Menschliches Mikrobiom

• The human microbiome has a great impact on health and wellbeing. Different diseases can be linked to the microbes in our body. Also in pregnancy the microbiome can play an important role, from perception via the period of gestation through to delivery and even beyond.
  A very important question here is the time point of first colonization of a young living being with microbes. Does the first contact already take place in the maternal body, contradicting the sterile womb hypothesis, or not until the point of delivery? Can microbes be inherited? There is a big discussion if the womb is colonized with microbes or not, especially regarding the placenta. It is known that in cases of intrauterine infections also infections of the womb may appear, leading to diverse pregnancy outcomes as preeclampsia, preterm birth or even still birth. But are living microbes only present in the placenta in cases of infection and disease or maybe also in healthy pregnancies? Our group is explicitly investigating this fundamental question.
  Regarding the matter of preterm birth we also investigate the microbiome of neonates with a gestational age lower than 37 weeks and what impact the different treatments in early live concerning the application of antibiotics, antimycotics, probiotics and nutrition have on their colonization by microbes.
  We investigate those topics regarding bacteria, archaea and fungi using next generation sequencing (NGS) and visualization via fluorescence in situ hybridization (FISH).
   
• Team: Christine Moissl-Eichinger, Charlotte Neumann, Manuela Pausan
   
• Kooperationspartner*innen: Stefan Kurath-Koller, Berndt Urlesberger, Berhard Resch, Christian Wadsack, Evelyn Jantscher-Krenn, Eva Weiß

• 10^14 Mikroorganismen leben in und auf unserem Körper. Diese mikrobielle Gemeinschaft ist immens wichtig für z.B. die optimale Verdauung der Nahrung, die Bereitstellung sekundärer Stoffe und den Schutz vor pathogenen Mikroorganismen. Eine Entgleisung des Mikrobioms (Dysbiose) geht einher mit weit verbreiteten Krankheitsbildern, z.B. Diabetes, Fettleibigkeit, entzündlichen Darmerkrankungen. Üblicherweise wird das sogenannte Mikrobiom bereits bei der vaginalen Geburt von der Mutter auf das Kind übertragen (aus Vagina, Darm).
  Bei Kaiserschnittkindern erfolgt zunächst die Übertragung der Mikroben von der Haut der Eltern, wobei nach und nach weitere Mikroorganismen aus Muttermilch und anderen Quellen folgen und den Verdauungstrakt des Babys bevölkern. Dieser Vorgang wird z.B. durch Oligosaccharide unterstützt, die in der Muttermilch vorkommen, und das Wachstum der nützlichen Mikroben fördert. Das Darmmikrobiom besteht aus Bakterien, Archaeen, Viren und Eukaryonten. Die Mehrzahl dieser Mikroorganismen sind Anaerobier, d.h. sie brauchen zum Wachstum keinen Sauerstoff, bzw. werden durch diesen sogar gehemmt oder abgetötet. Obwohl bei Kaiserschnittkindern auf den ersten Blick keine Übertragung solcher Anaerobier von Mutter auf Kind ersichtlich ist, werden auch diese Kinder zügig von Anaerobiern besiedelt; deren Übertragungsweg jedoch bleibt völlig unklar, da ein längerer Kontakt zum Luftsauerstoff für viele dieser Mikroben bereits hemmend wirkt. Insbesondere methanogene Archaeen sind für ihre Empfindlichkeit gegenüber Sauerstoff bekannt.
  Das Ziel dieser Studie ist es nun, zu untersuchen, ob bzw. wie strikt anaerobe Mikroorganismen von Mutter auf Kind übertragen werden und die Quellen dieser Mikroben zu erfassen. Die Mikroben verschiedener Körperstellen der Mutter (Vagina, Darm etc.) werden direkt vor der Geburt untersucht, sowie die Besiedelung des Kindes innerhalb der ersten Tage überprüft. Dabei liegt besonderer Augenmerk bei den Unterschieden vaginal geborener Kinder gegenüber Kaiserschnittkindern. Gleichzeitig soll die Rolle der Oligosaccharide bei der Ausbildung eines gesunden Mikrobioms überprüft werden.
   
