Representative Bacillus sp. AM1 from Gut Microbiota Harbor Versatile Molecular Pathways for Bisphenol A Biodegradation

Human gut microbiota harbors numerous microbial species with molecular enzymatic potential that impact on the eubiosis/dysbiosis and health/disease balances. Microbiota species isolation and description of their specific molecular features remain largely unexplored. In the present study, we focused on the cultivation and selection of species able to tolerate or biodegrade the endocrine disruptor bisphenol A (BPA), a xenobiotic extensively found in food plastic containers. Chemical xenobiotic addition methods for the directed isolation, culturing, Whole Genome Sequencing (WGS), phylogenomic identification, and specific gene-encoding searches have been applied to isolate microorganisms, assess their BPA metabolization potential, and describe encoded catabolic pathways. BPA-tolerant strains were isolated from 30% of infant fecal microbial culture libraries analyzed. Most isolated strains were phylogenetically related to the operational taxonomic group Bacillus amyloliquefaciens spp. Importantly, WGS analysis of microbial representative strain, Bacillus sp. AM1 identified the four complete molecular pathways involved on BPA degradation indicating its versatility and high potential to degrade BPA. Pathways for Exopolysaccharide (EPS) and Polyhydroxyalkanates (PHA) biopolymer synthesis were also identified and phenotypically confirmed by transmission electronic microscopy (TEM). These microbial biopolymers could generally contribute to capture and/or deposit xenobiotics.GP/EFSA/ENCO/380 2018/03/G04: OBEMIRISK: Knowledge platform for assessing the risk of Bisphenols on gut microbiota and its role in obesogenic phenotype: looking for biomarkersFEDERInfrastructure: IE_2019-198APC was funded by EIN-2019-10308

Rapid and simultaneous determination of histidine metabolism intermediates in human and mouse microbiota and biomatrices

European Food Safety Authority; FEDER-Infraestructure Consejeria de Economia, Conocimiento, Empresas y Universidad, Grant/Award Number: IE_2019-198Histidine metabolism is a key pathway physiologically involved in satiety, recognition memory, skin, and neural protection and allergic diseases. Microbiologicallyproduced imidazole propionate induces type II diabetes and interferes with glucose lowering drugs. Despite their determinant health implications, no single method simultaneously assesses histidine metabolites in urine, feces, and microbiota. The aim of this study was to develop a simple, rapid, and sensitive method for the determination of histidine and its major bioactive metabolites histamine, N-acetylhistamine, imidazole-4-acetate, cis-urocanate, trans-urocanate, glutamate and imidazole propionate, using ultrahigh-performance liquid chromatography with electrospray ionization tandem mass spectrometry. An innovative simple extraction method from small aliquots of human and mice urine, feces and microbial cell extracts was coupled to separation in a 6.5 min chromatographic run. The successful performance allowed accurate and precise quantification of all metabolites in mouse feces, suggesting broad exchange of histidine metabolites between the gut and mice. Higher urine histamine, histamine to histidine ratio, and imidazole-4-acetate pointed to an underlying inflammatory or allergic process in mice compared to human subjects. N-acetylhistamine and imidazole propionate were detected in human and mouse feces, confirming its origin from gut microbial metabolism. Our novel and robust analytical method captured histidine metabolism in a single assay that will facilitate broad and deep histidine metabolic phenotyping assessing the impact of microbiota on host health in large-scale human observational and interventional studies.European Food Safety AuthorityFEDER-Infraestructure Consejeria de Economia, Conocimiento, Empresas y Universidad IE_2019-19

