This page has only limited features, please log in for full access.
Project Goal: Analysis of industrial cooling liquid microbiomes
Current Stage: Experimental stage
Project Goal: Improve black soldier fly rearing
Current Stage: Experimental stage
Project Goal: Microbiomes of black soldier fly larvae reared by citizen scientists
Current Stage: Experimental stage
Project Goal: Introduce citizen scientists to insect farming
Current Stage: Finished
The human microbiome has emerged as a central research topic in human biology and biomedicine. Current microbiome studies generate high-throughput omics data across different body sites, populations, and life stages. Many of the challenges in microbiome research are similar to other high-throughput studies, the quantitative analyses need to address the heterogeneity of data, specific statistical properties, and the remarkable variation in microbiome composition across individuals and body sites. This has led to a broad spectrum of statistical and machine learning challenges that range from study design, data processing, and standardization to analysis, modeling, cross-study comparison, prediction, data science ecosystems, and reproducible reporting. Nevertheless, although many statistics and machine learning approaches and tools have been developed, new techniques are needed to deal with emerging applications and the vast heterogeneity of microbiome data. We review and discuss emerging applications of statistical and machine learning techniques in human microbiome studies and introduce the COST Action CA18131 “ML4Microbiome” that brings together microbiome researchers and machine learning experts to address current challenges such as standardization of analysis pipelines for reproducibility of data analysis results, benchmarking, improvement, or development of existing and new tools and ontologies.
Isabel Moreno-Indias; Leo Lahti; Miroslava Nedyalkova; Ilze Elbere; Gennady Roshchupkin; Muhamed Adilovic; Onder Aydemir; Burcu Bakir-Gungor; Enrique Carrillo-De Santa Pau; Domenica D’Elia; Mahesh S. Desai; Laurent Falquet; Aycan Gundogdu; Karel Hron; Thomas Klammsteiner; Marta B. Lopes; Laura Judith Marcos-Zambrano; Cláudia Marques; Michael Mason; Patrick May; Lejla Pašić; Gianvito Pio; Sándor Pongor; Vasilis J. Promponas; Piotr Przymus; Julio Saez-Rodriguez; Alexia Sampri; Rajesh Shigdel; Blaz Stres; Ramona Suharoschi; Jaak Truu; Ciprian-Octavian Truică; Baiba Vilne; Dimitrios Vlachakis; Ercument Yilmaz; Georg Zeller; Aldert L. Zomer; David Gómez-Cabrero; Marcus J. Claesson. Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions. Frontiers in Microbiology 2021, 12, 1 .
AMA StyleIsabel Moreno-Indias, Leo Lahti, Miroslava Nedyalkova, Ilze Elbere, Gennady Roshchupkin, Muhamed Adilovic, Onder Aydemir, Burcu Bakir-Gungor, Enrique Carrillo-De Santa Pau, Domenica D’Elia, Mahesh S. Desai, Laurent Falquet, Aycan Gundogdu, Karel Hron, Thomas Klammsteiner, Marta B. Lopes, Laura Judith Marcos-Zambrano, Cláudia Marques, Michael Mason, Patrick May, Lejla Pašić, Gianvito Pio, Sándor Pongor, Vasilis J. Promponas, Piotr Przymus, Julio Saez-Rodriguez, Alexia Sampri, Rajesh Shigdel, Blaz Stres, Ramona Suharoschi, Jaak Truu, Ciprian-Octavian Truică, Baiba Vilne, Dimitrios Vlachakis, Ercument Yilmaz, Georg Zeller, Aldert L. Zomer, David Gómez-Cabrero, Marcus J. Claesson. Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions. Frontiers in Microbiology. 2021; 12 ():1.