• Team: Christine Moissl-Eichinger, Charlotte Neumann
   
• Kooperationspartnerin: Evelyn Jantscher-Krenn

• The presence of microbes in the placenta is matter of investigations for the last years, but no satisfying conclusion could be drawn until today. The main reason here is that handling samples with low biomass, investigations take place around the minimal detection limit of the techniques used and that contaminations introduced during sample processing have huge impact. The specific role of bacteria colonizing the placenta is still unclear but it might be linked to health and pregnancy outcome. The placental microbiome is extensively discussed in context with inflammation and negative pregnancy outcomes, especially preterm birth (Tomlinson et al., 2017). The abundance of certain clinically relevant species differs between spontaneous preterm- and nonspontaneous preterm- or term-delivered placentas (Leon et al., 2018a). In cell culture of human placental cells the presence of bacteria has been associated with pro- as well as anti-inflammatory responses (Tomlinson et al., 2017).
  Aargard et al. (Aargaard, K. et al., 2016) claimed a unique placental microbiome by sequencing with 150-bp Illumina HiSeq and differentiated between a preterm birth-case cohort and a case-cohort with a remote history of antenatal infections. Apart from E.coli being the most abundant species found in the placentas, oral specimens like Prevotella tannnerae and nonpathogenic Neisseria species formed the placental microbiome. A weakness of this study was the lack of appropriate controls.
  Tomlinson et al. investigated the methylome of 84 preterm placentas and found 16 microbial species in 52% of the placentas, but in low numbers, and saw changes in the DNA methylation (Tomlinson et al., 2017).
  Bacterial infections have been linked with spontaneous preterm birth and in estimation 20-40% of preterm births have a history of intrauterine infections (Leon et al., 2018a). It was thought that the bacteria in the placenta derive from the urinary tract but the oral cavity as well as the vagina are also discussed as possible origins. Hematogenous transmission therefore might be a possible route for translocation (Tomlinson et al., 2017).
  Regarding the technical restrictions represented by detection limits as well as differentiation from possible contaminants it is not clear yet if the microbes claimed to be found in the placenta by those researchers actually really derive from the placenta itself or are introduced during sample-processing. Applying multiple technical as well as biological controls the presence of a distinct placental microbiome was rebutted by several publications (Leiby et al.)(Lauder et al., 2016)(Leon et al., 2018b)
  The approach mostly used in studies investigating the placental microbiome is based on PCR relying methods like Illumina sequencing and qPCR which is not sufficient to confirm or disprove the presence of microorganisms colonizing the placenta.
   
• Team: Christian Wadsack, Charlotte Neumann

The correspondence of the nasal microbiome and neuroplasticity in human olfaction.

• Background: The ability to smell is mediated by olfactory neurons in the ceiling of the nose, the olfactory mucosa, which is inhabited by numerous microorganisms. In general, human-associated microbes are intertwined with human health, disease and maybe even behavior. The microbiome communicates with the human body cells and affects functions of the brain and other tissues. People who have a normal olfactory capability are called normosmics.
  The loss of smell is an incisive event, caused by mechanical impact, infection or disease, or occurs subtly during ageing. Besides effects on psychological, social and behavioral performance and thus affecting the quality of life tremendously, the loss of the sense of smell induces a reorganization in the functional network structure of the human brain. People who have a reduces olfactory capability are called hyposmics; People who completely lost their olfactory sense are called anosmics.
  Smell training has been shown to improve olfactory function in healthy individuals or even after smell loss due to diseases (e.g. Alzheimer’s and Parkinson’s disease, or an infection) again.
  The microbiome (comprising trillions of microorganisms) is associated with the human body. It appears to have tremendous effects on health, disease, behavior and other aspects of human life and is capable to communicate with human body cells and affects functions of human tissues and even brain.
   
• Hypothesis: We propose that the nasal microbiome located in the olfactory area plays not only an important role in olfactory function and dysfunction but also in olfactory regain due to smell training along with reorganization of the brain.
   
