Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome
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The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service. -
The Oral Microbiome of Healthy Japanese People at the Age of 90
applied sciences Article The Oral Microbiome of Healthy Japanese People at the Age of 90 Yoshiaki Nomura 1,* , Erika Kakuta 2, Noboru Kaneko 3, Kaname Nohno 3, Akihiro Yoshihara 4 and Nobuhiro Hanada 1 1 Department of Translational Research, Tsurumi University School of Dental Medicine, Kanagawa 230-8501, Japan; [email protected] 2 Department of Oral bacteriology, Tsurumi University School of Dental Medicine, Kanagawa 230-8501, Japan; [email protected] 3 Division of Preventive Dentistry, Faculty of Dentistry and Graduate School of Medical and Dental Science, Niigata University, Niigata 951-8514, Japan; [email protected] (N.K.); [email protected] (K.N.) 4 Division of Oral Science for Health Promotion, Faculty of Dentistry and Graduate School of Medical and Dental Science, Niigata University, Niigata 951-8514, Japan; [email protected] * Correspondence: [email protected]; Tel.: +81-45-580-8462 Received: 19 August 2020; Accepted: 15 September 2020; Published: 16 September 2020 Abstract: For a healthy oral cavity, maintaining a healthy microbiome is essential. However, data on healthy microbiomes are not sufficient. To determine the nature of the core microbiome, the oral-microbiome structure was analyzed using pyrosequencing data. Saliva samples were obtained from healthy 90-year-old participants who attended the 20-year follow-up Niigata cohort study. A total of 85 people participated in the health checkups. The study population consisted of 40 male and 45 female participants. Stimulated saliva samples were obtained by chewing paraffin wax for 5 min. The V3–V4 hypervariable regions of the 16S ribosomal RNA (rRNA) gene were amplified by PCR. -
Bulleidia Extructa Gen. Nov., Sp. Nov., Isolated from the Oral Cavity
International Journal of Systematic and Evolutionary Microbiology (2000), 50, 979–983 Printed in Great Britain Bulleidia extructa gen. nov., sp. nov., isolated from the oral cavity Julia Downes,1 Bente Olsvik,†2 Sarah J. Hiom,1 David A. Spratt,1 Sarah L. Cheeseman,1 Ingar Olsen,2 Andrew J. Weightman3 and William G. Wade1 Author for correspondence: William G. Wade. Tel: j44 207 955 2849. Fax: j44 207 955 2847. e-mail: william.wade!kcl.ac.uk 1 Oral Microbiology Unit, Five strains of anaerobic non-sporing Gram-positive bacilli isolated from Division of Oral Medicine, advanced periodontitis (four strains) and a dentoalveolar abscess (one strain) Pathology, Microbiology and Immunology, Guy’s, that did not correspond to existing species were subjected to phenotypic and King’s and St Thomas’ genetic characterization. Following 16S rDNA sequence analysis, they were Dental Institute, found to constitute a novel branch of the low GMC Gram-positive division of King’s College London, Guy’s Hospital, London the phylogenetic tree related to Erysipelothrix rhusiopathiae and Holdemania SE1 9RT, UK filiformis. A new genus Bulleidia, and the species Bulleidia extructa, are 2 Institutt for oral biologi, proposed. Growth of B. extructa in broth media was poor but was enhanced by University of Oslo, the addition of fructose, glucose or maltose together with Tween 80. Glucose N-0316 Oslo, Norway and maltose were fermented and arginine was hydrolysed. Acetate, lactate 3 Cardiff School of and trace amounts of succinate were the end products of glucose Biosciences, Cardiff fermentation. The GMC content of the DNA of the type strain is 38 mol%. -
The Comparative Analysis of the Ruminal Bacterial Population in Reindeer (Rangifer Tarandus L.) from the Russian Arctic Zone: Regional and Seasonal Effects
