Background references

FISH

Commensal and Pathogenic Biofilms Alter Toll-Like Receptor Signaling in Reconstructed Human Gingiva.Front. Cell. Infect. Microbiol., 07 August 2019. Lin Shang, Dongmei Deng, Jeroen Kees Buskermolen, Sanne Roffel, Marleen Marga Janus, Bastiaan Philip Krom, Wim Crielaard and Susan Gibbs.

Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung. Nature Communications volume 10, Article number: 3397 (2019). Adrian Kordes, Matthias Preusse, Sven D. Willger, Peter Braubach, Danny Jonigk, Axel Haverich, Gregor Warnecke & Susanne Haussler

Fluorescence in Situ Hybridization (FISH) for the Diagnosis of Periprosthetic Joint Infection in Formalin-Fixed Paraffin-Embedded Surgical Tissues. JBJS: January 16, 2019 - Volume 101 - Issue 2 - p e5. Torsten Lippmann, Peter Braubach, Max Ettinger, Mark Kuehnel, Florian Laenger, Danny Jonigk.

Saliva-Derived Commensal and Pathogenic Biofilms in a Human Gingiva Model. Journal of Dental Research (2018), 97(2), 201 208. Buskermolen, J. K., Janus, M. M., Roffel, S., Krom, B. P., & Gibbs, S.

Prediction of transplant outcome after 24-hour ex vivo lung perfusion using the Organ Care System in a porcine lung transplantation model. American Journal of Transplantation. https://doi.org/10.1111/ajt.15075. Wiebke Sommer Jawad Salman Murat Avsar Klaus Hoeffler Katharina Jansson Thierry N. Siemeni Ann-Kathrin Knoefel Linda Ahrens Reza Poyanmehr Igor Tudorache Peter Braubach Danny Jonigk Axel Haverich Gregor Warnecke

Fluorescence In Situ Hybridization for Diagnosis of Whipple s Disease in Formalin-Fixed Paraffin-Embedded Tissue. Front. Med., 22 June 2017. https://doi.org/10.3389/fmed.2017.00087. Peter Braubach, Torsten Lippmann, Didier Raoult, Jean-Christophe Lagier, Ioannis Anagnostopoulos, Steffen Zender, Florian Peter L nger, Hans-Heinrich Kreipe, Mark Philipp K hnel and Danny Jonigk

Starter formula enriched in prebiotics and probiotics ensures normal growth of infants and promotes gut health: a randomized clinical trial. Pediatric Research (2017) doi:10.1038/pr.2016.270. Michael Radke, Jean-Charles Picaud, Andrea Loui, Gilles Cambonie, Dirk Faas, Harry N. Lafeber, Nanda de Groot, Sophie S. Pecquet, Philippe G. Steenhout and Jean-Michel Hascoet

Nasopharyngeal colonization with Streptococcus pneumoniae triggers dendritic cell-dependent antibody responses against invasive disease in mice. European Journal of Immunology (2017) DOI: 10.1002/eji.201646700. Anne Dommaschk, Nadine Ding, Meritxell Tort Tarres, Lara F. Bittersohl, Regina Maus, Jennifer Stolper, Danny Jonigk, Peter Braubach, Torsten Lippmann, Tobias Welte, Ulrich A. Maus.

The Microbiota in Gastrointestinal Pathophysiology: Implications for Human Health, Prebiotics, Probiotics, and Dysbiosis. Academic Press (2016). Floch, Martin H., Yehuda Ringel, and W. Allen Walker, eds.

Production Conditions Affect the In Vitro Anti-Tumoral Effects of a High Concentration Multi-Strain Probiotic Preparation. Plos One (2016) PLoS One 2016;11(9):e0163216. Epub Sep 22. Benedetta Cinque, Cristina La Torre, Francesca Lombardi, Paola Palumbo, Michel Van der Rest and Maria Grazia Cifone.

Milk digesta and milk protein fractions influence the adherence of Lactobacillus gasseri R and Lactobacillus casei FMP to human cultured cells. Food & Function (2016) DOI: 10.1039/C6FO00545D. Tereza Volstatova, Jaroslav Havlik, Miroslava Potuckovab and Martina Geigerovaa.

