TY  - JOUR
AB  - INTRODUCTION: Microbiome amplicon sequencing data are distorted by multiple protocol-dependent biases from bacterial DNA extraction, contamination, sequence errors, and chimeras, hindering clinical microbiome applications. In particular, extraction bias is a major confounder in sequencing-based microbiome analyses, with no correction method available to date. Here, we suggest using mock community controls to computationally correct extraction bias based on bacterial morphological properties. METHODS: We compared dilution series of 3 cell mock communities with an even or staggered composition. DNA of these mock, and additional skin microbiome samples, was extracted with 8 different extraction protocols (2 buffers, 2 extraction kits, 2 lysis conditions). Extracted DNA was sequenced (V1-V3 16S rRNA gene) together with corresponding DNA mocks. RESULTS: Microbiome composition was significantly different between extraction kits and lysis conditions, but not between buffers. Independent of the extraction protocol, chimera formation increased with higher input cell numbers. Contaminants originated mostly from buffers, and considerable cross-contamination was observed in low-input samples. Comparing the microbiome composition of the cell mocks to corresponding DNA mocks revealed taxon-specific protocol-dependent extraction bias. Strikingly, this extraction bias per species was predictable by bacterial cell morphology. Morphology-based computational correction of extraction bias significantly improved resulting microbial compositions when applied to different mock samples, even with different taxa. Equivalent correction of the skin samples showed a substantial impact on microbiome compositions. CONCLUSIONS: Our results indicate that higher DNA density increases chimera formation during PCR amplification. Furthermore, we show that computational correction of extraction bias based on bacterial cell morphology would be feasible using appropriate positive controls, thus constituting an important step toward overcoming protocol biases in microbiome analysis. Video Abstract.
AU  - Rauer, L.
AU  - De Tomassi, A.*
AU  - Müller, C.L.
AU  - Hülpüsch, C.*
AU  - Traidl-Hoffmann, C.
AU  - Reiger, M.
AU  - Neumann, A.U.
C1  - 73297
C2  - 56988
CY  - Campus, 4 Crinan St, London N1 9xw, England
TI  - De-biasing microbiome sequencing data: Bacterial morphology-based correction of extraction bias and correlates of chimera formation.
JO  - Microbiome
VL  - 13
IS  - 1
PB  - Bmc
PY  - 2025
SN  - 2049-2618
ER  - 

TY  - JOUR
AB  - BACKGROUND: The rhizosheath, a cohesive soil layer firmly adhering to plant roots, plays a vital role in facilitating water and mineral uptake. In pearl millet, rhizosheath formation is genetically controlled and influenced by root exudates. Here, we investigated the impact of root exudates on the microbiota composition, interactions, and assembly processes, and rhizosheath structure in pearl millet using four distinct lines with contrasting soil aggregation abilities. RESULTS: Utilizing 16S rRNA gene and ITS metabarcoding for microbiota profiling, coupled with FTICR-MS metabonomic analysis of metabolite composition in distinct plant compartments and root exudates, we revealed substantial disparities in microbial diversity and interaction networks. The ß-NTI analysis highlighted bacterial rhizosphere turnover driven primarily by deterministic processes, showcasing prevalent homogeneous selection in root tissue (RT) and root-adhering soil (RAS). Conversely, fungal communities were more influenced by stochastic processes. In bulk soil assembly, a combination of deterministic and stochastic mechanisms shapes composition, with deterministic factors exerting a more pronounced role. Metabolic profiles across shoots, RT, and RAS in different pearl millet lines mirrored their soil aggregation levels, emphasizing the impact of inherent plant traits on microbiota composition and unique metabolic profiles in RT and exudates. Notably, exclusive presence of antimicrobial compounds, including DIMBOA and H-DIMBOA, emerged in root exudates and RT of low aggregation lines. CONCLUSIONS: This research underscores the pivotal influence of root exudates in shaping the root-associated microbiota composition across pearl millet lines, entwined with their soil aggregation capacities. These findings underscore the interconnectedness of root exudates and microbiota, which jointly shape rhizosheath structure, deepening insights into soil-plant-microbe interactions and ecological processes shaping rhizosphere microbial communities. Deciphering plant-microbe interactions and their contribution to soil aggregation and microbiota dynamics holds promise for the advancement of sustainable agricultural strategies. Video Abstract.
AU  - Alahmad, A.*
AU  - Harir, M.
AU  - Fochesato, S.*
AU  - Tulumello, J.*
AU  - Walker, A.
AU  - Barakat, M.*
AU  - Ndour, P.M.S.*
AU  - Schmitt-Kopplin, P.
AU  - Cournac, L.*
AU  - Laplaze, L.*
AU  - Heulin, T.*
AU  - Achouak, W.*
C1  - 69018
C2  - 55193
CY  - Campus, 4 Crinan St, London N1 9xw, England
TI  - Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet.
JO  - Microbiome
VL  - 12
IS  - 1
PB  - Bmc
PY  - 2024
SN  - 2049-2618
ER  - 