Infant Gut Microbiota Associated with Fine Motor Skills

BACKGROUND: During early life, dynamic gut colonization and brain development co-occur with potential cross-talk mechanisms affecting behaviour. METHODS: We used 16S rRNA gene sequencing to examine the associations between gut microbiota and neurodevelopmental outcomes assessed by the Bayley Scales of Infant Development III in 71 full-term healthy infants at 18 months of age. We hypothesized that children would differ in gut microbial diversity, enterotypes obtained by Dirichlet multinomial mixture analysis and specific taxa based on their behavioural characteristics. RESULTS: In children dichotomized by behavioural trait performance in above- and below-median groups, weighted Unifrac b-diversity exhibited significant differences in fine motor (FM) activity. Dirichlet multinomial mixture modelling identified two enterotypes strongly associated with FM outcomes. When controlling for maternal pre-gestational BMI and breastfeeding for up to 3 months, the examination of signature taxa in FM groups showed that Turicibacter and Parabacteroides were highly abundant in the below-median FM group, while Collinsella, Coprococcus, Enterococcus, Fusobacterium, Holdemanella, Propionibacterium, Roseburia, Veillonella, an unassigned genus within Veillonellaceae and, interestingly, probiotic Bifidobacterium and Lactobacillus were more abundant in the above-median FM group. CONCLUSIONS: Our results suggest an association between enterotypes and specific genera with FM activity and may represent an opportunity for probiotic interventions relevant to treatment for motor disorders.Spanish Ministry of Innovation and ScienceJunta de Andalucía: Excellence Projects (P06-CTS-02341)Spanish Ministry of Economy and Competitiveness (BFU2012-40254-C03-02) and partially funded by the European Commission MyNewGut FP7 EU Project (Grant agreement n◦ 613979)MyNewGut FP7 EU Project (Grant agreement n◦ 613979)DynaHEALTH EU Project HORIZON 2020 (Grant agreement n◦ : 633595-2)Marie Curie post-doctoral fellowship (FP7, no. 329812, NutriOmics)Spanish Ministry of Education, Culture and Sports (FPU16/04587

Next Generation Probiotics for Neutralizing Obesogenic Effects: Taxa Culturing Searching Strategies

This work was carried out within the frame of GP/EFSA/ENCO/380 2018/03/G04: OBEMIRISK: Knowledge platform for assessing the risk of Bisphenols on gut microbiota and its role in obesogenic phenotype: looking for biomarkers. This research was also funded by FEDER-Infrastructure: IE_2019-198. A.L-M Incentivacion de la Investigacion. Plan Propio-UGR. K. Cerk is collaborating with UGR under the EU-FORA Programme (2020/2021).The combination of diet, lifestyle, and the exposure to food obesogens categorized into "microbiota disrupting chemicals" (MDC) could determine obesogenic-related dysbiosis and modify the microbiota diversity that impacts on individual health-disease balances, inducing altered pathogenesis phenotypes. Specific, complementary, and combined treatments are needed to face these altered microbial patterns and the specific misbalances triggered. In this sense, searching for next-generation beneficial microbes or next-generation probiotics (NGP) by microbiota culturing, and focusing on their demonstrated, extensive scope and well-defined functions could contribute to counteracting and repairing the effects of obesogens. Therefore, this review presents a perspective through compiling information and key strategies for directed searching and culturing of NGP that could be administered for obesity and endocrine-related dysbiosis by (i) observing the differential abundance of specific microbiota taxa in obesity-related patients and analyzing their functional roles, (ii) developing microbiota-directed strategies for culturing these taxa groups, and (iii) applying the successful compiled criteria from recent NGP clinical studies. New isolated or cultivable microorganisms from healthy gut microbiota specifically related to obesogens' neutralization effects might be used as an NGP single strain or in consortia, both presenting functions and the ability to palliate metabolic-related disorders. Identification of holistic approaches for searching and using potential NGP, key aspects, the bias, gaps, and proposals of solutions are also considered in this review.OBEMIRISK: Knowledge platform for assessing the risk of Bisphenols on gut microbiota and its role in obesogenic phenotype: looking for biomarkers GP/EFSA/ENCO/380 2018/03/G04FEDER-Infrastructure IE_2019-19

A synbiotics, long chain polyunsaturated fatty acids, and milk fat globule membranes supplemented formula modulates microbiota maturation and neurodevelopment