Early Benefits of a Starter Formula Enriched in Prebiotics and Probiotics on the Gut Microbiota of Healthy Infants Born to HIV+ Mothers: A Randomized Double-Blind Controlled Trial. Clin Med Insights Pediatr. (2016) 10: 119 130. Peter Cooper, Keith D. Bolton, Sithembiso Velaphi, Nanda de Groot, Shahram Emady-Azar, Sophie Pecquet, and Philippe Steenhout.

In vitro influence of dietary protein and fructooligosaccharides on metabolism of canine fecal microbiota. BMC Veterinary Research (2016) DOI: 10.1186/s12917-016-0672-1. Carlo Pinna, Carla Giuditta Vecchiato, Giuliano Zaghini, Monica Grandi, Eleonora Nannoni, Claudio Stefanelli and Giacomo Biagi.

Extracellular vesicle derived protein from Bifidobacterium longum alleviates food allergy through mast cell suppression. Journal of Allergy and Clinical Immunology Volume 137, Issue 2, February 2016, Pages 507 516. Jung-Hwan Kim, Eun-Ji Jeun, Chun-Pyo Hong, Seong-Hoon Kim, Min Seong Jang, Eun-Jung Lee, Sook Jin Moon, Chang Ho Yun, Sin-Hyeog Im, Seok-Geun Jeong, Beom-Young Park, Kyong-Tai Kim, Ju-Young Seoh, Yoon-Keun Kim, Sung-Jong Oh, Jun-Sang Ham, Bo-Gie Yang, Myoung Ho Jang.

Normal growth of infants receiving an infant formula containing Lactobacillus reuteri, galacto-oligosaccharides, and fructo-oligosaccharide: a randomized controlled trial. Maternal Health, Neonatology and Perinatology 2015 1:9. Le Ye Lee, Roshan Bharani, Agnihotri Biswas, Jiun Lee, Li n-Anh Tran, Sophie Pecquet and Philippe Steenhout.

Effects of yogurt dietary supplementation on the intestinal ecosystem of a population of Emperor tamarins (Saguinus imperator). Progress in Nutrition (2015); Vol. 17, N. 3: 231-237. Carlo Pinna, Eleonora Nannoni, Giulia Rigoni, Monica Grandi, Carla Giuditta Vecchiato, Caterina Spiezio, Camillo Sandri and Giacomo Biagi.

A new medium containing mupirocin, acetic acid, and norfloxacin for the selective cultivation of bifidobacteria. Anaerobe Volume 34, August 2015, Pages 27 33. Eva Vlkov , Hana Salmonov , Vera Bune ov , Martina Geigerov , Vojtech Rada and rka Musilov .

Selective growth-inhibitory effect of 8-hydroxyquinoline towards Clostridium difficile and Bifidobacterium longum subsp. longum in co-culture analysed by flow cytometry. Journal of Medical Microbiology (2014), 63, 1663 1669. Jitka Novakova, M ria D unkov , Sarka Musilova, Eva Vlkova, Ladislav Kokoska, Andr s Moya and Giuseppe D Auria.

Effect of UV irradiation (253.7 nm) on free Legionella and Legionella associated with its amoebae hosts. Water Research Volume 67, 15 December 2014, Pages 299 309. S lvia Cervero-Arag a, Regina Sommer, Rosa M. Araujo.

In vitro effect of dietary protein level and nondigestible oligosaccharides on feline fecal microbiota1. J. Anim. Sci. (2014) 92:5593 5602. Carlo Pinna, Claudio Stefanelli, and Giacomo Biagi

A Randomized Double Blind Controlled Safety Trial Evaluating d-Lactic Acid Production in Healthy Infants Fed a Lactobacillus reuteri-containing Formula. Nutr Metab Insights. 2014; 7: 19 27. Konstantinos Papagaroufalis, Aikaterini Fotiou, Delphine Egli, Li n-Anh Tran, and Philippe Steenhout.

In vitro selective inhibitory effect of 8-hydroxyquinoline against bifidobacteria and clostridia. Anaerobe Volume 22, August 2013, Pages 134 136. Jitka Novakovaa, Eva Vlkovab, Bela Bonusovaa, Vojtech Radab and Ladislav Kokoskaa.