TY  - JOUR
AB  - BACKGROUND: Darier's disease (DD) is a genodermatosis caused by mutations of the ATP2A2 gene leading to disrupted keratinocyte adhesion. Recurrent episodes of skin inflammation and infections with a typical malodour in DD indicate a role for microbial dysbiosis. Here, for the first time, we investigated the DD skin microbiome using a metabarcoding approach of 115 skin swabs from 14 patients and 14 healthy volunteers. Furthermore, we analyzed its changes in the context of DD malodour and the cutaneous DD transcriptome. RESULTS: We identified a disease-specific cutaneous microbiome with a loss of microbial diversity and of potentially beneficial commensals. Expansion of inflammation-associated microbes such as Staphylococcus aureus and Staphylococcus warneri strongly correlated with disease severity. DD dysbiosis was further characterized by abundant species belonging to Corynebacteria, Staphylococci and Streptococci groups displaying strong associations with malodour intensity. Transcriptome analyses showed marked upregulation of epidermal repair, inflammatory and immune defence pathways reflecting epithelial and immune response mechanisms to DD dysbiotic microbiome. In contrast, barrier genes including claudin-4 and cadherin-4 were downregulated. CONCLUSIONS: These findings allow a better understanding of Darier exacerbations, highlighting the role of cutaneous dysbiosis in DD inflammation and associated malodour. Our data also suggest potential biomarkers and targets of intervention for DD. Video Abstract.
AU  - Amar, Y.*
AU  - Rogner, D.*
AU  - Silva, R.*
AU  - Fösel, B.
AU  - Ud-Dean, M.
AU  - Lagkouvardos, I.*
AU  - Steimle-Grauer, S.A.*
AU  - Niedermeier, S.*
AU  - Kublik, S.
AU  - Jargosch, M.*
AU  - Heinig, M.
AU  - Thomas, J.
AU  - Eyerich, S.
AU  - Wikström, J.D.*
AU  - Schloter, M.
AU  - Eyerich, K.*
AU  - Biedermann, T.*
AU  - Köberle, M.*
C1  - 68064
C2  - 54542
CY  - Campus, 4 Crinan St, London N1 9xw, England
TI  - Darier's disease exhibits a unique cutaneous microbial dysbiosis associated with inflammation and body malodour.
JO  - Microbiome
VL  - 11
IS  - 1
PB  - Bmc
PY  - 2023
SN  - 2049-2618
ER  - 

TY  - JOUR
AB  - Following publication of the original article [1], the author reported that the name “Jakob Wikström” should be “Jakob D Wikström” This has been corrected above and the original article has been updated.
AU  - Amar, Y.*
AU  - Rogner, D.*
AU  - Silva, R.*
AU  - Fösel, B.
AU  - Ud-Dean, M.
AU  - Lagkouvardos, I.*
AU  - Steimle‑Grauer, S.A.*
AU  - Niedermeier, S.*
AU  - Kublik, S.
AU  - Jargosch, M.*
AU  - Heinig, M.
AU  - Thomas, J.
AU  - Eyerich, S.
AU  - Wikström, J.D.*
AU  - Schloter, M.
AU  - Eyerich, K.*
AU  - Biedermann, T.*
AU  - Köberle, M.*
C1  - 68279
C2  - 54704
CY  - Campus, 4 Crinan St, London N1 9xw, England
TI  - Correction: Darier’s disease exhibits a unique cutaneous microbial dysbiosis associated with inflammation and body malodour (Microbiome, (2023), 11, 1, (162), 10.1186/s40168-023-01587-x).
JO  - Microbiome
VL  - 11
IS  - 1
PB  - Bmc
PY  - 2023
SN  - 2049-2618
ER  - 