Supplementary data to this article can be found online at https://doi.org/10.1016/j.clnu.2022.05.013.Acknowledgments The authors wish to acknowledge the parents and children who participated in the study, and also the paediatricians and researchers of the EURISTIKOS team at the Department of Paediatrics as well as the Genetics Service at Centro de Instrumentación Científica e UGR for their contributions.Funding This project was supported by CDTI (Centro para el Desarrollo Tecnológico e Industrial) and FEDER (SMARTFOODS: IDI-20141206), Ordesa Laboratories, S.L. (Contract FE-UGR No. 3349), and The Spanish Ministry of Economy, Industry and Competitiveness, and partially supported by HORIZON 2020 EU DynaHEALTH Project (GA No.633595). Alicia Ruiz and Inmaculada Acuña were granted Ph.D. scholarships from the Spanish Ministry of Economy and Competitivity. Tomás Cerdó was granted a Ph.D. scholarship from Carlos III Health Institute. Natalia Sepúlveda-Valbuena was granted with a scholarship from Fundación Carolina, Madrid, Spain.Background & aims The critical window of concurrent developmental paths of the nervous system and gut microbiota in infancy provides an opportunity for nutritional interventions with potential health benefits later in life. Methods We compared the dynamics of gut microbiota maturation and explored its association with neurodevelopment at 12 months and 4 years of age in 170 full-term healthy infants fed a standard formula (SF) or a new formula (EF) based on standard formula supplemented with synbiotics, long chain polyunsaturated fatty acids (LC-PUFA) and bovine milk fat globule membranes (MFGM), including a breastfed reference group (BF). Results Using Dirichlet Multinomial Modelling, we characterized three microbial enterotypes (Mixed, anaerobic and aerobic profile; Bact, Bacteroides-dominant; Firm, Firmicutes-enriched) and identified a new enterotype dominated by an unidentified genus within Lachnospiraceae (U_Lach). Enterotypes were associated with age (Mixed with baseline, U_Lach with month 6, Bact and Firm with months 12 and 18). Trajectories or timely enterotype shifts in each infant were not random but strongly associated with type of feeding. Trajectories in SF shifted from initial Mixed to U_Lach, Bact or Firm at month. Microbiota maturation in EF split into a fast trajectory as in SF, and a slow trajectory with Mixed to U_Lach, Bact or Firm transitions at months 12 or 18, as in BF. EF infants with slow trajectories were more often in–home reared and born by vaginal delivery to mothers with pre-pregnancy lean BMI. At 12 months of age, language and expressive language scores were significantly higher in EF infants with fast trajectories than in BF. Neurodevelopmental outcomes were similar between EF infants with slow trajectories and BF at 12 months and 4 years of age. Conclusions Feeding a synbiotics, LC-PUFA and MFGM supplemented formula in a specific infant environment promoted probiotic growth and retarded gut microbiota maturation with similar neurodevelopment outcomes to breastfed infants.CDTI (Centro para el Desarrollo Tecnológico e Industrial) and FEDER (SMARTFOODS: IDI- 20141206)Ordesa Laboratories, S.L. (Contract FE-UGR No. 3349)Spanish Ministry of Economy, Industry and CompetitivenessHORIZON 2020 EU DynaHEALTH Project (GA No.633595

Contribución funcional y metabólica de la microbiota intestinal a la ingesta energética en el desarrollo de la obesidad

