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1. Outline of Fungi and fungus-like taxa

Author

Wijayawardene, NN, Hyde, KD, Al-Ani, LKT, Tedersoo, L, Haelewaters, D, Rajeshkumar, KC, Zhao, RL, Aptroot, A, Leontyev, DV, Saxena, RK, Tokarev, YS, Dai, DQ, Letcher, PM, Stephenson, SL, Ertz, D, Lumbsch, HT, Kukwa, M, Issi, IV, Madrid, H, Phillips, AJL, Selbmann, L, Pfliegler, WP, Horváth, E, Bensch, K, Kirk, PM, Kolaríková, K, Raja, HA, Radek, R, Papp, V, Dima, B, Ma, J, Malosso, E, Takamatsu, S, Rambold, G, Gannibal, PB, Triebel, D, Gautam, AK, Avasthi, S, Suetrong, S, Timdal, E, Fryar, SC, Delgado, G, Réblová, M, Doilom, M, Dolatabadi, S, Pawlowska, JZ, Humber, RA, Kodsueb, R, Sánchez-Castro, I, Goto, BT, Silva, DKA, de Souza, FA, Oehl, F, da Silva, GA, Silva, IR, Blaszkowski, J, Jobim, K, Maia, LC, Barbosa, FR, Fiuza, PO, Divakar, PK, Shenoy, BD, Castañeda-Ruiz, RF, Somrithipol, S, Lateef, AA, Karunarathna, SC, Tibpromma, S, Mortimer, PE, Wanasinghe, DN, Phookamsak, R, Xu, J, Wang, Y, Tian, F, Alvarado, P, Li, DW, Kušan, I, Matocec, N, Mešic, A, Tkalcec, Z, Maharachchikumbura, SSN, Papizadeh, M, Heredia, G, Wartchow, F, Bakhshi, M, Boehm, E, Youssef, N, Hustad, VP, Lawrey, JD, Santiago, ALCMA, Bezerra, JDP, Souza-Motta, CM, Firmino, AL, Tian, Q, Houbraken, J, Hongsanan, S, Tanaka, K, Dissanayake, AJ, Monteiro, JS, Grossart, HP, Suija, A, Wijayawardene, NN, Hyde, KD, Al-Ani, LKT, Tedersoo, L, Haelewaters, D, Rajeshkumar, KC, Zhao, RL, Aptroot, A, Leontyev, DV, Saxena, RK, Tokarev, YS, Dai, DQ, Letcher, PM, Stephenson, SL, Ertz, D, Lumbsch, HT, Kukwa, M, Issi, IV, Madrid, H, Phillips, AJL, Selbmann, L, Pfliegler, WP, Horváth, E, Bensch, K, Kirk, PM, Kolaríková, K, Raja, HA, Radek, R, Papp, V, Dima, B, Ma, J, Malosso, E, Takamatsu, S, Rambold, G, Gannibal, PB, Triebel, D, Gautam, AK, Avasthi, S, Suetrong, S, Timdal, E, Fryar, SC, Delgado, G, Réblová, M, Doilom, M, Dolatabadi, S, Pawlowska, JZ, Humber, RA, Kodsueb, R, Sánchez-Castro, I, Goto, BT, Silva, DKA, de Souza, FA, Oehl, F, da Silva, GA, Silva, IR, Blaszkowski, J, Jobim, K, Maia, LC, Barbosa, FR, Fiuza, PO, Divakar, PK, Shenoy, BD, Castañeda-Ruiz, RF, Somrithipol, S, Lateef, AA, Karunarathna, SC, Tibpromma, S, Mortimer, PE, Wanasinghe, DN, Phookamsak, R, Xu, J, Wang, Y, Tian, F, Alvarado, P, Li, DW, Kušan, I, Matocec, N, Mešic, A, Tkalcec, Z, Maharachchikumbura, SSN, Papizadeh, M, Heredia, G, Wartchow, F, Bakhshi, M, Boehm, E, Youssef, N, Hustad, VP, Lawrey, JD, Santiago, ALCMA, Bezerra, JDP, Souza-Motta, CM, Firmino, AL, Tian, Q, Houbraken, J, Hongsanan, S, Tanaka, K, Dissanayake, AJ, Monteiro, JS, Grossart, HP, and Suija, A