Chicago/Turabian StyleIsabel Moreno-Indias; Leo Lahti; Miroslava Nedyalkova; Ilze Elbere; Gennady Roshchupkin; Muhamed Adilovic; Onder Aydemir; Burcu Bakir-Gungor; Enrique Carrillo-De Santa Pau; Domenica D’Elia; Mahesh S. Desai; Laurent Falquet; Aycan Gundogdu; Karel Hron; Thomas Klammsteiner; Marta B. Lopes; Laura Judith Marcos-Zambrano; Cláudia Marques; Michael Mason; Patrick May; Lejla Pašić; Gianvito Pio; Sándor Pongor; Vasilis J. Promponas; Piotr Przymus; Julio Saez-Rodriguez; Alexia Sampri; Rajesh Shigdel; Blaz Stres; Ramona Suharoschi; Jaak Truu; Ciprian-Octavian Truică; Baiba Vilne; Dimitrios Vlachakis; Ercument Yilmaz; Georg Zeller; Aldert L. Zomer; David Gómez-Cabrero; Marcus J. Claesson. 2021. "Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions." Frontiers in Microbiology 12, no. : 1.
The number of microbiome-related studies has notably increased the availability of data on human microbiome composition and function. These studies provide the essential material to deeply explore host-microbiome associations and their relation to the development and progression of various complex diseases. Improved data-analytical tools are needed to exploit all information from these biological datasets, taking into account the peculiarities of microbiome data, i.e., compositional, heterogeneous and sparse nature of these datasets. The possibility of predicting host-phenotypes based on taxonomy-informed feature selection to establish an association between microbiome and predict disease states is beneficial for personalized medicine. In this regard, machine learning (ML) provides new insights into the development of models that can be used to predict outputs, such as classification and prediction in microbiology, infer host phenotypes to predict diseases and use microbial communities to stratify patients by their characterization of state-specific microbial signatures. Here we review the state-of-the-art ML methods and respective software applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on the application of ML in microbiome studies related to association and clinical use for diagnostics, prognostics, and therapeutics. Although the data presented here is more related to the bacterial community, many algorithms could be applied in general, regardless of the feature type. This literature and software review covering this broad topic is aligned with the scoping review methodology. The manual identification of data sources has been complemented with: (1) automated publication search through digital libraries of the three major publishers using natural language processing (NLP) Toolkit, and (2) an automated identification of relevant software repositories on GitHub and ranking of the related research papers relying on learning to rank approach.
Laura Judith Marcos-Zambrano; Kanita Karaduzovic-Hadziabdic; Tatjana Loncar Turukalo; Piotr Przymus; Vladimir Trajkovik; Oliver Aasmets; Magali Berland; Aleksandra Gruca; Jasminka Hasic; Karel Hron; Thomas Klammsteiner; Mikhail Kolev; Leo Lahti; Marta B. Lopes; Victor Moreno; Irina Naskinova; Elin Org; Inês Paciência; Georgios Papoutsoglou; Rajesh Shigdel; Blaz Stres; Baiba Vilne; Malik Yousef; Eftim Zdravevski; Ioannis Tsamardinos; Enrique Carrillo De Santa Pau; Marcus J. Claesson; Isabel Moreno-Indias; Jaak Truu. Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment. Frontiers in Microbiology 2021, 12, 1 .
AMA StyleLaura Judith Marcos-Zambrano, Kanita Karaduzovic-Hadziabdic, Tatjana Loncar Turukalo, Piotr Przymus, Vladimir Trajkovik, Oliver Aasmets, Magali Berland, Aleksandra Gruca, Jasminka Hasic, Karel Hron, Thomas Klammsteiner, Mikhail Kolev, Leo Lahti, Marta B. Lopes, Victor Moreno, Irina Naskinova, Elin Org, Inês Paciência, Georgios Papoutsoglou, Rajesh Shigdel, Blaz Stres, Baiba Vilne, Malik Yousef, Eftim Zdravevski, Ioannis Tsamardinos, Enrique Carrillo De Santa Pau, Marcus J. Claesson, Isabel Moreno-Indias, Jaak Truu. Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment. Frontiers in Microbiology. 2021; 12 ():1.
Chicago/Turabian StyleLaura Judith Marcos-Zambrano; Kanita Karaduzovic-Hadziabdic; Tatjana Loncar Turukalo; Piotr Przymus; Vladimir Trajkovik; Oliver Aasmets; Magali Berland; Aleksandra Gruca; Jasminka Hasic; Karel Hron; Thomas Klammsteiner; Mikhail Kolev; Leo Lahti; Marta B. Lopes; Victor Moreno; Irina Naskinova; Elin Org; Inês Paciência; Georgios Papoutsoglou; Rajesh Shigdel; Blaz Stres; Baiba Vilne; Malik Yousef; Eftim Zdravevski; Ioannis Tsamardinos; Enrique Carrillo De Santa Pau; Marcus J. Claesson; Isabel Moreno-Indias; Jaak Truu. 2021. "Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment." Frontiers in Microbiology 12, no. : 1.