animals Article The Comparative Analysis of the Ruminal Bacterial Population in Reindeer (Rangifer tarandus L.) from the Russian Arctic Zone: Regional and Seasonal Effects Larisa A. Ilina 1,*, Valentina A. Filippova 1 , Evgeni A. Brazhnik 1 , Andrey V. Dubrovin 1, Elena A. Yildirim 1 , Timur P. Dunyashev 1, Georgiy Y. Laptev 1, Natalia I. Novikova 1, Dmitriy V. Sobolev 1, Aleksandr A. Yuzhakov 2 and Kasim A. Laishev 2 1 BIOTROF + Ltd., 8 Malinovskaya St, Liter A, 7-N, Pushkin, 196602 St. Petersburg, Russia; fi[email protected] (V.A.F.); [email protected] (E.A.B.); [email protected] (A.V.D.); [email protected] (E.A.Y.); [email protected] (T.P.D.); [email protected] (G.Y.L.); [email protected] (N.I.N.); [email protected] (D.V.S.) 2 Department of Animal Husbandry and Environmental Management of the Arctic, Federal Research Center of Russian Academy Sciences, 7, Sh. Podbel’skogo, Pushkin, 196608 St. Petersburg, Russia; [email protected] (A.A.Y.); [email protected] (K.A.L.) * Correspondence: [email protected] Simple Summary: The reindeer (Rangifer tarandus) is a unique ruminant that lives in arctic areas characterized by severe living conditions. Low temperatures and a scarce diet containing a high Citation: Ilina, L.A.; Filippova, V.A.; proportion of hard-to-digest components have contributed to the development of several adaptations Brazhnik, E.A.; Dubrovin, A.V.; that allow reindeer to have a successful existence in the Far North region. These adaptations include Yildirim, E.A.; Dunyashev, T.P.; Laptev, G.Y.; Novikova, N.I.; Sobolev, the microbiome of the rumen—a digestive organ in ruminants that is responsible for crude fiber D.V.; Yuzhakov, A.A.; et al. -
Specificity in Legume-Rhizobia Symbioses
International Journal of Molecular Sciences Review Specificity in Legume-Rhizobia Symbioses Mitchell Andrews * and Morag E. Andrews Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand; [email protected] * Correspondence: [email protected]; Tel.: +64-3-423-0692 Academic Editors: Peter M. Gresshoff and Brett Ferguson Received: 12 February 2017; Accepted: 21 March 2017; Published: 26 March 2017 Abstract: Most species in the Leguminosae (legume family) can fix atmospheric nitrogen (N2) via symbiotic bacteria (rhizobia) in root nodules. Here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. The Leguminosae was divided into three sub-families, the Caesalpinioideae, Mimosoideae and Papilionoideae. Bradyrhizobium spp. were the exclusive rhizobial symbionts of species in the Caesalpinioideae, but data are limited. Generally, a range of rhizobia genera nodulated legume species across the two Mimosoideae tribes Ingeae and Mimoseae, but Mimosa spp. show specificity towards Burkholderia in central and southern Brazil, Rhizobium/Ensifer in central Mexico and Cupriavidus in southern Uruguay. These specific symbioses are likely to be at least in part related to the relative occurrence of the potential symbionts in soils of the different regions. Generally, Papilionoideae species were promiscuous in relation to rhizobial symbionts, but specificity for rhizobial genus appears to hold at the tribe level for the Fabeae (Rhizobium), the genus level for Cytisus (Bradyrhizobium), Lupinus (Bradyrhizobium) and the New Zealand native Sophora spp. (Mesorhizobium) and species level for Cicer arietinum (Mesorhizobium), Listia bainesii (Methylobacterium) and Listia angolensis (Microvirga). -
Breast Milk Microbiota: a Review of the Factors That Influence Composition
Published in "Journal of Infection 81(1): 17–47, 2020" which should be cited to refer to this work. ✩ Breast milk microbiota: A review of the factors that influence composition ∗ Petra Zimmermann a,b,c,d, , Nigel Curtis b,c,d a Department of Paediatrics, Fribourg Hospital HFR and Faculty of Science and Medicine, University of Fribourg, Switzerland b Department of Paediatrics, The University of Melbourne, Parkville, Australia c Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, Australia d Infectious Diseases Unit, The Royal Children’s Hospital Melbourne, Parkville, Australia s u m m a r y Breastfeeding is associated with considerable health benefits for infants. Aside from essential nutrients, immune cells and bioactive components, breast