scholarly journals Description and Genome Analysis of Methylotetracoccus aquaticus sp. nov. , a Novel Tropical Wetland Methanotroph, with the Amended Description of Methylotetracoccus gen. nov.

2020 ◽  
Author(s):  
Monali Rahalkar ◽  
Kumal Khatri ◽  
Jyoti Mohite ◽  
Pranitha Pandit ◽  
Rahul Bahulikar
Keyword(s):  
Single Species ◽  
Morphological Characters ◽  
Culture Collection ◽  
Freshwater Wetland ◽  
Microbial Culture ◽  
Culture Collections ◽  
Genome Data ◽  
Fame Analysis ◽  
Wide Range ◽  
Fame Profile

We enriched and isolated a novel gammproteobacterial methanotroph; strain FWC3, from tropical freshwater wetland, near Nagaon beach, Alibag, India. FWC3 is a coccoid, flesh pink/peach pigmented, non-motile methanotroph and the cells are present in pairs and as tetracocci. The culture can grow on methane (20%) as well as on a wide range of methanol from concentrations (0.02%-5%). Based on the comparison of genome data, FAME analysis, morphological characters and biochemical characters, FWC3 belongs to the tentatively and newly but not validly described genus ‘Methylotetracoccus’ of which only a single species strain was described, Methylotetracoccus oryzae C50C1. The ANI index between FWC3 and C50C1 strains is 94%, and the DDH value is 55.7%, less than the cut-off values 96% and 70%, respectively. The genome size of FWC3 is smaller (3.4 Mbp) compared to that of C50C1 (4.8 Mbp). Additionally, the FAME profile of FWC3 shows differences in cell wall fatty acid profiles compared to Methylotetracoccus oryzae C50C1. Also, there are other differences on the morphological, physiological and genomic levels. We propose FWC3 to be a member of a novel species of the genus Methylotetracoccus, for which the name Methylotetracoccus aquaticus is proposed. Also, an amended description of the genus Methylotetracoccus gen. nov. is given here. FWC3 is available in two international culture collections with the accession numbers: MCC 4198 (Microbial Culture collection, India) and JCM 33786 (Japan Collection of Microorganisms, Japan).

scholarly journals WFCC-MIRCEN: world data centre for microorganisms

2006 ◽  
Vol 27 (1) ◽  
pp. 13
Author(s):  
Hideaki Sugawara
Keyword(s):  
Strategic Plan ◽  
Culture Collection ◽  
Microbial Culture ◽  
Culture Collections ◽  
World Data ◽  
Data Centre ◽  
The 1960S

In the 1960s, microbiology and culture collection experts met several times to develop a strategic plan to foster microbial culture collections. They quickly recognised that statistics on the activities of culture collections worldwide were not available and that there was a need for a ?world directory of collections of cultures of microorganisms? that accumulated information on culture collections. It was obvious also that a world data centre for microorganisms was required to develop and maintain the directory.

scholarly journals In Silico Comparison Shows that the Pan-Genome of a Dairy-Related Bacterial Culture Collection Covers Most Reactions Annotated to Human Microbiomes

2020 ◽  
Vol 8 (7) ◽  
pp. 966 ◽  
Author(s):  
Thomas Roder ◽  
Daniel Wüthrich ◽  
Cornelia Bär ◽  
Zahra Sattari ◽  
Ueli von Ah ◽  
...  
Keyword(s):  
Dietary Patterns ◽  
In Silico ◽  
Bacterial Culture ◽  
In Silico Analysis ◽  
Culture Collection ◽  
Microbial Culture ◽  
Enzymatic Reactions ◽  
Culture Collections ◽  
Pan Genome ◽  
Dairy Research

The diversity of the human microbiome is positively associated with human health. However, this diversity is endangered by Westernized dietary patterns that are characterized by a decreased nutrient variety. Diversity might potentially be improved by promoting dietary patterns rich in microbial strains. Various collections of bacterial cultures resulting from a century of dairy research are readily available worldwide, and could be exploited to contribute towards this end. We have conducted a functional in silico analysis of the metagenome of 24 strains, each representing one of the species in a bacterial culture collection composed of 626 sequenced strains, and compared the pathways potentially covered by this metagenome to the intestinal metagenome of four healthy, although overweight, humans. Remarkably, the pan-genome of the 24 strains covers 89% of the human gut microbiome’s annotated enzymatic reactions. Furthermore, the dairy microbial collection covers biological pathways, such as methylglyoxal degradation, sulfate reduction, γ-aminobutyric (GABA) acid degradation and salicylate degradation, which are differently covered among the four subjects and are involved in a range of cardiometabolic, intestinal, and neurological disorders. We conclude that microbial culture collections derived from dairy research have the genomic potential to complement and restore functional redundancy in human microbiomes.