Canteens represent an essential food supply hub for educational institutions, companies, and business parks. Many people in these locations rely on a guaranteed service with consistent quality. It is an ongoing challenge to satisfy the demand for sufficient serving numbers, portion sizes, and menu variations to cover food intolerances and different palates of customers. However, overestimating this demand or fluctuating quality of dishes leads to an inevitable loss of unconsumed food due to leftovers. In this study, the food waste fraction of canteen leftovers was identified as an optimal diet for black soldier fly (Hermetia illucens) larvae based on 50% higher consumption and 15% higher waste reduction indices compared with control chicken feed diet. Although the digestibility of food waste was nearly twice as high, the conversion efficiency of ingested and digested chicken feed remains unparalleled (17.9 ± 0.6 and 37.5 ± 0.9 in CFD and 7.9 ± 0.9 and 9.6 ± 1.0 in FWD, respectively). The oil separator waste fraction, however, inhibited biomass gain by at least 85% and ultimately led to a larval mortality of up to 96%. In addition to monitoring larval development, we characterized physicochemical properties of pre- and post-process food waste substrates. High-throughput amplicon sequencing identified Firmicutes, Proteobacteria, and Bacteroidota as the most abundant phyla, and Morganella, Acinetobacter, and certain Lactobacillales species were identified as indicator species. By using metagenome imputation, we additionally gained insights into the functional spectrum of gut microbial communities. We anticipate that the results will contribute to the development of decentralized waste-management sites that make use of larvae to process food waste as it has become common practice for biogas plants.
Thomas Klammsteiner; Andreas Walter; Tajda Bogataj; Carina D. Heussler; Blaž Stres; Florian M. Steiner; Birgit C. Schlick-Steiner; Heribert Insam. Impact of Processed Food (Canteen and Oil Wastes) on the Development of Black Soldier Fly (Hermetia illucens) Larvae and Their Gut Microbiome Functions. Frontiers in Microbiology 2021, 12, 1 .
AMA StyleThomas Klammsteiner, Andreas Walter, Tajda Bogataj, Carina D. Heussler, Blaž Stres, Florian M. Steiner, Birgit C. Schlick-Steiner, Heribert Insam. Impact of Processed Food (Canteen and Oil Wastes) on the Development of Black Soldier Fly (Hermetia illucens) Larvae and Their Gut Microbiome Functions. Frontiers in Microbiology. 2021; 12 ():1.
Chicago/Turabian StyleThomas Klammsteiner; Andreas Walter; Tajda Bogataj; Carina D. Heussler; Blaž Stres; Florian M. Steiner; Birgit C. Schlick-Steiner; Heribert Insam. 2021. "Impact of Processed Food (Canteen and Oil Wastes) on the Development of Black Soldier Fly (Hermetia illucens) Larvae and Their Gut Microbiome Functions." Frontiers in Microbiology 12, no. : 1.
Today, insect applications for food and feed are of strong economic, ecological and social interest. Despite their tremendous potential, insects still elicit negative associations in the mindset of Western consumers, which is attributed to a lack of knowledge and scarce opportunities for engagement in this topic. The citizen science project ‘six-legged livestock’ aims to increase the potential of the insect Hermetia illucens (black soldier fly), merging the topics ‘waste re-valorisation’ and ‘protein production’ as a cross-link to circular economy. Workshops were held in four school classes, involving 89 pupils, aged 15 to 18 years old. Making use of organic wastes, participating school classes ran eight rearing systems containing a total of 1800 H. illucens larvae. In the four-week experiments, the pupils monitored larval growth and development. Evidently, the pupils were highly motivated to run their rearing systems and fulfil their working tasks. Furthermore, negative associations with insects, including phobia and scepticism decreased, while excitement for the topic increased after hands-on work with the insects. The presented project may be considered an innovative approach paving the way for the establishment of insects as an important educational tool, since they are still underrepresented in scholarly curricula, despite the public outrage over insect decline.