• Methods: To investigate the association between nasal microbiome and the sense of smell we combine imaging biomarkers with measures obtained from microbiome phylogenetic and functional analyses. Therefore, the basic functions and characteristics (microbial diversity and abundance) of the nasal microbiota of normosmics and anosmic volunteers before and after smell training is determined and results are correlated with olfactory function. Additionally, combined neuroimaging measures from functional and structural connectivity, as well as morphological characteristics were collected and their correspondence with olfactory function, dysfunction and regain will be investigated.
   
• Previous results: Our completed pilot study showed that the microbial profile at the olfactory mucosa mirrors the capability to smell. Volunteers with impaired smelling capacity had an increase of specific (anaerobic) microbial groups. Understanding the microbial community in the olfactory mucosa will increase therapeutic opportunities and possibly allow monitoring and predicting smell therapy success in future. https://www.nature.com/articles/s41598-018-19438-3
   
• Perspectives: The integrational approach in combining these fields will focus on increasing therapeutic opportunities and monitoring and predicting therapy success in the future. The project marries two highly uprising fields of human life science – microbiome research and neuroimaging. Especially due to the mixture of methods and approaches with aiming at the same target, this study has the potential of generating profound knowledge on understanding the sense of smell.
   
• Team: Christina Kumpitsch, Veronika Schöpf (Uni Graz), Florian Fischmeister (Uni Graz)

• Approximately 11% of all life births worldwide were born prematurely in 2010, i.e. before 37 weeks of gestational age (GA), with incidence rates increasing over the past years. Prematurity may be caused by several factors and necessitates intensive care treatment over months. Long-term morbidities are common among this patient cohort.
  Mortality shows inverse proportion to GA with necrotizing enterocolitis (NEC) being the most common life-threatening emergency of the gastrointestinal tract with a prevalence rate of 7-11% in very low birth weight (VLBW; <1.500g) infants, and an overall prevalence rate of 1-5% of infants in neonatal intensive care units (NICUs). Mortality rate associated with NEC is up to 30% and fatality rates are inversely proportional with birth weight and GA. Although NEC is a multifactorial disease - primarily associated with intestinal immaturity - the concept of “risk factors” for NEC remains controversial; however, the greatest risk factor is prematurity itself.
  The newborn infants´ microbiome originate mainly from vertical transmission of maternal microbiota during delivery, and probably even before. Rapidly maturing throughout the first year of life and becoming more or less permanent by three years of age, the individual intestinal microbiome is regulated interactively by initial colonising microbiota, genetic factors, intestinal development, dietary factors, and environmental factors.
  In the gut of preterm infants, microbial diversity is reduced with a preponderance of pathogenic organisms. Preterm infants having concurrent immunologic impairment, low intestinal microbiota diversity and predominant intestinal pathogens represent an example of dysbiosis. Microbial dysbiosis preceding NEC in preterm infants is characterized by increased relative abundances of Proteobacterales and decreased relative abundances of Firmicutes and Bacteroidetes.
  Probiotics may be protective by several potential mechanisms including increasing intestinal barrier function and modification of host response to microbial products. It is not known to what extent the microbiome is influenced by hospital regimens during the first days of life, including use of different probiotics for prevention of NEC.
  Here, we aimed to characterize the differences of intestinal microbiota composition and abundance with regard to different hospital regimens for NEC prophylaxis.
   
• Team: Charlotte Neumann, Stefan Kurath-Koller, Bernhard Resch, Berndt Urlesberger

• Background: Chronic rhinosinusitis (CRS) is a common disease which affects 16% of the population’s paranasal sinuses. It is categorized in CRS with (CRSwP) and without (CRSsP) polyps (fleshy swellings due to inflammation). Although it is suggested to be an inflammatory instead of an infectious disease, microbes might contribute to initiation and progression of the inflammation.
   