Abstract

This article provides an outline of the classification of the kingdom Fungi (including fossil fungi. i.e. dispersed spores, mycelia, sporophores, mycorrhizas). We treat 19 phyla of fungi. These are Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. The placement of all fungal genera is provided at the class-, order- and family-level. The described number of species per genus is also given. Notes are provided of taxa for which recent changes or disagreements have been presented. Fungus-like taxa that were traditionally treated as fungi are also incorporated in this outline (i.e. Eumycetozoa, Dictyosteliomycetes, Ceratiomyxomycetes and Myxomycetes). Four new taxa are introduced: Amblyosporida ord. nov. Neopereziida ord. nov. and Ovavesiculida ord. nov. in Rozellomycota, and Protosporangiaceae fam. nov. in Dictyosteliomycetes. Two different classifications (in outline section and in discussion) are provided for Glomeromycota and Leotiomycetes based on recent studies. The phylogenetic reconstruction of a four-gene dataset (18S and 28S rRNA, RPB1, RPB2) of 433 taxa is presented, including all currently described orders of fungi.

Published
2020

2. Outline of Fungi and fungus-like taxa

Author

Wijayawardene, N. N., Hyde, K. D., Al-Ani, L. K. T., Tedersoo, L., Haelewaters, D., Rajeshkumar, K. C., Zhao, R. L., Aptroot, A., Leontyev, D., V, Saxena, R. K., Tokarev, Y. S., Dai, D. Q., Letcher, P. M., Stephenson, S. L., Ertz, D., Lumbsch, H. T., Kukwa, M., Issi, I., V, Madrid, H., Phillips, A. J. L., Selbmann, L., Pfliegler, W. P., Horvath, E., Bensch, K., Kirk, P. M., Kolarikova, K., Raja, H. A., Radek, R., Papp, V, Dima, B., Ma, J., Malosso, E., Takamatsu, S., Rambold, G., Gannibal, P. B., Triebel, D., Gautam, A. K., Avasthi, S., Suetrong, S., Timdal, E., Fryar, S. C., Delgado, G., Reblova, M., Doilom, M., Dolatabadi, S., Pawlowska, J. Z., Humber, R. A., Kodsueb, R., Sanchez-Castro, I, Goto, B. T., Silva, D. K. A., de Souza, F. A., Oehl, F. R., da Silva, G. A., Silva, I. R., Blaszkowski, J., Jobim, K., Maia, L. C., Barbosa, F. R., Fiuza, P. O., Divakar, P. K., Shenoy, B. D., Castaneda-Ruiz, R. F., Somrithipol, S., Lateef, A. A., Karunarathna, S. C., Tibpromma, S., Mortimer, P. E., Wanasinghe, D. N., Phookamsak, R., Xu, J., Wang, Y., Tian, F., Alvarado, P., Li, D. W., Kusan, I, Matocec, N., Mesic, A., Tkalcec, Z., Maharachchikumbura, S. S. N., Papizadeh, M., Heredia, G., Wartchow, F., Bakhshi, M., Boehm, E., Youssef, N., Hustad, V. P., Lawrey, J. D., Santiago, A. L. C. M. A., Bezerra, J. D. P., Souza-Motta, C. M., Firmino, A. L., Tian, Q., Houbraken, J., Hongsanan, S., Tanaka, K., Dissanayake, A. J., Monteiro, J. S., Grossart, H. P., Suija, A., Weerakoon, G., Etayo, J., Tsurykau, A., Vazquez, V., Mungai, P., Damm, U., Li, Q. R., Zhang, H., Boonmee, S., Lu, Y. Z., Becerra, A. G., Kendrick, B., Brearley, F. Q., Motiejunaite, J., Sharma, B., Khare, R., Gaikwad, S., Wijesundara, D. S. A., Tang, L. Z., He, M. Q., Flakus, A., Rodriguez-Flakus, P., Zhurbenko, M. P., McKenzie, E. H. C., Stadler, M., Bhat, D. J., Liu, J. K., Raza, M., Jeewon, R., Nassonova, E. S., Prieto, M., Jayalal, R. G. U., Erdogdu, M., Yurkov, A., Schnittler, M., Shchepin, O. N., Novozhilov, Y. K., Silva-Filho, A. G. S., Gentekaki, E., Liu, P., Cavender, J. C., Kang, Y., Mohammad, S., Zhang, L. F., Xu, R. F., Li, Y. M., Dayarathne, M. C., Ekanayaka, A. H., Wen, T. C., Deng, C. Y., Pereira, O. L., Navathe, S., Hawksworth, D. L., Fan, X. L., Dissanayake, L. S., Kuhnert, E., Thines, M., Wijayawardene, N. N., Hyde, K. D., Al-Ani, L. K. T., Tedersoo, L., Haelewaters, D., Rajeshkumar, K. C., Zhao, R. L., Aptroot, A., Leontyev, D., V, Saxena, R. K., Tokarev, Y. S., Dai, D. Q., Letcher, P. M., Stephenson, S. L., Ertz, D., Lumbsch, H. T., Kukwa, M., Issi, I., V, Madrid, H., Phillips, A. J. L., Selbmann, L., Pfliegler, W. P., Horvath, E., Bensch, K., Kirk, P. M., Kolarikova, K., Raja, H. A., Radek, R., Papp, V, Dima, B., Ma, J., Malosso, E., Takamatsu, S., Rambold, G., Gannibal, P. B., Triebel, D., Gautam, A. K., Avasthi, S., Suetrong, S., Timdal, E., Fryar, S. C., Delgado, G., Reblova, M., Doilom, M., Dolatabadi, S., Pawlowska, J. Z., Humber, R. A., Kodsueb, R., Sanchez-Castro, I, Goto, B. T., Silva, D. K. A., de Souza, F. A., Oehl, F. R., da Silva, G. A., Silva, I. R., Blaszkowski, J., Jobim, K., Maia, L. C., Barbosa, F. R., Fiuza, P. O., Divakar, P. K., Shenoy, B. D., Castaneda-Ruiz, R. F., Somrithipol, S., Lateef, A. A., Karunarathna, S. C., Tibpromma, S., Mortimer, P. E., Wanasinghe, D. N., Phookamsak, R., Xu, J., Wang, Y., Tian, F., Alvarado, P., Li, D. W., Kusan, I, Matocec, N., Mesic, A., Tkalcec, Z., Maharachchikumbura, S. S. N., Papizadeh, M., Heredia, G., Wartchow, F., Bakhshi, M., Boehm, E., Youssef, N., Hustad, V. P., Lawrey, J. D., Santiago, A. L. C. M. A., Bezerra, J. D. P., Souza-Motta, C. M., Firmino, A. L., Tian, Q., Houbraken, J., Hongsanan, S., Tanaka, K., Dissanayake, A. J., Monteiro, J. S., Grossart, H. P., Suija, A., Weerakoon, G., Etayo, J., Tsurykau, A., Vazquez, V., Mungai, P., Damm, U., Li, Q. R., Zhang, H., Boonmee, S., Lu, Y. Z., Becerra, A. G., Kendrick, B., Brearley, F. Q., Motiejunaite, J., Sharma, B., Khare, R., Gaikwad, S., Wijesundara, D. S. A., Tang, L. Z., He, M. Q., Flakus, A., Rodriguez-Flakus, P., Zhurbenko, M. P., McKenzie, E. H. C., Stadler, M., Bhat, D. J., Liu, J. K., Raza, M., Jeewon, R., Nassonova, E. S., Prieto, M., Jayalal, R. G. U., Erdogdu, M., Yurkov, A., Schnittler, M., Shchepin, O. N., Novozhilov, Y. K., Silva-Filho, A. G. S., Gentekaki, E., Liu, P., Cavender, J. C., Kang, Y., Mohammad, S., Zhang, L. F., Xu, R. F., Li, Y. M., Dayarathne, M. C., Ekanayaka, A. H., Wen, T. C., Deng, C. Y., Pereira, O. L., Navathe, S., Hawksworth, D. L., Fan, X. L., Dissanayake, L. S., Kuhnert, E., and Thines, M.