scholarly journals Evaluating species in Botryosphaeriales

2021 ◽  
Author(s):  
W. Zhang ◽  
J.Z. Groenewald ◽  
L. Lombard ◽  
R.K. Schumacher ◽  
A.J.L. Phillips ◽  
...  
Keyword(s):  
South Africa ◽  
Woody Plants ◽  
Phylogenetic Analyses ◽  
Culture Collection ◽  
Morphological Data ◽  
Culture Collections ◽  
Future Studies ◽  
The Past ◽  
Wide Range ◽  
Solid Foundation

The Botryosphaeriales (Dothideomycetes) includes numerous endophytic, saprobic, and plant pathogenic species associated with a wide range of symptoms, most commonly on woody plants. In a recent phylogenetic treatment of 499 isolates in the culture collection (CBS) of the Westerdijk Institute, we evaluated the families and genera accommodated in this order of important fungi. The present study presents multigene phylogenetic analyses for an additional 230 isolates, using ITS, tef1, tub2, LSU and rpb2 loci, in combination with morphological data. Based on these data, 58 species are reduced to synonymy, and eight novel species are described. They include Diplodia afrocarpi (Afrocarpus, South Africa), Dothiorella diospyricola (Diospyros, South Africa), Lasiodiplodia acaciae (Acacia, Indonesia), Neofusicoccum podocarpi (Podocarpus, South Africa), N. rapaneae (Rapanea, South Africa), Phaeobotryon ulmi (Ulmus, Germany), Saccharata grevilleae (Grevillea, Australia) and S. hakeiphila (Hakea, Australia). The results have clarified the identity of numerous isolates that lacked Latin binomials or had been deposited under incorrect names in the CBS collection in the past. They also provide a solid foundation for more in-depth future studies on taxa in the order. Sequences of the tef1, tub2 and rpb2 genes proved to be the most reliable markers. At the species level, results showed that the most informative genes were inconsistent, but that a combination of four candidate barcodes (ITS, tef1, tub2 and rpb2) provided reliable resolution. Furthermore, given the large number of additional isolates included in this study, and newly generated multigene DNA datasets, several species could also be reduced to synonymy. The study illustrates the value of reassessing the identity of older collections in culture collections utilising modern taxonomic frameworks and methods.

scholarly journals New ECCO model documents for Material Deposit and Transfer Agreements in compliance with the Nagoya Protocol

2020 ◽  
Vol 367 (5) ◽  
Author(s):  
Gerard Verkley ◽  
Giancarlo Perrone ◽  
Mery Piña ◽  
Amber Hartman Scholz ◽  
Jörg Overmann ◽  
...  
Keyword(s):  
Code Of Conduct ◽  
Relevant Information ◽  
Culture Collection ◽  
Benefit Sharing ◽  
Microbial Culture ◽  
Material Transfer ◽  
Access And Benefit Sharing ◽  
Culture Collections ◽  
Material Transfer Agreement ◽  
The Status

ABSTRACT The European Culture Collections’ Organisation presents two new model documents for Material Deposit Agreement (MDA) and Material Transfer Agreement (MTA) designed to enable microbial culture collection leaders to draft appropriate agreement documents for, respectively, deposit and supply of materials from a public collection. These tools provide guidance to collections seeking to draft an MDA and MTA, and are available in open access to be used, modified, and shared. The MDA model consists of a set of core fields typically included in a ‘deposit form’ to collect relevant information to facilitate assessment of the status of the material under access and benefit sharing (ABS) legislation. It also includes a set of exemplary clauses to be included in ‘terms and conditions of use’ for culture collection management and third parties. The MTA model addresses key issues including intellectual property rights, quality, safety, security and traceability. Reference is made to other important tools such as best practices and code of conduct related to ABS issues. Besides public collections, the MDA and MTA model documents can also be useful for individual researchers and microbial laboratories that collect or receive microbial cultures, keep a working collection, and wish to share their material with others.

scholarly journals ITEM - agro-food microbial culture collection: The importance of toxigenic fungi in the fight against mycotoxins

2014 ◽  
pp. 7-14
Author(s):  
Francesca Fanelli ◽  
Antonio Logrieco
Keyword(s):  
Biological Sciences ◽  
Fungal Pathogens ◽  
Industrial Applications ◽  
Culture Collection ◽  
Microbial Culture ◽  
Fungal Culture ◽  
Culture Collections ◽  
Fungal Isolation ◽  
Toxigenic Fungi ◽  
Fungal Biology