TY  - JOUR
AB  - BACKGROUND: Bariatric surgery remains the most effective therapy for adiposity reduction and remission of type 2 diabetes. Although different bariatric procedures associate with pronounced shifts in the gut microbiota, their functional role in the regulation of energetic and metabolic benefits achieved with the surgery are not clear. METHODS: To evaluate the causal as well as the inherent therapeutic character of the surgery-altered gut microbiome in improved energy and metabolic control in diet-induced obesity, an antibiotic cocktail was used to eliminate the gut microbiota in diet-induced obese rats after gastric bypass surgery, and gastric bypass-shaped gut microbiota was transplanted into obese littermates. Thorough metabolic profiling was combined with omics technologies on samples collected from cecum and plasma to identify adaptions in gut microbiota-host signaling, which control improved energy balance and metabolic profile after surgery. RESULTS: In this study, we first demonstrate that depletion of the gut microbiota largely reversed the beneficial effects of gastric bypass surgery on negative energy balance and improved glucolipid metabolism. Further, we show that the gastric bypass-shaped gut microbiota reduces adiposity in diet-induced obese recipients by re-activating energy expenditure from metabolic active brown adipose tissue. These beneficial effects were linked to improved glucose homeostasis, lipid control, and improved fatty liver disease. Mechanistically, these effects were triggered by modulation of taurine metabolism by the gastric bypass gut microbiota, fostering an increased abundance of intestinal and circulating taurine-conjugated bile acid species. In turn, these bile acids activated gut-restricted FXR and systemic TGR5 signaling to stimulate adaptive thermogenesis. CONCLUSION: Our results establish the role of the gut microbiome in the weight loss and metabolic success of gastric bypass surgery. We here identify a signaling cascade that entails altered bile acid receptor signaling resulting from a collective, hitherto undescribed change in the metabolic activity of a cluster of bacteria, thereby readjusting energy imbalance and metabolic disease in the obese host. These findings strengthen the rationale for microbiota-targeted strategies to improve and refine current therapies of obesity and metabolic syndrome. Video Abstract Bariatric Surgery (i.e. RYGB) or the repeated fecal microbiota transfer (FMT) from RYGB donors into DIO (diet-induced obesity) animals induces shifts in the intestinal microbiome, an effect that can be impaired by oral application of antibiotics (ABx). Our current study shows that RYGB-dependent alterations in the intestinal microbiome result in an increase in the luminal and systemic pool of Taurine-conjugated Bile acids (TCBAs) by various cellular mechanisms acting in the intestine and the liver. TCBAs induce signaling via two different receptors, farnesoid X receptor (FXR, specifically in the intestines) and the G-protein-coupled bile acid receptor TGR5 (systemically), finally resulting in metabolic improvement and advanced weight management. BSH, bile salt hydrolase; BAT brown adipose tissue.
AU  - Münzker, J.*
AU  - Haase, N.*
AU  - Till, A.*
AU  - Sucher, R.*
AU  - Haange, S.B.*
AU  - Nemetschke, L.*
AU  - Gnad, T.*
AU  - Jäger, E.*
AU  - Chen, J.*
AU  - Riede, S.J.*
AU  - Chakaroun, R.*
AU  - Massier, L.*
AU  - Kovacs, P.*
AU  - Ost, M.*
AU  - Rolle-Kampczyk, U.*
AU  - Jehmlich, N.*
AU  - Weiner, J.*
AU  - Heiker, J.T.
AU  - Klöting, N.
AU  - Seeger, G.*
AU  - Morawski, M.*
AU  - Keitel, V.*
AU  - Pfeifer, A.*
AU  - von Bergen, M.*
AU  - Heeren, J.*
AU  - Krügel, U.*
AU  - Fenske, W.K.*
C1  - 65534
C2  - 52319
TI  - Functional changes of the gastric bypass microbiota reactivate thermogenic adipose tissue and systemic glucose control via intestinal FXR-TGR5 crosstalk in diet-induced obesity.
JO  - Microbiome
VL  - 10
IS  - 1
PY  - 2022
SN  - 2049-2618
ER  - 