Effect of probiotics on the fecal microflora after radiotherapy: A pilot study. Indian Journal of Pathology and Microbiology, 2013. J Timko.

Emulsion Encapsulation of Bifidobacterium animalis subsp. lactis BB12 with the addition of Lecithin. Czech J. Food Sci. Vol. 31, 2013, No. 3: 270 274. Ivana Lisov , rka Hor ckov , Renata Kov cov , Vojtech Rada and Milada Plockov .

Lactobacillus Genus Identification Isolated from Gastrointestinal Tract of Chickens after Bee Products Application Using FISH and RTQ PCR Methods. Animal Science and Biotechnologies, 2013, 46; 127-132. Miroslava Kac niov , Peter Ha c k, Henrieta Arp ov , Adriana Pavelkov , Jana Petrov , Luk Hleba, Jaroslav Pochop, Katar na Rovn .

Growth of infant fecal bacteria on commercial prebiotics. Folia Microbiologica July 2012, Volume 57, Issue 4, pp 273-275. Vera Bune ov , Eva Vlkov , Vojtech Rada, Vladim ra Knazovick , rka Rockov , Martina Geigerov and Matej Bo ik.,

Identification of Bifidobacterium strains from faeces of lambs. Small Ruminant Research Volume 105, Issues 1 3, June 2012, Pages 355 360. Vera Bune ov a, Eva Vlkov a, Jir Killera, Vojtech Radaa and rka Rockov a.

Effect of honey and starter culture on growth, acidification, sensory properties and bifidobacteria cell counts in fermented skimmed milk. Afr. J. Microbiol. Res. Vol. 6 No. 3 486-498. 2012. Ali Riazi and Hasnia Ziar

Occurrence of bifidobacteria and lactobacilli in digestive tract of some freshwater fishes. BIOLOGIA Volume 67, Number 2 (2012), 411-416. Eva Vlkov , Luk Kalous, Vera Bune ov , Katerina Rylkov , Radana Svetl kov and Vojtech Rada.

In vitro and In vivo antimicrobial activity of propolis on the microbiota from gastrointestinal tract of chickens. Journal of Environmental Science and Health, Part A: Toxic/Hazardous Substances and Environmental Engineering Volume 47, Issue 11, 2012. Miroslava Kac niov , Katar na Rovn , Henrieta Arp ov , Juraj Cubon, Luk Hleba, Jaroslav Pochop, Simona Kunov and Peter Ha c k.

Effects of Prebiotic-Containing Infant Formula on Gastrointestinal Tolerance and Fecal Microbiota in a Randomized Controlled Trial. J Parenter Enteral Nutr January 2012 vol. 36 no. 1 suppl 95S-105S. Hannah D. Holscher, RD1,* Kristin L. Faust, Laura A. Czerkies, Richard Litov, Ekhard E. Ziegler, Herschel Lessin, Terry Hatch, Shumei Sun, Kelly A.

Staphylococcus aureus directly activates eosinophils via platelet-activating factor receptor. Journal of Leukocyte Biology vol. 92 no. 2 333-341. Koa Hosoki, Akiko Nakamura, Mizuho Nagao, Yukiko Hiraguchi, Hisashi Tanida, Reiko Tokuda, Hideo Wada, Tsutomu Nobori, Shigeru Suga and Takao Fujisawa.

Improved growth of toddlers fed a milk containing synbiotics. Asia Pac J Clin Nutr 2011;20 (1):69-76. Agus Firmansyah, Pramita G Dwipoerwantoro, Muzal Kadim, Safira Alatas, Nelly Conus, Leilani Lestarina, Florilene Bouisset, Philippe Steenhout.

Molecular analysis of faecal and duodenal samples reveals significantly higher prevalence and numbers of Pseudomonas aeruginosa in IBS. J Med Microbiol. (2011) Feb;60(Pt 2):236-45 A. P. M. Kerckhoffs, K. Ben-Amor, M. Samsom, M. E. van der Rest, J. de Vogel, J. Knol and L. M. A. Akkermans.