Published
2020

3. Notes for genera: Ascomycota

Author

Wijayawardene, Nalin N., Hyde, K.D., Rajeshkumar, Kunhiraman C., Hawksworth, D.L., Madrid, H., Kirk, P.M., Braun, U., Singh, R.V., Crous, P. W., Kukwa, M., Lücking, R., Kurtzman, Cletus P., Yurkov, A., Haelewaters, D., Aptroot, A., Thorsten Lumbsch, H., Timdal, E., Ertz, D., Etayo, Javier, Phillips, Alan J. L., Groenewald, J. Z., Papizadeh, M., Selbmann, Laura, Dayarathne, Monika C., Weerakoon, G., Gareth Jones, E.B., Suetrong, S., Tian, Q., Castañeda-Ruiz, R.F., Bahkali, A.H., Pang, K.L., Tanaka, K., Dai, Dong Qin, Sakayaroj, J., Hujslová, M., Lombard, L., Shenoy, B.D., Suija, A., Maharachchikumbura, Sajeewa S. N., Thambugala, K.M., Wanasinghe, D.N., Sharma, B.O., Gaikwad, S., Pandit, G., Zucconi, L., Onofri, Silvano, Egidi, E., Raja, H.A., Kodsueb, R., Pérez-Ortega, Sergio, Prieto, M., Quijada, L., Wijayawardene, Nalin N., Hyde, K.D., Rajeshkumar, Kunhiraman C., Hawksworth, D.L., Madrid, H., Kirk, P.M., Braun, U., Singh, R.V., Crous, P. W., Kukwa, M., Lücking, R., Kurtzman, Cletus P., Yurkov, A., Haelewaters, D., Aptroot, A., Thorsten Lumbsch, H., Timdal, E., Ertz, D., Etayo, Javier, Phillips, Alan J. L., Groenewald, J. Z., Papizadeh, M., Selbmann, Laura, Dayarathne, Monika C., Weerakoon, G., Gareth Jones, E.B., Suetrong, S., Tian, Q., Castañeda-Ruiz, R.F., Bahkali, A.H., Pang, K.L., Tanaka, K., Dai, Dong Qin, Sakayaroj, J., Hujslová, M., Lombard, L., Shenoy, B.D., Suija, A., Maharachchikumbura, Sajeewa S. N., Thambugala, K.M., Wanasinghe, D.N., Sharma, B.O., Gaikwad, S., Pandit, G., Zucconi, L., Onofri, Silvano, Egidi, E., Raja, H.A., Kodsueb, R., Pérez-Ortega, Sergio, Prieto, M., and Quijada, L.

Abstract

Knowledge of the relationships and thus the classification of fungi, has developed rapidly with increasingly widespread use of molecular techniques, over the past 10-15 years, and continues to accelerate. Several genera have been found to be polyphyletic, and their generic concepts have subsequently been emended. New names have thus been introduced for species which are phylogenetically distinct from the type species of particular genera. The ending of the separate naming of morphs of the same species in 2011, has also caused changes in fungal generic names. In order to facilitate access to all important changes, it was desirable to compile these in a single document. The present article provides a list of generic names of Ascomycota (approximately 6500 accepted names published to the end of 2016), including those which are lichen-forming. Notes and summaries of the changes since the last edition of ‘Ainsworth & Bisby’s Dictionary of the Fungi’ in 2008 are provided. The notes include the number of accepted species, classification, type species (with location of the type material), culture availability, life-styles, distribution, and selected publications that have appeared since 2008. This work is intended to provide the foundation for updating the ascomycete component of the “Without prejudice list of generic names of Fungi” published in 2013, which will be developed into a list of protected generic names. This will be subjected to the XIXth International Botanical Congress in Shenzhen in July 2017 agreeing to a modification in the rules relating to protected lists, and scrutiny by procedures determined by the Nomenclature Committee for Fungi (NCF). The previously invalidly published generic names Barriopsis, Collophora (as Collophorina), Cryomyces, Dematiopleospora, Heterospora (as Heterosporicola), Lithophila, Palmomyces (as Palmaria) and Saxomyces are validated, as are two previously invalid family names, Bartaliniaceae and Wiesneriomycetaceae. Four species of L