Proyectos y contratos que han financiado la Tesis Doctoral 1: Reference FP7-KBBE-2013-7 Title: MyNewGut: Microbiome Influence on Energy balance and Brain Development- Function Put into Action to Tackle Diet-related Diseases and Behavior IP at UGR: Dra.Cristina Campoy Colaborator at UGR: Dr.Antonio Suárez Funding Organism: FP7 Cooperation Theme 2 Food, Agriculture, Fisheries and Biotechnologies Time: 01/01/2014-31/12-2019 Funding (€) 8.973.268 2: Reference BFU2012-40254-C03-01 Title: PREOBE-2nd Follow-up: IP: Dra.Cristina Campoy Colaborator at UGR: Dr.Antonio Suárez Funding Organism: MINECO Time: 01/01-2013-31/12-16 Funding (€): 197.468 3: Reference: 2921 Title: Search for novel functional ingredients for infant formulas to improve human neurodevelopment IPs: Dr.Antonio Suárez and Dra.Cristina Campoy Funding Organism: Fondo Tecnológico. C.D.T.I. Ministerio de Ciencia e Innovación. Fundación Empresa – UGR Company: Laboratorios ORDESA S.L. Time: 01/01/09-31/12/18 Funding (€): 45.000, 30.000, extended for 2019. 4: Proyecto Internacional EFSA. Agencia Europea De Seguridad Alimentaria: OBEMIRISK Consortium-Partnering Grant - Project EFSA -Coordinadora: Margarita Aguilera Gómez. (Universidad de Granada).31/10/2018-31/05/2021. 200.484 € 5: Proyecto Internacional – Programa Eufora- Hosting Sites - Coordinadora EFSA: Margarita Aguilera Gómez. (Universidad de Granada). 01/09/2021-31/08/2022. 28.000 € Klara Cerk-Bioinformatica-Metagenómica-Microbiota-Obesidad-EDC 6: Proyecto Europa Investiga-MICIN: Identificación del rol patofisiologico de la microbiota alterada por xenobióticos de la dieta en pacientes con desórdenes hormonales- Laboratorio de referencia (INYTA-Departamento de Microbiología). 01/06/2019- 31/05/2021. 8.500 € EUROS 7: Proyecto Infraestructura: Laboratorio de referencia de microbiota humana: Estación de manipulación de microorganismos en anaerobiosis y accesorios para la optimización y armonización del análisis fenotípico y genotípico de la microbiota y su impacto en nutrición y salud". 190.407 € (29-12-2020-29-12-2022) 8: Proyecto FIS ISCIII: Influence of endocrine disrupters chemicals on gut microbiota: a missed link in childhood obesity (ENDOMICROMICS) 111.320 € (01-01-2021-31-12- 2023)La microbiota intestinal humana es una comunidad microbiana densa y diversa que contribuye en gran medida a la salud y enfermedad del organismo. Las comunidades microbianas intestinales han coevolucionado con el huésped para desarrollar una relación mutualista, lo que influye en la homeostasis metabólica, el sistema endocrino, la función cerebral y la disponibilidad de macronutrientes. Las etapas tempranas de la vida son de especial interés, donde el establecimiento y la influencia de la microbiota intestinal puede tener consecuencias a largo plazo. El conocimiento acumulado sobre la microbiota intestinal está produciendo un cambio en el enfoque de los estudios, que previamente trataban de contestar a la pregunta de ¿qué microorganismos la componen?, hacia la pregunta ¿qué función tienen esos microorganismos? Para intentar contestarlas se han realizado estudios metabólicos y enzimáticos que permitan describir mejor los efectos de la microbiota intestinal sobre la salud/enfermedad del huésped, concretamente en obesidad y en alteraciones cognitivas, y diseñar una estrategia racional para clasificar, identificar y ensayar consorcios de microbiota humana en modelos murinos gnotobióticos. Concretamente, el estudio se ha centrado en la actividad enzimática glicosidasa y su impacto en el metabolismo de carbohidratos en relación a la obesidad. Asimismo, se ha estudiado la relación de la microbiota con el neurodesarrollo infantil a través del metabolismo de la histidina, y ha sido posible gracias al desarrollo de un método rápido, preciso y simultáneo para medir la histidina y sus metabolitos bioactivos usando UHPLC-MS/MS. Los hallazgos muestran que el fenotipo de obesidad se transmite madre-hijo-ratón a través de transferencia efectiva de la microbiota. Además, el metabolismo microbiano asocia con el perfil de neurodesarrollo de niños, y la asociación se mantiene en los ratones receptores de la microbiota, mostrando diferencias significativas en el metabolismo de la histidina. Conocer mejor las vías de comunicación entre la microbiota y el huésped es el camino para entender su influencia en la salud y en multitud de trastornos metabólicos y neurológicos con el fin de encontrar posibles enfoques terapéuticos y diagnósticos.Human gut microbiota is a dense and diverse microbial community that contributes greatly to the health and disease balance. Gut microbial communities have co-evolved with the host to develop a mutualistic relationship, influencing metabolic homeostasis, the endocrine system, brain function, and macronutrient availability. Early life stages are of exceptional interest, because the establishment and influence of the gut taxa microbiota can trigger long-term health consequences. The increased knowledge about the intestinal microbiota is producing a change of paradigm and focus of the studies, which were previously used to answer the question of what intestinal microbiota is producing?, towards the question what function do these microbes have? To try to answer these questions, a metabolic and enzymatic study has been carried out to better describe the effects of the intestinal microbiota on the host health/disease equilibrium, specifically in obesity and cognitive alterations; and to design a rational strategy to classify, identify and test microbiota consortia in gnotobiotic murine models. Specially, the study has focused on glycosidase enzymatic activity, its impact on carbohydrate metabolism, in relation to obesity. Likewise, the relationship of the microbiota with childhood neurodevelopment through histidine metabolism has been studied. That has been facilitated throught the development of a specific, rapid, precise and simultaneous method to measure histidine and its bioactive metabolites using UHPLC-MS/ MS. The overall results show that the obesity phenotype is transmitted from mother-child-mouse through the effective transfer of the microbiota. In addition, specific microbial metabolism is associated with the neurodevelopmental profile of children, and the association was maintained in microbiota recipient mice, showing significant differences in the histidine metabolism. Therefore, contribution and more scientific evidence for knowing the communication pathways between the microbiota and the host is the way to better understand their influence on metabolic and neurological disorders and ultimately on health in order to find new therapeutic and diagnostic approaches.Tesis Univ. Granada.FP7-KBBE-2013-7 FP7 Cooperation Theme 2 FoodBFU2012-40254-C03-01 MINECO2921 Fondo Tecnológico. C.D.T.I. Ministerio de Ciencia e Innovación. Fundación Empresa – UGRProyecto Internacional EFSA. Agencia Europea De Seguridad Alimentaria: OBEMIRISK Consortium-Partnering Grant - Project EFSAProyecto Internacional – Programa Eufora- Hosting Sites - Coordinadora EFSAProyecto Europa Investiga-MICI