TY  - JOUR
AB  - BACKGROUND: Caloric restriction can delay the development of metabolic diseases ranging from insulin resistance to type 2 diabetes and is linked to both changes in the composition and metabolic function of the gut microbiota and immunological consequences. However, the interaction between dietary intake, the microbiome, and the immune system remains poorly described. RESULTS: We transplanted the gut microbiota from an obese female before (AdLib) and after (CalRes) an 8-week very-low-calorie diet (800 kcal/day) into germ-free mice. We used 16S rRNA sequencing to evaluate taxa with differential abundance between the AdLib- and CalRes-microbiota recipients and single-cell multidimensional mass cytometry to define immune signatures in murine colon, liver, and spleen. Recipients of the CalRes sample exhibited overall higher alpha diversity and restructuring of the gut microbiota with decreased abundance of several microbial taxa (e.g., Clostridium ramosum, Hungatella hathewayi, Alistipi obesi). Transplantation of CalRes-microbiota into mice decreased their body fat accumulation and improved glucose tolerance compared to AdLib-microbiota recipients. Finally, the CalRes-associated microbiota reduced the levels of intestinal effector memory CD8+ T cells, intestinal memory B cells, and hepatic effector memory CD4+ and CD8+ T cells. CONCLUSION: Caloric restriction shapes the gut microbiome which can improve metabolic health and may induce a shift towards the naïve T and B cell compartment and, thus, delay immune senescence. Understanding the role of the gut microbiome as mediator of beneficial effects of low calorie diets on inflammation and metabolism may enhance the development of new therapeutic treatment options for metabolic diseases. TRIAL REGISTRATION: NCT01105143 , "Effects of negative energy balance on muscle mass regulation," registered 16 April 2010. Video Abstract.
AU  - Sbierski-Kind, J.*
AU  - Grenkowitz, S.*
AU  - Schlickeiser, S.*
AU  - Sandforth, A.
AU  - Friedrich, M.*
AU  - Kunkel, D.*
AU  - Glauben, R.*
AU  - Brachs, S.*
AU  - Mai, K.*
AU  - Thürmer, A.*
AU  - Radonić, A.*
AU  - Drechsel, O.*
AU  - Turnbaugh, P.J.*
AU  - Bisanz, J.E.*
AU  - Volk, H.D.*
AU  - Spranger, J.*
AU  - Jumpertz von Schwartzenberg, R.
C1  - 64741
C2  - 51946
TI  - Effects of caloric restriction on the gut microbiome are linked with immune senescence.
JO  - Microbiome
VL  - 10
IS  - 1
PY  - 2022
SN  - 2049-2618
ER  - 

TY  - JOUR
AB  - BACKGROUND: Inflammatory bowel diseases (IBDs) including Crohn's disease (CD) and ulcerative colitis (UC) are characterized by chronic and debilitating gut inflammation. Altered bacterial communities of the intestine are strongly associated with IBD initiation and progression. The gut virome, which is primarily composed of bacterial viruses (bacteriophages, phages), is thought to be an important factor regulating and shaping microbial communities in the gut. While alterations in the gut virome have been observed in IBD patients, the contribution of these viruses to alterations in the bacterial community and heightened inflammatory responses associated with IBD patients remains largely unknown. RESULTS: Here, we performed in vivo microbial cross-infection experiments to follow the effects of fecal virus-like particles (VLPs) isolated from UC patients and healthy controls on bacterial diversity and severity of experimental colitis in human microbiota-associated (HMA) mice. Shotgun metagenomics confirmed that several phages were transferred to HMA mice, resulting in treatment-specific alterations in the gut virome. VLPs from healthy and UC patients also shifted gut bacterial diversity of these mice, an effect that was amplified during experimental colitis. VLPs isolated from UC patients specifically altered the relative abundance of several bacterial taxa previously implicated in IBD progression. Additionally, UC VLP administration heightened colitis severity in HMA mice, as indicated by shortened colon length and increased pro-inflammatory cytokine production. Importantly, this effect was dependent on intact VLPs. CONCLUSIONS: Our findings build on recent literature indicating that phages are dynamic regulators of bacterial communities in the gut and implicate the intestinal virome in modulating intestinal inflammation and disease. Video Abstract.
AU  - Sinha, A.*
AU  - Li, Y.*
AU  - Mirzaei, M.K.
AU  - Shamash, M.*
AU  - Samadfam, R.*
AU  - King, I.L.*
AU  - Maurice, C.F.*
C1  - 65654
C2  - 52853
TI  - Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis.
JO  - Microbiome
VL  - 10
IS  - 1
PY  - 2022
SN  - 2049-2618
ER  - 