milk also contains a diverse range of microbes, which are important for maintaining mammary and infant health. In this review, we summarise studies that have Keywords: investigated the composition of the breast milk microbiota and factors that might influence it. Microbiome We identified 44 studies investigating 3105 breast milk samples from 2655 women. Several studies Diversity reported that the bacterial diversity is higher in breast milk than infant or maternal faeces. The maxi- Delivery mum number of each bacterial taxonomic level detected per study was 58 phyla, 133 classes, 263 orders, Caesarean 596 families, 590 genera, 1300 species and 3563 operational taxonomic units. Furthermore, fungal, ar- GBS chaeal, eukaryotic and viral DNA was also detected. The most frequently found genera were Staphylococ- Antibiotics cus, Streptococcus Lactobacillus, Pseudomonas, Bifidobacterium, Corynebacterium, Enterococcus, Acinetobacter, BMI Rothia, Cutibacterium, Veillonella and Bacteroides. There was some evidence that gestational age, delivery Probiotics mode, biological sex, parity, intrapartum antibiotics, lactation stage, diet, BMI, composition of breast milk, Smoking Diet HIV infection, geographic location and collection/feeding method influence the composition of the breast milk microbiota. -
Integrating Taxonomic, Functional, and Strain-Level Profiling of Diverse
TOOLS AND RESOURCES Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 Francesco Beghini1†, Lauren J McIver2†, Aitor Blanco-Mı´guez1, Leonard Dubois1, Francesco Asnicar1, Sagun Maharjan2,3, Ana Mailyan2,3, Paolo Manghi1, Matthias Scholz4, Andrew Maltez Thomas1, Mireia Valles-Colomer1, George Weingart2,3, Yancong Zhang2,3, Moreno Zolfo1, Curtis Huttenhower2,3*, Eric A Franzosa2,3*, Nicola Segata1,5* 1Department CIBIO, University of Trento, Trento, Italy; 2Harvard T.H. Chan School of Public Health, Boston, United States; 3The Broad Institute of MIT and Harvard, Cambridge, United States; 4Department of Food Quality and Nutrition, Research and Innovation Center, Edmund Mach Foundation, San Michele all’Adige, Italy; 5IEO, European Institute of Oncology IRCCS, Milan, Italy Abstract Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and *For correspondence: phylogenetic profiling of metagenomes newly developed to build on the largest set of reference [email protected] (CH); sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of [email protected] (EAF); taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These [email protected] (NS) methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and †These authors contributed IBD (1635 metagenomes and 817 metatranscriptomes). -
Effect of Co-Inoculation of Bradyrhizobium And
agronomy Article Effect of Co-Inoculation of Bradyrhizobium and Trichoderma on Growth, Development, and Yield of Arachis hypogaea L. (Peanut) Ravi Teja Kumar Reddy Neelipally 1, Ambrose O. Anoruo 1,* and Shad Nelson 2 1 Department of Agriculture, Agribusiness and Environmental Sciences, College of Agriculture, Natural Resources & Human Sciences, Texas A&M University, Kingsville, TX 78363, USA; [email protected] 2 College of Agriculture, Natural Resources & Human Sciences, Texas A&M University, Kingsville, TX 78363, USA; [email protected] * Correspondence: [email protected] Received: 20 August 2020; Accepted: 14 September 2020; Published: 17 September 2020 Abstract: Cultivation of the peanut (Arachis hypogaea L.) on the same land contributes to the accumulation of root exudates, leading to increased soil pathogens and decreased yield. Trichoderma harzianum is a naturally occurring endophytic biocontrol fungus that can enhance plant growth, nutrient uptake, and tolerance to biotic and abiotic stresses. Separately, Bradyrhizobium spp. is a biological nitrogen-fixing (BNF) bacterium favoring nodule formation in peanut roots which promotes nitrogen fixation. The dynamics of the symbiotic association between these two organisms were evaluated in the laboratory and greenhouse conditions. Peanuts were cultivated in pots inoculated with either Bradyrhizobium or Trichoderma or both to evaluate growth, development, and yield. The in vitro study results showed that seeds treated with Trichoderma had better germination and seedling biomass (p = 0.0008) compared to the other treatments. On the other hand, the results of greenhouse studies showed that seeds inoculated with both microbes, and those inoculated with Bradyrhizobium alone had higher dry biomass (p < 0.0001) as well as higher chlorophyll content (p < 0.0001) compared to the other treatments. -