Survival of bifidobacteria in adult intestinal tract. Folia Microbiologica. 2010 55(3), 281-285. M. Grmanov , E. Vlkov , V. Rada and I. Homutov

Comparison of three methods to enumerate gut microbiota of weanling piglets fed insoluble dietary fibre differing in lignin content. 2010 The Journal of Agricultural Science, 148: 225-232. A. Peterson, K. J. Domig, K. Schedle, W. Windisch and W. Kneife.

Lactobacillus reuteri DSM 17938 in Infantile Colic: A Randomized, Double-Blind, Placebo-Controlled Trial. 2010 PEDIATRICS 126(3): 526-533. F. Savino, L. Cordisco, V. Tarasco, E. Palumeri, R. Calabrese, R. Oggero, S. Roos, D. Matteuzzi.

Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients. World J Gastroenterol. 2009 15(23): 2887 2892 A. P.M. Kerckhoffs, M. Samsom, M. E. van der Rest, J. de Vogel, J. Knol, K. Ben-Amor, and L. M.A. Akkermans.

Intestinal microbiota in exclusively breast-fed infants with blood-streaked stools.Folia Microbiologica. 2009 54(2): 167-171. J. Nevoral, V. Rada, E. Vlkov , K. Bl hov , J. Bronsk , D. Bub kov and J. Killer.

Selection of probiotic bifidobacteria for lambs. Czech J. Anim. Sci., 2009 54(12): 552 565. E. Vlkov , M. Grmanov , V. Rada, I. Homutov , S. Dubn .

Interactions between salivary Bifidobacterium adolescentis and other oral bacteria: in vitro coaggregation and coadhesion assays. FEMS Microbiology Letters (2008) Volume 281, Issue 2, pages 183 189, April 2008. S. Nagaoka, K. Hojo, S. Murata, T. Mori, T. Ohshima and N. Maeda

Effect of food preservatives on the growth of spoilage lactobacilli isolated from mayonnaise-based sauces. Food Control 2008, 19(7):706-713. J. Fialov a, J. Chumchalov a, K. Mikov b and I. Hru ov a.

Critical Evaluation of Diagnosing Bacterial Overgrowth in the Proximal Small Intestine. Journal of Clinical Gastroenterology. 2008, 42(10):1095-1102. A.P.M. Kerckhoffs, M.R. Visser, M. Samsom, M.E. van der Rest, J. de Vogel, W. Harmsen, L.M.A. Akkermans.

In vitro comparison of the prebiotic effects of two inulin-type fructans. 2008 Anaerobe 14(5): 280-286. A. Pompei, L. Cordisco, S. Raimondi, A. Amaretti, U. M. Pagnoni, D. Matteuzzi and M. Rossi

Occurrence of bifidobacteria in faeces of calves fed milk or a combined diet. Archives of Animal Nutrition, 2008 62(5): 359 - 365. E. Vlkova, V. Rada, I. Trojanova, J. Killer, M. Scaronmehilova, Z. Molatov

Auto-aggregation and Co-aggregation ability in bifidobacteria and clostridia. Folia Microbiol. 2008, 53: 263-269. E. Vlkov , V. Rada, M. Smehilova and J. Killer.

Administration of Folate-Producing Bifidobacteria Enhances Folate Status in Wistar Rats. J. Nutr. 2007, 137:2742-2746. A. Pompei, L. Cordisco, A. Amaretti, S. Zanoni, S. Raimondi, D. Matteuzzi and M. Rossi.

Occurrence of Bifidobacterium in the intestine of newborns by fluorescence in situ hybridization. Comparative Immunology, Microbiology and Infectious diseases. 2006, 29:345-352. E. Bezirtzogloua, V. Maipab, N. Chotourad, E. Apazidoud, A. Tsiotsiasa, C. Voidaroua, D. Kostakisc and A. Alexopoulosa.

Comparison of bacterial flora and enzymatic activity in faeces of infants and calves. FEMS Microbiology Letters. 2006, 258:25-28. V. Rada, E. Vlkov , J. Nevoral, I. Trojanov

Distribution of Bifidobacteria in the gastrointestinal tract of Calves. Folia Microbiol. 2006, 51:325-328. E. Vlkov , I. Trojanov and V. Rada.