Infant gut microbiota contributes to cognitive performance in mice

Work in the author’s laboratories was performed on resources provided by the Spanish Health and Science Ministries (PREOBE project P06-CTS-02341, BFU2012-40254-C03-01, and PID2020-114269GB-I00), Junta de Andalucía, and UFZ-Germany. T.C. participated in the PhD program in biomedicine at UGR, was a fellowship of the FPI program (BES-2013-065133) funded by the Spanish Ministry of Economy and Competitiveness, and is currently supported by the ‘‘Sara Borrell’’ program (CD21/00187) of the Carlos III Institute. I.A., S.M.-M., and A.R.-R. were granted PhD scholarships (FPU) from the Spanish Ministry of Economy and Competitiveness. A.R.-R. currently holds a María Zambrano Next Generation EU-Talent Reincorporation from UGR.Gut microbiota has been related to infant neurodevelopment. Here, an association between infant composite cognition with gut microbiota composition was established as soon as 6 months. Higher diversity and evenness characterized microbial communities of infants with composite cognition above (Inf-aboveCC) versus below (Inf-belowCC) median values. Metaproteomic and metabolomic analyses established an association between microbial histidine ammonia lyase activity and infant histidine metabolome with cognition. Fecal transplantation from Inf-aboveCC versus Inf-belowCC donors into germ-free mice showed that memory, assessed by novel object recognition test, was a transmissible trait. Furthermore, Inf-aboveCC mice were enriched in species previously linked to cognition belonging to Bacteroides, Phaeicola and Bifidobacterium. Finally, Inf-aboveCC mice showed differential faecal histidine, hippocampal urocanate and histidine-urocanate-glutamate ratios compared to Inf-aboveCC mice. Overall, these findings reveal a causative role of gut microbiota on infant cognition pointing at modulation of histidine metabolite levels as a potential underlying mechanism.Spanish Health and Science Ministries (PREOBE project P06-CTS-02341, BFU2012-40254-C03-01, PID2020-114269GB-I00)Junta de AndalucíaUFZ-GermanySpanish Ministry of Economy and Competitiveness BES-2013-065133Carlos III Institute (CD21/00187)María Zambrano Next Generation EU-Talent ReincorporationUG