TY  - JOUR
AB  - Background: The identification of microbiota based on next-generation sequencing (NGS) of extracted DNA has drastically improved our understanding of the role of microbial communities in health and disease. However, DNA-based microbiome analysis cannot per se differentiate between living and dead microorganisms. In environments such as the skin, host defense mechanisms including antimicrobial peptides and low cutaneous pH result in a high microbial turnover, likely resulting in high numbers of dead cells present and releasing substantial amounts of microbial DNA. NGS analyses may thus lead to inaccurate estimations of microbiome structures and consequently functional capacities. Results: We investigated in this study the feasibility of a Benzonase-based approach (BDA) to pre-digest unprotected DNA, i.e., of dead microbial cells, as a method to overcome these limitations, thus offering a more accurate assessment of the living microbiome. A skin mock community as well as skin microbiome samples were analyzed using 16S rRNA gene sequencing and metagenomics sequencing after DNA extraction with and without a Benzonase digest to assess bacterial diversity patterns. The BDA method resulted in less reads from dead bacteria both in the skin mock community and skin swabs spiked with either heat-inactivated bacteria or bacterial-free DNA. This approach also efficiently depleted host DNA reads in samples with high human-to-microbial DNA ratios, with no obvious impact on the microbiome profile. We further observed that low biomass samples generate an α-diversity bias when the bacterial load is lower than 10  CFU and that Benzonase digest is not sufficient to overcome this bias. Conclusions: The BDA approach enables both a better assessment of the living microbiota and depletion of host DNA reads. [MediaObject not available: see fulltext.] Graphical abstract: [Figure not available: see fulltext.]
AU  - Amar, Y.
AU  - Lagkouvardos, I.*
AU  - Silva, R.L.
AU  - Ishola, O.A.
AU  - Fösel, B.
AU  - Kublik, S.
AU  - Schöler, A.
AU  - Niedermeier, S.*
AU  - Bleuel, R.
AU  - Zink, A.
AU  - Neuhaus, K.*
AU  - Schloter, M.
AU  - Biedermann, T.
AU  - Köberle, M.*
C1  - 62168
C2  - 50687
CY  - Campus, 4 Crinan St, London N1 9xw, England
TI  - Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA.
JO  - Microbiome
VL  - 9
IS  - 1
PB  - Bmc
PY  - 2021
SN  - 2049-2618
ER  - 

TY  - JOUR
AB  - Background: The gut microbiome impacts human health through various mechanisms and is involved in the development of a range of non-communicable diseases. Diet is a well-known factor influencing microbe-host interaction in health and disease. However, very few findings are based on large-scale analysis using population-based studies. Our aim was to investigate the cross-sectional relationship between habitual dietary intake and gut microbiota structure in the Cooperative Health Research in the Region of Augsburg (KORA) FF4 study. Results: Fecal microbiota was analyzed using 16S rRNA gene amplicon sequencing. Latent Dirichlet allocation (LDA) was applied to samples from 1992 participants to identify 20 microbial subgroups within the study population. Each participant’s gut microbiota was subsequently described by a unique composition of these 20 subgroups. Associations between habitual dietary intake, assessed via repeated 24-h food lists and a Food Frequency Questionnaire, and the 20 subgroups, as well as between prevalence of metabolic diseases/risk factors and the subgroups, were assessed with multivariate-adjusted Dirichlet regression models. After adjustment for multiple testing, eight of 20 microbial subgroups were significantly associated with habitual diet, while nine of 20 microbial subgroups were associated with the prevalence of one or more metabolic diseases/risk factors. Subgroups 5 (Faecalibacterium, Lachnospiracea incertae sedis, Gemmiger, Roseburia) and 14 (Coprococcus, Bacteroides, Faecalibacterium, Ruminococcus) were particularly strongly associated with diet. For example, participants with a high probability for subgroup 5 were characterized by a higher Alternate Healthy Eating Index and Mediterranean Diet Score and a higher intake of food items such as fruits, vegetables, legumes, and whole grains, while participants with prevalent type 2 diabetes mellitus were characterized by a lower probability for subgroup 5. Conclusions: The associations between habitual diet, metabolic diseases, and microbial subgroups identified in this analysis not only expand upon current knowledge of diet-microbiota-disease relationships, but also indicate the possibility of certain microbial groups to be modulated by dietary intervention, with the potential of impacting human health. Additionally, LDA appears to be a powerful tool for interpreting latent structures of the human gut microbiota. However, the subgroups and associations observed in this analysis need to be replicated in further studies. [MediaObject not available: see fulltext.].
AU  - Breuninger, T.
AU  - Wawro, N.
AU  - Breuninger, J.*
AU  - Reitmeier, S.*
AU  - Clavel, T.*
AU  - Six-Merker, J.
AU  - Pestoni, G.*
AU  - Rohrmann, S.*
AU  - Rathmann, W.*
AU  - Peters, A.
AU  - Grallert, H.
AU  - Meisinger, C.
AU  - Haller, D.*
AU  - Linseisen, J.
C1  - 61641
C2  - 50167
CY  - Campus, 4 Crinan St, London N1 9xw, England
TI  - Associations between habitual diet, metabolic disease, and the gut microbiota using latent Dirichlet allocation.
JO  - Microbiome
VL  - 9
IS  - 1
PB  - Bmc
PY  - 2021
SN  - 2049-2618
ER  - 