Molecular typing methods show different fingerprints for the faecal bacterial composition in irritable bowel syndrome (IBS) patients and healthy subjects. European Journal of Gastroenterology & Hepatology. 2006, 18: 427-437. A. P. M. Kerckhoffs, M. Samsom, G.P. van Berge Henegouwen, A. J. P. M. Smout, M. E. van der Rest, J. Knol, E. A. F. van Tol and L. M. A. Akkermans.

Growth during the first 6 months of life in infants using formula enriched with Lactobacillus rhamnosus GG: double-blind, randomized trial. Journal of Human Nutrition and Dietetics. 2006, 19:51-58. N. Vendt, H. Gr nberg, T. Tuure, O. Malminiemi, E. Wuolijoki, V. Tillmann, E. Sepp and R. Korpela.

Activity and Cellular localization of amylases of rabbit cecal bacteria. Folia Microbiol. 2006, 51:309-312. K.Sirotek, M. Marounek and O. Suchorska.

Nucleic acid-based methods for the detection of bacterial pathogens: Present and future considerations for the clinical laboratory. Clinica Chimica Acta. 2006, 363:206-220. E.A. Mothershed and A.M. Whitney.

Bifidobacterium-selective isolation and enumeration from chicken caeca by a modified oligosaccharide. Letters in Applied Microbiology, 2005, 41: 355-360. S.N. Thitaram, G.R. Siragusa and A. Hinton.

Detection of infant faecal bifidobacteria by enzymatic methods. Journal of microbiological methods, 2005, 60: 365-373. E. Vlkov , J. Nevoralb, B. Jencikovac, J. Kopečnýd, J. Godefrooije, I. Trojanov and V. Rada.

Fermentation of Fructooligosaccharides and Inulin by Bifidobacteria: a Comparative Study of Pure and Fecal Culture. Applied and Environmental Microbiology, 2005, 71: 6150-6158,. M. Rossi, C. Corradini, A. Amaretti, M. Nicolini, A. Pompei, S. Zanoni, and D. Matteuzzi.

Growth in Cecal Mucus Facilitates Colonization of the Mouse Intestinal Tract by Methicillin-Resistant Staphylococcus aureus. The Journal of Infectious Diseases, 2005, 192: 1621–1627. D. M. Gries, N. J. Pultz, and C. J. Donskey.

Enumeration, Isolation and Identification of Bifidobacteria from dairy products. Acta Agriculturae Slovenica, 2004, 84:31-36. E. Vlkova, V. Rada and I. Trojanova.

High-performance anion-exchange chromatography coupled with pulsed amperometric detection and capillary zone electrophoresis with indirect ultra violet detection as powerful tools to evaluate prebiotic properties of fructooligosaccharides and inulin. 2004 Journal of Chromatography A 1054, (1-2): 165-173. C. Corradini, F. Bianchi, D. Matteuzzi, A. Amoretti, M. Rossi and S. Zanoni.

Prebiotic effects of a wheat germ preparation in human healthy subjects. Food Microbiology. 2004, 21:119-124. D. Matteuzzi, E. Swennena, M. Rossia, T. Hartman and V. Lebet.

Bifidobacterium psychraerophilum sp. nov. and Aeriscardovia aeriphila gen. nov., sp. nov., isolated from a porcine caecum. Int J Syst Evol Microbiol 2004, 54: 401-406; P. J. Simpson, R. P. Ross, G. F. Fitzgerald and C. Stanton.

Mechanisms by Which Anaerobic Microbiota Inhibit the Establishment in Mice of Intestinal Colonization by Vancomycin-Resistant Enterococcus. The Journal of Infectious Diseases, 2003, 191: 949–956. N. J. Pultz, U. Stiefel, S. Subramanyan, M. S. Helfand, and C. J. Donskey.

Isolation, Identification and Characterization of Rabbit Caecal Mucinolytic Bacteria. ACTA VET. BRNO 2003, 72: 365–370. K. Sirotek, E. Santos, V. Benda, M. Marounek.

Quantification of Uncultured Ruminococcus obeum-Like Bacteria in Human Fecal Samples by Fluorescent In Situ Hybridization and Flow Cytometry Using 16S rRNA-Targeted Probes. Applied and Environmental Microbiology, 2002 68: 4225 4232. E. G. Zoetendal, K. Ben-Amor, H. J. M. Harmsen, F. Schut, A. D. L. Akkermans and W. M. de Vos.

