overcoming the electron acceptor limitation and maximizing metabolic oxidation. Microbial electroremediating cells (MERCs) are devices that can perform such a bioelectroventing. We also report an overall profile of the (14) C-ATR metabolites and (14) C mass balance in response to the different treatments. The objective of this work was to use MERC principles, under different configurations, to stimulate soil bacteria to achieve the complete biodegradation of the herbicide (14) C-atrazine (ATR) to (14) CO2 in soils. Our study concludes that using electrodes at a positive potential [+600 mV (versus Ag/AgCl)] ATR mineralization was enhanced by 20-fold when compared to natural attenuation in electrode-free controls. Furthermore, ecotoxicological analysis of the soil after the bioelectroventing treatment revealed an effective clean-up in < 20 days. The impact of electrodes on soil bioremediation suggests a promising future for this emerging environmental technology. AU - Domínguez-Garay, A.* AU - Quejigo, J.R.* AU - Dörfler, U. AU - Schroll, R. AU - Esteve-Núñez, A.* C1 - 51385 C2 - 43206 CY - Hoboken SP - 50-62 TI - Bioelectroventing: An electrochemical-assisted bioremediation strategy for cleaning-up atrazine-polluted soils. JO - Microb. Biotechnol. VL - 11 IS - 1 PB - Wiley PY - 2017 SN - 1751-7907 ER - TY - JOUR AB - The effects of different anthropic activities (vineyard: phytosanitary protection; winery: pressing and sulfiting) on the fungal populations of grape berries were studied. The global diversity of fungal populations (moulds and yeasts) was performed by pyrosequencing. The anthropic activities studied modified fungal diversity. Thus, a decrease in biodiversity was measured for three successive vintages for the grapes of the plot cultivated with Organic protection compared to plots treated with Conventional and Ecophyto protections. The fungal populations were then considerably modified by the pressing-clarification step. The addition of sulfur dioxide also modified population dynamics and favoured the domination of the species Saccharomyces cerevisiae during fermentation. The non-targeted chemical analysis of musts and wines by FT-ICR-MS showed that the wines could be discriminated at the end of alcoholic fermentation as a function of adding SO2 or not, but also and above all as a function of phytosanitary protection, regardless of whether these fermentations took place in the presence of SO2 or not. Thus, the existence of signatures in wines of chemical diversity and microbiology linked to vineyard protection has been highlighted. AU - Grangeteau, C.* AU - Roullier-Gall, C. AU - Rousseaux, S.* AU - Gougeon, R.D.* AU - Schmitt-Kopplin, P. AU - Alexandre, H.* AU - Guilloux-Benatier, M.* C1 - 50103 C2 - 42103 CY - Hoboken SP - 354-370 TI - Wine microbiology is driven by vineyard and winery anthropogenic factors. JO - Microb. Biotechnol. VL - 10 IS - 2 PB - Wiley PY - 2017 SN - 1751-7907 ER - TY - JOUR AB - Cyanides are highly toxic and produced by various microorganisms as defence strategy or to increase their competitiveness. As degradation is the most efficient way of detoxification, some microbes developed the capability to use cyanides as carbon and nitrogen source. However, it is not clear if this potential also helps to lower cyanide concentrations in roadside soils where deicing salt application leads to significant inputs of ferrocyanide. The question remains if biodegradation in soils can occur without previous photolysis. By conducting a microcosm experiment using soils with/without pre-exposition to road salts spiked with (13) C-labelled ferrocyanide, we were able to confirm biodegradation and in parallel to identify bacteria using ferrocyanide as C source via DNA stable isotope probing (DNA-SIP), TRFLP fingerprinting and pyrosequencing. Bacteria assimilating (13) C were highly similar in the pre-exposed soils, belonging mostly to Actinomycetales (Kineosporia, Mycobacterium, Micromonosporaceae). In the soil without pre-exposition, bacteria belonging to Acidobacteria (Gp3, Gp4, Gp6), Gemmatimonadetes (Gemmatimonas) and Gammaproteobacteria (Thermomonas, Xanthomonadaceae) used ferrocyanide as C source but not the present Actinomycetales. This indicated that (i) various bacteria are able to assimilate ferrocyanide-derived C and (ii) long-term exposition to ferrocyanide applied with deicing salts leads to Actinomycetales outcompeting other microorganisms for the use of ferrocyanide as C source. AU - Gschwendtner, S. AU - Mansfeldt, T.* AU - Kublik, S. AU - Touliari, E. AU - Buegger, F. AU - Schloter, M. C1 - 48632 C2 - 41236 CY - Hoboken SP - 502-513 TI - Long-term ferrocyanide application via deicing salts promotes the establishment of actinomycetales assimilating ferrocyanide-derived carbon in soil. JO - Microb. Biotechnol. VL - 9 IS - 4 PB - Wiley-blackwell PY - 2016 SN - 1751-7907 ER - TY - JOUR AB - The absence of suitable terminal electron acceptors (TEA) in soil might limit the oxidative metabolism of environmental microbial populations. Microbial electroremediating cells (MERCs) consist in a variety of bioelectrochemical devices that aim to overcome electron acceptor limitation and maximize metabolic oxidation with the purpose of enhancing the biodegradation of a pollutant in the environment. The objective of this work was to use MERCs principles for stimulating soil bacteria to achieve the complete biodegradation of the herbicide (14) C-isoproturon (IPU) to (14) CO2 in soils. Our study concludes that using electrodes at a positive potential [+600 mV (versus Ag/AgCl)] enhanced the mineralization by 20-fold respect the electrode-free control. We also report an overall profile of the (14) C-IPU metabolites and a (14) C mass balance in response to the different treatments. The remarkable impact of electrodes on the microbial activity of natural communities suggests a promising future for this emerging environmental technology that we propose to name bioelectroventing. AU - Quejigo, J.R. AU - Dörfler, U. AU - Schroll, R. AU - Esteve-Núñez, A.* C1 - 47913 C2 - 39750 CY - Hoboken SP - 369-380 TI - Stimulating soil microorganisms for mineralizing the herbicide isoproturon by means of microbial electroremediating cells. JO - Microb. Biotechnol. VL - 9 IS - 3 PB - Wiley-blackwell PY - 2016 SN - 1751-7907 ER - TY - JOUR AB - Therapeutic vaccines are currently developed for chronic viral infections, such as human papillomavirus (HPV), human immunodeficiency virus (HIV), herpesvirus and hepatitis B (HBV) and C (HCV) virus infections. As an alternative to antiviral treatment or to support only partially effective therapy a therapeutic vaccine shall activate the patient's immune system to fight and finally control or ideally even eliminate the virus. Whereas the success of prophylactic vaccination is based on rapid neutralization of the invading pathogen by antibodies, virus control and elimination of infected cells require T cells. Therefore, induction of a multi-specific and multifunctional T-cell response against key viral antigens is a paradigm of therapeutic vaccination - besides activation of a humoral immune response to limit virus spread. In this review, we describe options to develop a therapeutic vaccine for chronic viral infections using HBV as a promising example. AU - Kutscher, S. AU - Bauer, T. AU - Dembek, C.J. AU - Sprinzl, M.F. AU - Protzer, U. C1 - 6702 C2 - 29139 SP - 270-282 TI - Design of therapeutic vaccines: Hepatitis B as an example. JO - Microb. Biotechnol. VL - 5 IS - 2 PB - Society for Applied Microbiology and Blackwell Publishing Ltd. PY - 2012 SN - 1751-7907 ER -