TY  - JOUR
AB  - BACKGROUND: The hyperarid core of the Atacama Desert is an extremely harsh environment thought to be colonized by only a few heterotrophic bacterial species. Current concepts for understanding this extreme ecosystem are mainly based on the diversity of these few species, yet a substantial area of the Atacama Desert hyperarid topsoil is covered by expansive boulder accumulations, whose underlying microbiomes have not been investigated so far. With the hypothesis that these sheltered soils harbor uniquely adapted microbiomes, we compared metagenomes and geochemistry between soils below and beside boulders across three distantly located boulder accumulations in the Atacama Desert hyperarid core. RESULTS: Genome-resolved metagenomics of eleven samples revealed substantially different microbial communities in soils below and beside boulders, despite the presence of shared species. Archaea were found in significantly higher relative abundance below the boulders across all samples within distances of up to 205 km. These key taxa belong to a novel genus of ammonia-oxidizing Thaumarchaeota, Candidatus Nitrosodeserticola. We resolved eight mid-to-high quality genomes of this genus and used comparative genomics to analyze its pangenome and site-specific adaptations. Ca. Nitrosodeserticola genomes contain genes for ammonia oxidation, the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway, and acetate utilization indicating a chemolithoautotrophic and mixotrophic lifestyle. They also possess the capacity for tolerating extreme environmental conditions as highlighted by the presence of genes against oxidative stress and DNA damage. Site-specific adaptations of the genomes included the presence of additional genes for heavy metal transporters, multiple types of ATP synthases, and divergent genes for aquaporins. CONCLUSION: We provide the first genomic characterization of hyperarid soil microbiomes below the boulders in the Atacama Desert, and report abundant and highly adapted Thaumarchaeaota with ammonia oxidation and carbon fixation potential. Ca. Nitrosodeserticola genomes provide the first metabolic and physiological insight into a thaumarchaeal lineage found in globally distributed terrestrial habitats characterized by various environmental stresses. We consequently expand not only the known genetic repertoire of Thaumarchaeota but also the diversity and microbiome functioning in hyperarid ecosystems. Video Abstract.
AU  - Hwang, Y.*
AU  - Schulze-Makuch, D.*
AU  - Arens, F.L.*
AU  - Saenz Medina, J.S.
AU  - Adam, P.S.*
AU  - Sager, C.*
AU  - Bornemann, T.L.V.*
AU  - Zhao, W.*
AU  - Zhang, Y.*
AU  - Airo, A.*
AU  - Schloter, M.
AU  - Probst, A.J.*
C1  - 63621
C2  - 51606
CY  - Campus, 4 Crinan St, London N1 9xw, England
TI  - Leave no stone unturned: Individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core.
JO  - Microbiome
VL  - 9
IS  - 1
PB  - Bmc
PY  - 2021
SN  - 2049-2618
ER  - 

TY  - JOUR
AB  - The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role.
AU  - Berg, G.*
AU  - Rybakova, D.*
AU  - Fischer, D.
AU  - Cernava, T.*
AU  - Vergès, M.C.C.*
AU  - Charles, T.*
AU  - Chen, X.*
AU  - Cocolin, L.*
AU  - Eversole, K.*
AU  - Corral, G.H.*
AU  - Kazou, M.*
AU  - Kinkel, L.*
AU  - Lange, L.*
AU  - Lima, N.*
AU  - Loy, A.*
AU  - Macklin, J.A.*
AU  - Maguin, E.*
AU  - Mauchline, T.*
AU  - McClure, R.*
AU  - Mitter, B.*
AU  - Ryan, M.*
AU  - Sarand, I.*
AU  - Smidt, H.*
AU  - Schelkle, B.*
AU  - Roume, H.*
AU  - Kiran, G.S.*
AU  - Selvin, J.*
AU  - Souza, R.S.C.d.*
AU  - van Overbeek, L.*
AU  - Singh, B.K.*
AU  - Wagner, M.*
AU  - Walsh, A.*
AU  - Sessitsch, A.*
AU  - Schloter, M.
C1  - 59638
C2  - 48907
CY  - Campus, 4 Crinan St, London N1 9xw, England
TI  - Microbiome definition re-visited: Old concepts and new challenges.
JO  - Microbiome
VL  - 8
IS  - 1
PB  - Bmc
PY  - 2020
SN  - 2049-2618
ER  - 