Lantibiotics Produced by Oral Inhabitants As a Trigger for Dysbiosis of Human Intestinal Microbiota
International Journal of Molecular Sciences Article Lantibiotics Produced by Oral Inhabitants as a Trigger for Dysbiosis of Human Intestinal Microbiota Hideo Yonezawa 1,* , Mizuho Motegi 2, Atsushi Oishi 2, Fuhito Hojo 3 , Seiya Higashi 4, Eriko Nozaki 5, Kentaro Oka 4, Motomichi Takahashi 1,4, Takako Osaki 1 and Shigeru Kamiya 1 1 Department of Infectious Diseases, Kyorin University School of Medicine, Tokyo 181-8611, Japan; [email protected] (M.T.); [email protected] (T.O.); [email protected] (S.K.) 2 Division of Oral Restitution, Department of Pediatric Dentistry, Graduate School, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; [email protected] (M.M.); [email protected] (A.O.) 3 Institute of Laboratory Animals, Graduate School of Medicine, Kyorin University School of Medicine, Tokyo 181-8611, Japan; [email protected] 4 Central Research Institute, Miyarisan Pharmaceutical Co. Ltd., Tokyo 114-0016, Japan; [email protected] (S.H.); [email protected] (K.O.) 5 Core Laboratory for Proteomics and Genomics, Kyorin University School of Medicine, Tokyo 181-8611, Japan; [email protected] * Correspondence: [email protected] Abstract: Lantibiotics are a type of bacteriocin produced by Gram-positive bacteria and have a wide spectrum of Gram-positive antimicrobial activity. In this study, we determined that Mutacin I/III and Smb (a dipeptide lantibiotic), which are mainly produced by the widespread cariogenic bacterium Streptococcus mutans, have strong antimicrobial activities against many of the Gram-positive bacteria which constitute the intestinal microbiota. -
A Review of the Source and Function of Microbiota in Breast Milk
68 A Review of the Source and Function of Microbiota in Breast Milk M. Susan LaTuga, MD, MSPH1 Alison Stuebe, MD, MSc2,3 Patrick C. Seed, MD, PhD4 1 Department of Pediatrics, Division of Neonatology, Albert Einstein Address for correspondence M. Susan LaTuga, MD, MSPH, Albert College of Medicine, Bronx, New York Einstein College of Medicine, 1601 Tenbroeck Ave, 2nd floor, Bronx, NY 2 Department of Obstetrics and Gynecology, University of North 10461 (e-mail: mlatuga@montefiore.org). Carolina School of Medicine 3 Department of Maternal and Child Health, Gillings School of Global Public Health, Chapel Hill, North Carolina 4 Department of Pediatrics, Division of Infectious Diseases, Duke University, Durham, North Carolina Semin Reprod Med 2014;32:68–73 Abstract Breast milk contains a rich microbiota composed of viable skin and non-skin bacteria. The extent of the breast milk microbiota diversity has been revealed through new culture-independent studies using microbial DNA signatures. However, the extent to which the breast milk microbiota are transferred from mother to infant and the function of these breast milk microbiota for the infant are only partially understood. Here, we appraise hypotheses regarding the formation of breast milk microbiota, including retrograde infant-to-mother transfer and enteromammary trafficking, and we review current knowledge of mechanisms determining the extent of breast milk microbiota transfer from mother to infant. We highlight known functions of constituents in the breast milk microbiota—to enhance immunity, liberate nutrients, synergize with breast Keywords milk oligosaccharides to enhance intestinal barrier function, and strengthen a functional ► enteromammary gut–brain axis. We also consider the pathophysiology of maternal mastitis with respect trafficking to a dysbiosis or abnormal shift in the breast milk microbiota. -