Molecular microbial analysis of Bifidobacterium isolates from different environments by the species-specific amplified ribosomal DNA restriction analysis (ARDRA). FEMS Microbiology Ecology 2001, 36: 113-121. M. Ventura, M. Elli, R. Reniero, R. Zink.

A Molecular View of the Intestinal Ecosystem. Curr. Issues Intestinal. Microbiol. 2000, 1:1-12. E.E. Vaughan, F. Schut, H.G.H.J. Heilig, E.G. Zoetendal, W.M. de Vos, A.D.L. Akkermans.

Method for the rapid determination of Bacteria. Patent WO/1999/054502. G.J. Jansen, J.E. Degener, G. W. Welling.

Methods and materials for determining relative abundance of microorganisms in mixed populations. Patent US 6107033. G. W. Welling, F. Schut, P. S. Langendijk, G. J. Jansen, M. H. F. Wilkingson, and P. Elffrich.

Quantitative Measurements of Intestinal Ecology by Digital Image Analysed Microscopy. Bioscience and Microflora. 1998, 17: 7-14. M. H. F. WILKINSON and Frits SCHUT.

T(D)GGE

Ipsat P1A, a Recombinant {beta}-lactamase, Prevents the Emergence of Antimicrobial Resistance in Gut Microflora of Healthy Subjects During Intravenous Administration of Ampicillin. Antimicrob Agents Chemother. 2009 Mar 23. A.M. Tarkkanen, T. Heinonen, R. J gi, S. Mentula, M.E. van der Rest, C.J. Donskey, T. Kemppainen, K. Gurbanov, C.E. Nord.

Orally administered targeted recombinant Beta-lactamase prevents ampicillin-induced selective pressure on the gut microbiota: a novel approach to reducing antimicrobial resistance. Antimicrob Agents Chemother. 2004 Jan;48(1):75-9. J. Harmoinen, S. Mentula, M. Heikkil , M.E. van der Rest, P.J. Rajala-Schultz, C.J. Donskey, R. Frias, P. Koski, N. Wickstrand, H. Jousimies-Somer, E. Westermarck, K. Lindevall.

Denaturing gradient gel electrophoresis analysis to study bacterial community structure in pockets of periodontitis patients. Oral Microbiology and Immunology. 2003, 18:59-65. V. Zijnge, H. J. M. Harmsen, J. W. Kleinfelder, M. E. van der Rest, J. E. Degener and G. W. Welling.

Mitox DNA - Mitochondrial toxicity assay

A novel mutation in FBXL4 in a Norwegian child with encephalomyopathic mitochondrial DNA depletion syndrome 13. European Journal of Medical Genetics (2016) Volume 59, Issue 6, Pages 342-346. Tuva Bar y, Christeen Ramane J. Pedurupillay, Yngve T. Bliksrud, Magnhild Rasmussen, Asbj rn Holmgren, Magnus D. Vigeland, Timothy Hughes, Maaike Brink, Richard Rodenburg, B rd Nedregaard.

Mitochondrial DNA Parameters in Blood of Infants Receiving Lopinavir/Ritonavir or Lamivudine Prophylaxis to Prevent Breastfeeding Transmission of HIV-1. J. Clin. Med. 2020, 9(9), 2972. Audrey Monnin,Nicolas Nagot,Marianne Periès,Roselyne Vallo,Nicolas Meda,Mandisa Singata-Madliki,James K. Tumwine,Chipepo Kankasa,Nobubelo Ngandu,Ameena Goga,Pascal Reynier,Thorkild Tylleskär,Philippe Van de Perre and Jean-Pierre Molès

Health Outcomes at School Age among Children Who Are HIV-Exposed but Uninfected with Detected Mitochondrial DNA Depletion at One Year. J. Clin. Med. 2020 9(11), 3680. Audrey Monnin,Nicolas Nagot,Sabrina Eymard-Duvernay,Nicolas Meda,James K. Tumwine,Thorkild Tylleskär,Philippe Van de Perre and Jean-Pierre Molès.