TY  - JOUR
AB  - An amendment to this paper has been published and can be accessed via the original article.
AU  - Berg, G.*
AU  - Rybakova, D.*
AU  - Fischer, D.
AU  - Cernava, T.*
AU  - Vergès, M.C.C.*
AU  - Charles, T.*
AU  - Chen, X.*
AU  - Cocolin, L.*
AU  - Eversole, K.*
AU  - Corral, G.H.*
AU  - Kazou, M.*
AU  - Kinkel, L.*
AU  - Lange, L.*
AU  - Lima, N.*
AU  - Loy, A.*
AU  - Macklin, J.A.*
AU  - Maguin, E.*
AU  - Mauchline, T.*
AU  - McClure, R.*
AU  - Mitter, B.*
AU  - Ryan, M.*
AU  - Sarand, I.*
AU  - Smidt, H.*
AU  - Schelkle, B.*
AU  - Roume, H.*
AU  - Kiran, G.S.*
AU  - Selvin, J.*
AU  - de Souza, R.S.C.*
AU  - van Overbeek, L.*
AU  - Singh, B.K.*
AU  - Wagner, M.*
AU  - Walsh, A.*
AU  - Sessitsch, A.*
AU  - Schloter, M.
C1  - 59971
C2  - 49806
CY  - Campus, 4 Crinan St, London N1 9xw, England
TI  - Microbiome definition re-visited: Old concepts and new challenges (vol 8, 103, 2020).
JO  - Microbiome
VL  - 8
IS  - 1
PB  - Bmc
PY  - 2020
SN  - 2049-2618
ER  - 

TY  - JOUR
AB  - BackgroundAquaculture is on the rise worldwide, and the use of antibiotics is fostering higher production intensity. However, recent findings suggest that the use of antibiotics comes at the price of increased antibiotic resistance. Yet, the effect of the oral administration of antibiotics on the mobility of microbial resistance genes in the fish gut is not well understood. In the present study, Piaractus mesopotamicus was used as a model to evaluate the effect of the antimicrobial florfenicol on the diversity of the gut microbiome as well as antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) using a metagenomic approach.ResultsThe total relative abundance of ARGs and MGEs significantly increased during the antibiotic exposure. Additionally, phage integrases, transposases, and transposons flanking ARGs accumulated in the gut microbiome of P. mesopotamicus because of the antibiotic exposure. MGEs co-occurring with ARGs showed a significant positive correlation with the total ARGs found. Furthermore, shifts in the gut microbiome towards well-known putative pathogens such as Salmonella, Plesiomonas, and Citrobacter were observed following florfenicol treatment. Mainly Plesiomonas and Citrobacter harbored genes that code for multidrug and phenicol efflux pumps. Moreover, several genes related to RNA processing and modification, cell motility, SOS response, and extracellular structure were enriched due to the antibiotic application. The observed effects were visible during the complete application phase and disappeared at the post-exposure phase.ConclusionsOur findings suggest that the oral administration of antibiotics increases the potential for MGE-mediated exchange of ARGs in the gut of fish and could contribute to the enrichment and dispersion of ARGs in aquaculture systems. Importantly, this increase in the potential for ARGs exchange could be an effect of changes in community structure and/or ARG mobilization.
AU  - Saenz Medina, J.S.
AU  - Marques, T.V.*
AU  - Barone, R.S.C.*
AU  - Cyrino, J.E.P.*
AU  - Kublik, S.
AU  - Nesme, J.
AU  - Schloter, M.
AU  - Rath, S.*
AU  - Vestergaard, G.
C1  - 55528
C2  - 46383
CY  - Campus, 4 Crinan St, London N1 9xw, England
TI  - Oral administration of antibiotics increased the potential mobility of bacterial resistance genes in the gut of the fish Piaractus mesopotamicus.
JO  - Microbiome
VL  - 7
IS  - 1
PB  - Bmc
PY  - 2019
SN  - 2049-2618
ER  - 