Fungal culture collections are important to biologists, microbiologists, epidemiologists and others involved in health and natural sciences. The improvement of techniques and methods for fungal isolation and preservation has contributed to maintain large microbial collections, which represent a rich source of biological sciences research, especially taxonomic, pathological and biodiversity studies as well as industrial applications. The collection centers are responsible for repository reference strains and for the maintenance of these microorganisms. The ITEM Microbial Culture Collection of ISPA (Institute of Sciences and of Food Production) includes more than 10,000 strains belonging to various agro-food microorganisms with phytopathological and toxicological significance. These microorganisms are mainly fungal pathogens belonging to toxigenic genera of Fusarium, Aspergillus, Alternaria, and Penicillium. This collection is a remarkable resource in the fight against mycotoxins: the increasing number of toxigenic fungi included in this collection ensures an original genetic source for biotechnological applications in several fields of research, contributing to knowledge improvement about fungal biology and strategies development for reducing mycotoxin contamination.

scholarly journals The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections

2015 ◽  
Vol 81 (17) ◽  
pp. 5671-5674 ◽  
Author(s):  
Kyria Boundy-Mills ◽  
Matthias Hess ◽  
A. Rick Bennett ◽  
Matthew Ryan ◽  
Seogchan Kang ◽  
...  
Keyword(s):  
United States ◽  
Science Research ◽  
The United States ◽  
Culture Collection ◽  
Microbial Culture ◽  
Culture Collections ◽  
Research Education ◽  
Education Industry ◽  
Microbial Resources ◽  
The University

ABSTRACTThe mission of the United States Culture Collection Network (USCCN;http://usccn.org) is “to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind.” Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections.

scholarly journals Overview of the Genetic Diversity of African Macrotermes (Termitidae: Macrotermitinae) and Implications for Taxonomy, Ecology and Food Science

Insects ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 518
Author(s):  
Bronwyn Egan ◽  
Zwannda Nethavhani ◽  
Barbara van Asch
Keyword(s):  
Negative Impact ◽  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Food Science ◽  
Cryptic Diversity ◽  
African Species ◽  
Genetic Groups ◽  
Wide Range ◽  
Coi Sequences ◽  
High Level

Macrotermes termites play important ecological roles and are consumed by many communities as a delicacy and dietary complement throughout Africa. However, lack of reliable morphological characters has hampered studies of Macrotermes diversity in a wide range of scientific fields including ecology, phylogenetics and food science. In order to place our preliminary assessment of the diversity of Macrotermes in South Africa in context, we analysed a comprehensive dataset of COI sequences for African species including new and publicly available data. Phylogenetic reconstruction and estimates of genetic divergence showed a high level of incongruity between species names and genetic groups, as well as several instances of cryptic diversity. We identified three main clades and 17 genetic groups in the dataset. We propose that this structure be used as a background for future surveys of Macrotermes diversity in Africa, thus mitigating the negative impact of the present taxonomic uncertainties in the genus. The new specimens collected in Limpopo fell into four distinct genetic groups, suggesting that the region harbours remarkable Macrotermes diversity relative to other African regions surveyed in previous studies. This work shows that African Macrotermes have been understudied across the continent, and that the genus contains cryptic diversity undetectable by classic taxonomy. Furthermore, these results may inform future taxonomic revisions in Macrotermes, thus contributing to advances in termitology.

scholarly journals Sequence data from isolated lichen-associated melanized fungi enhance delimitation of two new lineages within Chaetothyriomycetidae

2021 ◽  
Vol 20 (7) ◽  
pp. 911-927
Author(s):  
Lucia Muggia ◽  
Yu Quan ◽  
Cécile Gueidan ◽  
Abdullah M. S. Al-Hatmi ◽  
Martin Grube ◽  
...  
Keyword(s):  
Sequence Data ◽  
Single Species ◽  
Sister Group ◽  
Asexual Propagation ◽  
Dna Sequence Data ◽  
Wide Range ◽  
The Family ◽  
Rock Inhabiting Fungi ◽  
Stable Habitat