• Hypothesis: We hypothesize that the nasal microbiome of healthy people differs from that of CRS patients. Moreover, we expect that the two CRS groups (CRSwP and CRSsP) exhibit differences in their nasal microbiome, as the presence of polyps creates new microenvironments in the nasal cavity.
   
• Methods: Nasal microbial composition and community profiles of the healthy nasal cavity are determined and compared to CRS patients with and without polyps. To assess bacterial and archaeal loads, absolute abundance in the samples is additionally determined.
   
• Perspectives: We are aiming to use the gained knowledge on the role of the nasal microbiome in polyp formation and disease severity to propose new therapy options for CRS patients.
   
• Team: Christina Kumpitsch, Axel Wolf

• Background: Adenoid hypertrophy is a disturbing condition of the air circulation due to enlarged adenoids in the upper aerodigestive tract which obstruct breathing. During childhood adenoid size increases (reaching maximal size in the age of 6 or 7) before it starts to regress in adolescence again. Therefore, adenoid hypertrophy is not as common in adults compared to children. Symptoms of this obstructive condition are difficulties in breathing through the nose, snoring, rhinorrhea and more. If the symptoms are too severe, the adenoids have to be removed surgically. Previous studies have already shown that several bacterial species contribute to an infectious adenoid hypertrophy.
   
• Hypothesis: The nasal microbiome is influenced by the size of the adenoids or even vice versa. Therefore, we assume that the microbial profile in the nose of children with adenoid hypertrophy differ from children without this condition.
   
• Methods: Nasal microbial community profile is determined to compare children with and without adenoid hypertrophy.
   
• Perspectives: Better knowledge of the associations between the nasal microbiome and adenoid hypertrophy might help to reduce the burden of this obstructive condition and prevent small children from surgical interventions.
   
• Team: Christina Kumpitsch, Axel Wolf

• Background: The Gut-Brain axis describes the two-way communication between the brain and the gastrointestinal tract. One way to communicate are signals of the microbes in the gut, since microbial metabolites are able to influence the human body tissues, even the brain. Microbial dysbiosis in the gut can affect mood, memory, emotionality, pain, general susceptibility to stress and maybe personality.
  Dietary habits as well as obesity/BMI can affect the composition of the human gut microbiome and the metabolite composition which affects the brain and thereof has maybe also an impact on the mental state. The OCEAN personality test helps to grade human personality traits – regardless of age, sex or nationality – in 5 basic features. In detail, these traits to evaluate personality are openness, conscientiousness, extroversion, agreeableness and neuroticism – short “OCEAN “.
   
• Hypothesis: Individual dietary habits modulate the microbiome composition in the gut, and hence influence individual’s personality, indirectly.
   
• Methods: Microbial composition and community structure together with its metabolites are investigated and correlated with dietary questionnaires, brain images (MRI) and OCEAN personality tests.
   
• Perspectives: New insights into the connection between the human brain, especially the personality, and the microbes in the gastrointestinal tract are achieved. Knowledge about association of diet and microbiome composition in the gut might help to treat mental problems.
   
• Team: Christina Kumpitsch, Florian Fischmeister (Uni Graz)

• Introduction: The objective of bladder augmentation is to create a low-pressure storage reservoir of sufficient capacity to preserve upper urinary tract function and establish urinary continence when maximal medical therapy is unsuccessful . Several techniques, including ileocystoplasty (ICP) or colocystoplasty (CCP), have been described. However, it is well known that bladder augmentation can be associated with a variety of long-term complications, including excessive mucus production, electrolyte imbalances, metabolic acidosis, somatic growth retardation, vitamin B12 deficiency, and the formation of bladder calculi. Histological changes and tumor formation in the augmented bladder are the most severe postoperative complications. Furthermore, recurrent urinary tract infections (UTIs) represent a significant problem.
  Next-generation sequencing (NGS) techniques have provided novel insights into the microbiome of the urinary bladder (UB), which until now has been suspected to be sterile. However, there is a growing body of evidence suggesting that even the healthy urinary tract harbors a variety of microbial species, termed the urinary microbiome. Furthermore, disruptions of the microbiome of the UB have been demonstrated in urological disorders such as urgency urinary incontinence, overactive bladder, and urolithiasis.
  Before bladder augmentation, the intestinal segments (ISs) host a dense and complex microbial ecosystem serving numerous immunological, metabolic, and defensive functions. Augmentation of the native UB with ISs exposes this alimentary microbiota to a completely different microenvironment. At present, however, little is known about the fate of the intestinal mucosal microbiome after bladder augmentation. The aim of the present long-term postoperative observational study was therefore to intraindividually compare the local bacterial microbiome of the native UB and the IS in children after bladder augmentation.
   