TY  - JOUR
AB  - BACKGROUND: Natural oil seeps offer the opportunity to study the adaptation of ecosystems and the associated microbiota to long-term oil exposure. In the current study, we investigated a land-to-sea transition ecosystem called "Keri Lake" in Zakynthos Island, Greece. This ecosystem is unique due to asphalt oil springs found at several sites, a phenomenon already reported 2500 years ago. Sediment microbiomes at Keri Lake were studied, and their structure and functional potential were compared to other ecosystems with oil exposure histories of various time periods.RESULTS: Replicate sediment cores (up to 3-m depth) were retrieved from one site exposed to oil as well as a non-exposed control site. Samples from three different depths were subjected to chemical analysis and metagenomic shotgun sequencing. At the oil-exposed site, we observed high amounts of asphalt oil compounds and a depletion of sulfate compared to the non-exposed control site. The numbers of reads assigned to genes involved in the anaerobic degradation of hydrocarbons were similar between the two sites. The numbers of denitrifiers and sulfate reducers were clearly lower in the samples from the oil-exposed site, while a higher abundance of methanogens was detected compared to the non-exposed site. Higher abundances of the genes of methanogenesis were also observed in the metagenomes from other ecosystems with a long history of oil exposure, compared to short-term exposed environments.CONCLUSIONS: The analysis of Keri Lake metagenomes revealed that microbiomes in the oil-exposed sediment have a higher potential for methanogenesis over denitrification/sulfate reduction, compared to those in the non-exposed site. Comparison with metagenomes from various oil-impacted environments suggests that syntrophic interactions of hydrocarbon degraders with methanogens are favored in the ecosystems with a long-term presence of oil.
AU  - Michas, A.
AU  - Vestergaard, G.
AU  - Trautwein, K.*
AU  - Avramidis, P.*
AU  - Hatzinikolaou, D.G.*
AU  - Vorgias, C.E.*
AU  - Wilkes, H.*
AU  - Rabus, R.*
AU  - Schloter, M.
AU  - Schöler, A.
C1  - 51860
C2  - 43526
CY  - London
SP  - 118
TI  - More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis.
JO  - Microbiome
VL  - 5
IS  - 1
PB  - Biomed Central Ltd
PY  - 2017
SN  - 2049-2618
ER  - 

TY  - JOUR
AU  - Michas, A.
AU  - Vestergaard, G.
AU  - Trautwein, K.*
AU  - Hatzinikolaou, D.G.*
AU  - Vorgias, C.E.*
AU  - Wilkes, H.*
AU  - Rabus, R.*
AU  - Schloter, M.
AU  - Schöler, A.
C1  - 52098
C2  - 43707
CY  - London
TI  - Erratum: Correction to: More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis (Microbiome (2017) 5 1 (118)).
JO  - Microbiome
VL  - 5
IS  - 1
PB  - Biomed Central Ltd
PY  - 2017
SN  - 2049-2618
ER  - 

TY  - JOUR
AB  - BACKGROUND: The development of anti-islet cell autoimmunity precedes clinical type 1 diabetes and occurs very early in life. During this early period, dietary factors strongly impact on the composition of the gut microbiome. At the same time, the gut microbiome plays a central role in the development of the infant immune system. A functional model of the association between diet, microbial communities, and the development of anti-islet cell autoimmunity can provide important new insights regarding the role of the gut microbiome in the pathogenesis of type 1 diabetes. RESULTS: A novel approach was developed to enable the analysis of the microbiome on an aggregation level between a single microbial taxon and classical ecological measures analyzing the whole microbial population. Microbial co-occurrence networks were estimated at age 6 months to identify candidates for functional microbial communities prior to islet autoantibody development. Stratification of children based on these communities revealed functional associations between diet, gut microbiome, and islet autoantibody development. Two communities were strongly associated with breast-feeding and solid food introduction, respectively. The third community revealed a subgroup of children that was dominated by Bacteroides abundances compared to two subgroups with low Bacteroides and increased Akkermansia abundances. The Bacteroides-dominated subgroup was characterized by early introduction of non-milk diet, increased risk for early autoantibody development, and by lower abundances of genes for the production of butyrate via co-fermentation of acetate. By combining our results with information from the literature, we provide a refined functional hypothesis for a protective role of butyrate in the pathogenesis of type 1 diabetes. CONCLUSIONS: Based on functional traits of microbial communities estimated from co-occurrence networks, we provide evidence that alterations in the composition of mucin degrading bacteria associate with early development of anti-islet cell autoimmunity. We hypothesize that lower levels of Bacteroides in favor of increased levels of Akkermansia lead to a competitive advantage of acetogens compared to sulfate reducing bacteria, resulting in increased butyrate production via co-fermentation of acetate. This hypothesis suggests that butyrate has a protective effect on the development of anti-islet cell autoantibodies.
AU  - Endesfelder, D.
AU  - Engel, M.
AU  - Davis-Richardson, A.G.*
AU  - Ardissone, A.N.*
AU  - Achenbach, P.
AU  - Hummel, S.
AU  - Winkler, C.
AU  - Atkinson, M.*
AU  - Schatz, D.*
AU  - Triplett, E.W.*
AU  - Ziegler, A.-G.
AU  - zu Castell, W.
C1  - 48488
C2  - 41113
CY  - London
TI  - Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production.
JO  - Microbiome
VL  - 4
IS  - 1
PB  - Biomed Central Ltd
PY  - 2016
SN  - 2049-2618
ER  -