AbstractLichen thalli provide a long-lived and stable habitat for colonization by a wide range of microorganisms. Increased interest in these lichen-associated microbial communities has revealed an impressive diversity of fungi, including several novel lineages which still await formal taxonomic recognition. Among these, members of the Eurotiomycetes and Dothideomycetes usually occur asymptomatically in the lichen thalli, even if they share ancestry with fungi that may be parasitic on their host. Mycelia of the isolates are characterized by melanized cell walls and the fungi display exclusively asexual propagation. Their taxonomic placement requires, therefore, the use of DNA sequence data. Here, we consider recently published sequence data from lichen-associated fungi and characterize and formally describe two new, individually monophyletic lineages at family, genus, and species levels. The Pleostigmataceae fam. nov. and Melanina gen. nov. both comprise rock-inhabiting fungi that associate with epilithic, crust-forming lichens in subalpine habitats. The phylogenetic placement and the monophyly of Pleostigmataceae lack statistical support, but the family was resolved as sister to the order Verrucariales. This family comprises the species Pleostigma alpinum sp. nov., P. frigidum sp. nov., P. jungermannicola, and P. lichenophilum sp. nov. The placement of the genus Melanina is supported as a lineage within the Chaetothyriales. To date, this genus comprises the single species M. gunde-cimermaniae sp. nov. and forms a sister group to a large lineage including Herpotrichiellaceae, Chaetothyriaceae, Cyphellophoraceae, and Trichomeriaceae. The new phylogenetic analysis of the subclass Chaetothyiomycetidae provides new insight into genus and family level delimitation and classification of this ecologically diverse group of fungi.

scholarly journals COLMENA: A Culture Collection of Native Microorganisms for Harnessing the Agro-Biotechnological Potential in Soils and Contributing to Food Security

Diversity ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 337
Author(s):  
Sergio de los Santos-Villalobos ◽  
Alondra María Díaz-Rodríguez ◽  
María Fernanda Ávila-Mascareño ◽  
Andrea Denisse Martínez-Vidales ◽  
Fannie Isela Parra-Cota
Keyword(s):  
Food Security ◽  
Plant Growth ◽  
Field Trials ◽  
Culture Collection ◽  
Microbial Culture ◽  
Biotechnological Potential ◽  
Global Food Security ◽  
Beneficial Effects ◽  
Plant Growth Promoting

COLMENA is a microbial culture collection dedicated to the characterization, classification, preservation, and transferal of native microorganisms isolated from various agro-systems and other ecosystems in Mexico. This collection aims to protect microbial diversity, reducing soil degradation, but also exploiting its agro-biotechnological potential. So far, COLMENA has isolated and cryopreserved soil microorganisms from different crops in two major agricultural regions in Mexico, the Yaqui Valley, Sonora, and the Fuerte Valley, Sinaloa. COLMENA has specialized in the identification and characterization of microbial strains with metabolic capacities related to the promotion of plant growth and the biocontrol of phytopathogens. Thus, COLMENA has identified several promising plant growth-promoting microbial (PGPM) strains due to their metabolic and genetic potentials and their beneficial effects in vivo and field trials. These findings demonstrate the biotechnological potential of these strains for their future use in profitable agricultural alternatives focused on enhancing global food security. To share the knowledge and results of the COLMENA team’s scientific research, a virtual platform was created, where the database of the studied and preserved microorganisms is available to professionals, researchers, agricultural workers, and anyone who is interested.

scholarly journals Dissecting host-associated communities with DNA barcodes

2016 ◽  
Vol 371 (1702) ◽  
pp. 20150328 ◽  
Author(s):  
Christopher C. M. Baker ◽  
Leonora S. Bittleston ◽  
Jon G. Sanders ◽  
Naomi E. Pierce
Keyword(s):  
Species Interactions ◽  
Morphological Characters ◽  
South American ◽  
Dna Barcodes ◽  
Substantial Variation ◽  
East African ◽  
Pitcher Plant ◽  
Genome Data ◽  
Symbiotic Interactions ◽  
Database Connectivity

DNA barcoding and metabarcoding methods have been invaluable in the study of interactions between host organisms and their symbiotic communities. Barcodes can help identify individual symbionts that are difficult to distinguish using morphological characters, and provide a way to classify undescribed species. Entire symbiont communities can be characterized rapidly using barcoding and especially metabarcoding methods, which is often crucial for isolating ecological signal from the substantial variation among individual hosts. Furthermore, barcodes allow the evolutionary histories of symbionts and their hosts to be assessed simultaneously and in reference to one another. Here, we describe three projects illustrating the utility of barcodes for studying symbiotic interactions: first, we consider communities of arthropods found in the ant-occupied domatia of the East African ant-plant Vachellia ( Acacia ) drepanolobium ; second, we examine communities of arthropod and protozoan inquilines in three species of Nepenthes pitcher plant in South East Asia; third, we investigate communities of gut bacteria of South American ants in the genus Cephalotes . Advances in sequencing and computation, and greater database connectivity, will continue to expand the utility of barcoding methods for the study of species interactions, especially if barcoding can be approached flexibly by making use of alternative genetic loci, metagenomes and whole-genome data. This article is part of the themed issue ‘From DNA barcodes to biomes’.

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