Populations of Bradyrhizobium Japonicum
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Feb. 1987, p. 315-319 Vol. 53, No. 2 0099-2240/87/020315-05$02.00/0 Copyright © 1987, American Society for Microbiology Long-Term Effects of Metal-Rich Sewage Sludge Application on Soil Populations of Bradyrhizobium japonicum B. K. KINKLE,1 J. S. ANGLE,'* AND H. H. KEYSER2 Department of Agronomy, University of Maryland, College Park, Maryland 20742,1 and Nitrogen Fixation and Soybean Genetics Laboratory, U.S. Department of Agriculture, Agricultural Resear-ch Stationi, Beltsv'ille, Maryland 207052 Received 27 October 1986/Accepted 5 November 1986 The application of sewage sludge to land may increase the concentration of heavy metals in soil. Of considerable concern is the effect of heavy metals on soil microorganisms, especially those involved in the biocycling of elements important to soil productivity. Bradyrhizobiumjaponicum is a soil bacterium involved in symbiotic nitrogen fixation with Glycine max, the common soybean. To examine the effect of metal-rich sludge application on B. japonicum, the MICs for Pb, Cu, Al, Fe, Ni, Zn, Cd, and Hg were determined in minimal media by using laboratory reference strains representing 11 common serogroups of B. japonicum. Marked differences were found among the B. japonicum strains for sensitivity to Cu, Cd, Zn, and Ni. Strain USDA 123 was most sensitive to these metals, whereas strain USDA 122 was most resistant. In field studies, a silt loam soil amended 11 years ago with 0, 56, or 112 Mg of digested sludge per ha was examined for total numbers of B. japonicum by using the most probable number method. Nodule isolates from soybean nodules grown on this soil were serologically typed, and their metal sensitivity was determined. -
Advances in Biochemistry and Biotechnology Bacterial
Advances in Biochemistry and Biotechnology Degrassi G and Carpentieri-Pipolo V. Adv Biochem Biotechnol 5: 1099. Review Article DOI: 10.29011/2574-7258.001099 Bacterial Endophytes Associated to Crops: Novel Practices for Sustainable Agriculture Giuliano Degrassi1*, Valeria Carpentieri-Pipolo2 1Industrial Biotechnology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Parque Tecnológico Miguelete, San Martín, Buenos Aires, República Argentina 2Embrapa Trigo, Rodovia BR-285, Km 294, 99050-970, Passo Fundo, Rio Grande do Sul, Brazil. *Corresponding author: Giuliano Degrassi, Industrial Biotechnology Group, International Centre for Genetic Engineering and Bio- technology (ICGEB), Parque Tecnológico Miguelete, Av. General Paz N° 5445, B1650WAB San Martín, Buenos Aires, República Argentina Citation: Degrassi G and Carpentieri-Pipolo V (2020) Bacterial Endophytes Associated to Crops: Novel Practices for Sustainable Agriculture. Adv Biochem Biotechnol 5: 1099. DOI: 10.29011/2574-7258.001099 Received Date: 16 April, 2020; Accepted Date: 20 May, 2020; Published Date: 25 May, 2020 Abstract For many decades, rhizosphere bacteria have been studied for their potential to promote crop growth and control certain pathogens. Compared to the studies conducted, there are relatively few examples of microbial inoculants based on rhizosphere bacteria that have had commercial success, mainly due to the strong competition present in the rhizosphere. In the last twenty years, studies on endophytes have multiplied, also and above all as a possible alternative to rhizobacteria, for the development of microbial inoculants capable of replacing some agrochemicals and reducing the environmental impact of agronomic management of crops. This minireview summarizes the most important characteristics and qualities of endophytic bacteria and describes the path that can be followed to identify and deepen the knowledge of candidates suitable for the development of microbial inocu- lants.