Andreas Walter; Thomas Klammsteiner; Magdalena Gassner; Carina Desirée Heussler; Suzanne Kapelari; Markus Schermer; Heribert Insam. Black Soldier Fly School Workshops as Means to Promote Circular Economy and Environmental Awareness. Sustainability 2020, 12, 9574 .
AMA StyleAndreas Walter, Thomas Klammsteiner, Magdalena Gassner, Carina Desirée Heussler, Suzanne Kapelari, Markus Schermer, Heribert Insam. Black Soldier Fly School Workshops as Means to Promote Circular Economy and Environmental Awareness. Sustainability. 2020; 12 (22):9574.
Chicago/Turabian StyleAndreas Walter; Thomas Klammsteiner; Magdalena Gassner; Carina Desirée Heussler; Suzanne Kapelari; Markus Schermer; Heribert Insam. 2020. "Black Soldier Fly School Workshops as Means to Promote Circular Economy and Environmental Awareness." Sustainability 12, no. 22: 9574.
Because of its nutritious properties, the black soldier fly has emerged as one of the most popular species in advancing circular economy through the re-valorization of anthropogenic organic wastes to insect biomass. Black soldier fly frass accumulates as a major by-product in artificial rearing set-ups and harbors great potential to complement or replace commercial fertilizers. We applied frass from larvae raised on different diets in nitrogen-equivalent amounts as soil amendment, comparing it to NH4NO3 fertilizer as a control. While the soil properties did not reveal any difference between mineral fertilizer and frass, principal component analysis showed significant differences that are mainly attributed to nitrate and dissolved nitrogen contents. We did not find significant differences in the growth of perennial ryegrass between the treatments, indicating that frass serves as a rapidly acting fertilizer comparable to NH4NO3. While the abundance of coliform bacteria increased during frass maturation, after application to the soil, they were outcompeted by gram-negatives. We thus conclude that frass may serve as a valuable fertilizer and does not impair the hygienic properties of soils.
Thomas Klammsteiner; Veysel Turan; Marina Fernández-Delgado Juárez; Simon Oberegger; Heribert Insam. Suitability of Black Soldier Fly Frass as Soil Amendment and Implication for Organic Waste Hygienization. Agronomy 2020, 10, 1578 .
AMA StyleThomas Klammsteiner, Veysel Turan, Marina Fernández-Delgado Juárez, Simon Oberegger, Heribert Insam. Suitability of Black Soldier Fly Frass as Soil Amendment and Implication for Organic Waste Hygienization. Agronomy. 2020; 10 (10):1578.
Chicago/Turabian StyleThomas Klammsteiner; Veysel Turan; Marina Fernández-Delgado Juárez; Simon Oberegger; Heribert Insam. 2020. "Suitability of Black Soldier Fly Frass as Soil Amendment and Implication for Organic Waste Hygienization." Agronomy 10, no. 10: 1578.
An organism’s gut microbiome handles most of the metabolic processes associated with food intake and digestion but can also strongly affect health and behavior. A stable microbial core community in the gut provides general metabolic competences for substrate degradation and is robust against extrinsic disturbances like changing diets or pathogens. Black Soldier Fly larvae (BSFL; Hermetia illucens) are well known for their ability to efficiently degrade a wide spectrum of organic materials. The ingested substrates build up the high fat and protein content in their bodies that make the larvae interesting for the animal feedstuff industry. In this study, we subjected BSFL to three distinct types of diets carrying a low bioburden and assessed the diets’ impact on larval development and on the composition of the bacterial and archaeal gut community. No significant impact on the gut microbiome across treatments pointed us to the presence of a predominant core community backed by a diverse spectrum of low-abundance taxa. Actinomyces spp., Dysgonomonas spp., and Enterococcus spp. as main members of this community provide various functional and metabolic skills that could be crucial for the thriving of BSFL in various environments. This indicates that the type of diet could play a lesser role in guts of BSFL than previously assumed and that instead a stable autochthonous collection of bacteria provides the tools for degrading of a broad range of substrates. Characterizing the interplay between the core gut microbiome and BSFL helps to understand the involved degradation processes and could contribute to further improving large-scale BSFL rearing.