• Objective: The aim was to compare the mucosal microbiome of the native UB vs the augmented intestinal segment (IS) using NGS.
   
• Study design: Twelve children after bladder augmentation (ICP n = 6, CCP n = 6) were included. Biopsies were taken during routine postoperative cystoscopy from the native UB and the IS. Specimens underwent whole-genome DNA extraction, 16S rRNA gene amplification, NGS, and Quantitative Insights Into Microbial Ecology (QIIME) data analysis. Downstream statistical data analyses were performed in Calypso.
   
• Results: Patients' median age at the time of surgery was 11 years (6–17 years), and the median interval between augmentation and sampling was 7 years (4–13 years). α-Diversity (Shannon diversity index) was not significantly different between IS vs UB, ICP vs CCP, and male vs female. No general differences in the overall bacterial pattern (β-diversity) were found between IS, UB, ICP, and CCP groups. The groups overlapped in principal coordinate analysis (PCoA) and non-metric multidimensional scaling (NMDS) analysis (Figure). Age at sampling had a statistically significant influence on β-diversity at the genus level. Corynebacterium, Pseudoxanthomonas, Lactobacillus, Flavobacterium, and Micrococcus were the most dominating taxa detected over all samples. There was an obvious dominance of the genus Corynebacterium in the samples taken from the UB and IS in both ICP and CCP patients. Limitations of this study include the relatively small number of patients
   
• Conclusion: After bladder augmentation, the native UB and augmented ISs (ICP and CCP) host similar microbiota despite their distinct differences of originating mucosal anatomy

• Background: Preterm birth is one of the leading causes of neonatal mortality. The causes for spontaneous preterm birth (PTB) are multifactorial and often remain unknown. In this study, we tested the hypothesis that human milk oligosaccharides (HMOs) in blood and urine modulate the maternal urinary and vaginal microbiome and influence the risk for PTB. We analyzed the vaginal and urinary microbiome of a cross-sectional cohort of women with and without preterm labor, and correlated our findings with measurements of metabolites and HMOs in urine and blood. We identified several microbial signatures associated with short cervix, PTB and/or preterm contractions such as Lactobacillus jensenii, L. gasseri, Ureaplasma sp. and Gardnerella sp.. Additionally, we observed associations between sialylated HMOs, in particular 3'-sialyllactose, with PTB, short cervix and increased inflammation, and confirmed an influence of HMOs on the microbiome profile. Identifying serum and urinary HMOs and several key microorganisms associated with PTB, our findings point at two distinct processes modulating the risk for PTB. One process seems to be driven by sterile inflammation, characterized by increased concentrations of sialylated HMOs in serum. Another process might be microbiome-mediated, potentially driven by secretor-associated HMOs in urine. Our results support current efforts to improve diagnostics and therapeutic strategies.
   
• Importance: Causes for preterm birth often remain elusive. We investigated whether circulating human milk oligosaccharides (HMOs) might be involved in modulating urinary and vaginal microbiome promoting or preventing preterm birth. We here identified HMOs and key microbial taxa associated with indicators of preterm birth. Based on our results, we propose two models how HMOs might modulate risk for preterm birth: 1) by changes in HMOs associated with sterile inflammation (microbiome-independent) and 2) by HMO-driven shifts in microbiome (microbiome-dependent). Our findings will guide current efforts to better predict the risk for PTB in seemingly healthy pregnant women, and also provide appropriate preventive strategies.