Thomas Klammsteiner; Andreas Walter; Tajda Bogataj; Carina D. Heussler; Blaž Stres; Florian M. Steiner; Birgit C. Schlick-Steiner; Wolfgang Arthofer; Heribert Insam. The Core Gut Microbiome of Black Soldier Fly (Hermetia illucens) Larvae Raised on Low-Bioburden Diets. Frontiers in Microbiology 2020, 11, 993 .
AMA StyleThomas Klammsteiner, Andreas Walter, Tajda Bogataj, Carina D. Heussler, Blaž Stres, Florian M. Steiner, Birgit C. Schlick-Steiner, Wolfgang Arthofer, Heribert Insam. The Core Gut Microbiome of Black Soldier Fly (Hermetia illucens) Larvae Raised on Low-Bioburden Diets. Frontiers in Microbiology. 2020; 11 ():993.
Chicago/Turabian StyleThomas Klammsteiner; Andreas Walter; Tajda Bogataj; Carina D. Heussler; Blaž Stres; Florian M. Steiner; Birgit C. Schlick-Steiner; Wolfgang Arthofer; Heribert Insam. 2020. "The Core Gut Microbiome of Black Soldier Fly (Hermetia illucens) Larvae Raised on Low-Bioburden Diets." Frontiers in Microbiology 11, no. : 993.
Thomas Klammsteiner; Andreas Walter; Heinrich Pan; Magdalena Gassner; Carina Desirée Heussler; Markus Schermer; Heribert Insam. On everyone’s lips: insects for food and feed. Proceedings of 5th Austrian Citizen Science Conference 2019 — PoS(ACSC2019) 2020, 366, 006 .
AMA StyleThomas Klammsteiner, Andreas Walter, Heinrich Pan, Magdalena Gassner, Carina Desirée Heussler, Markus Schermer, Heribert Insam. On everyone’s lips: insects for food and feed. Proceedings of 5th Austrian Citizen Science Conference 2019 — PoS(ACSC2019). 2020; 366 ():006.
Chicago/Turabian StyleThomas Klammsteiner; Andreas Walter; Heinrich Pan; Magdalena Gassner; Carina Desirée Heussler; Markus Schermer; Heribert Insam. 2020. "On everyone’s lips: insects for food and feed." Proceedings of 5th Austrian Citizen Science Conference 2019 — PoS(ACSC2019) 366, no. : 006.
Cooling and lubrication agents like triethanolamine (TEA) are essential for many purposes in industry. Due to biodegradation, they need continuous replacement, and byproducts of degradation may be toxic. This study investigates an industrial (1,200 m³) cooling-lubrication circuit (CLC) that has been in operation for 20 years and is supposedly in an ecological equilibrium, thus offering a unique habitat. Next-generation (Illumina Miseq 16S rRNA amplicon) sequencing was used to profile the CLC-based microbiota and relate it to TEA and bicine dynamics at the sampling sites, influent, machine rooms, biofilms and effluent. Pseudomonas pseudoalcaligenes dominated the effluent and influent sites, while Alcaligenes faecalis dominated biofilms, and both species were identified as the major TEA degrading bacteria. It was shown that a 15 min heat treatment at 50°C was able to slow down the growth of both species, a promising option to control TEA degradation at large scale.
Thomas Klammsteiner; Heribert Insam; Maraike Probst. Microbiota in a cooling-lubrication circuit and an option for controlling triethanolamine biodegradation. Biofouling 2018, 34, 519 -531.
AMA StyleThomas Klammsteiner, Heribert Insam, Maraike Probst. Microbiota in a cooling-lubrication circuit and an option for controlling triethanolamine biodegradation. Biofouling. 2018; 34 (5):519-531.
Chicago/Turabian StyleThomas Klammsteiner; Heribert Insam; Maraike Probst. 2018. "Microbiota in a cooling-lubrication circuit and an option for controlling triethanolamine biodegradation." Biofouling 34, no. 5: 519-531.