Published
2017

4. Fungal Planet description sheets: 281–319

Author

Crous, P.W., Wingfield, M.J., Schumacher, R.K., Summerell, B.A., Giraldo, A., Gené, J., Guarro, J., Wanasinghe, D.N., Hyde, K.D., Camporesi, E., Gareth Jones, E.B., Thambugala, K.M., Malysheva, E.F., Malysheva, V.F., Acharya, K., Álvarez, J., Alvarado, P., Assefa, A., Barnes, C.W., Bartlett, J.S., Blanchette, R.A., Burgess, T.I., Carlavilla, J.R., Coetzee, M.P.A., Damm, U., Decock, C.A., Breeÿen, A. den, Vries, B. de, Dutta, A.K., Holdom, D.G., Rooney-Latham, S., Manjón, J.L., Marincowitz, S., Mirabolfathy, M., Moreno, G., Nakashima, C., Papizadeh, M., Shahzadeh Fazeli, S.A., Amoozegar, M.A., Romberg, M.K., Shivas, R.G., Stalpers, J.A., Stielow, B., Stukely, M.J.C., Swart, W.J., Tan, Y.P., Bank, M. van der, Wood, A.R., Zhang, Y., Groenewald, J.Z., Crous, P.W., Wingfield, M.J., Schumacher, R.K., Summerell, B.A., Giraldo, A., Gené, J., Guarro, J., Wanasinghe, D.N., Hyde, K.D., Camporesi, E., Gareth Jones, E.B., Thambugala, K.M., Malysheva, E.F., Malysheva, V.F., Acharya, K., Álvarez, J., Alvarado, P., Assefa, A., Barnes, C.W., Bartlett, J.S., Blanchette, R.A., Burgess, T.I., Carlavilla, J.R., Coetzee, M.P.A., Damm, U., Decock, C.A., Breeÿen, A. den, Vries, B. de, Dutta, A.K., Holdom, D.G., Rooney-Latham, S., Manjón, J.L., Marincowitz, S., Mirabolfathy, M., Moreno, G., Nakashima, C., Papizadeh, M., Shahzadeh Fazeli, S.A., Amoozegar, M.A., Romberg, M.K., Shivas, R.G., Stalpers, J.A., Stielow, B., Stukely, M.J.C., Swart, W.J., Tan, Y.P., Bank, M. van der, Wood, A.R., Zhang, Y., and Groenewald, J.Z.

Abstract

Novel species of fungi described in the present study include the following from South Africa: Alanphillipsia aloeicola from Aloe sp., Arxiella dolichandrae from Dolichandra unguiscati, Ganoderma austroafricanum from Jacaranda mimosifolia, Phacidiella podocarpi and Phaeosphaeria podocarpi from Podocarpus latifolius, Phyllosticta mimusopisicola from Mimusops zeyheri and Sphaerulina pelargonii from Pelargonium sp. Furthermore, Barssia maroccana is described from Cedrus atlantica (Morocco), Codinaea pini from Pinus patula (Uganda), Crucellisporiopsis marquesiae from Marquesia acuminata (Zambia), Dinemasporium ipomoeae from Ipomoea pes-caprae (Vietnam), Diaporthe phragmitis from Phragmites australis (China), Marasmius vladimirii from leaf litter (India), Melanconium hedericola from Hedera helix (Spain), Pluteus albotomentosus and Pluteus extremiorientalis from a mixed forest (Russia), Rachicladosporium eucalypti from Eucalyptus globulus (Ethiopia), Sistotrema epiphyllum from dead leaves of Fagus sylvatica in a forest (The Netherlands), Stagonospora chrysopyla from Scirpus microcarpus (USA) and Trichomerium dioscoreae from Dioscorea sp. (Japan). Novel species from Australia include: Corynespora endiandrae from Endiandra introrsa, Gonatophragmium triuniae from Triunia you

Published
2014

5. Fungal Planet description sheets: 281–319

Author

Crous, P.W. (Pedro Willem), Wingfield, M.J., Schumacher, R.K., Summerell, B.A., Giraldo, A., Gené, J., Guarro, J., Wanasinghe, D.N., Hyde, K.D., Camporesi, E., Gareth Jones, E.B., Thambugala, K.M., Malysheva, E.F., Malysheva, V.F., Acharya, K., Álvarez, J., Alvarado, P., Assefa, A., Barnes, C.W., Bartlett, J.S., Blanchette, R.A., Burgess, T.I., Carlavilla, J.R., Coetzee, M.P.A., Damm, U., Decock, C.A., Breeÿen, A. den, Vries, B. de, Dutta, A.K., Holdom, D.G., Rooney-Latham, S., Manjón, J.L., Marincowitz, S., Mirabolfathy, M., Moreno, G., Nakashima, C., Papizadeh, M., Shahzadeh Fazeli, S.A., Amoozegar, M.A., Romberg, M.K., Shivas, R.G., Stalpers, J.A., Stielow, B., Stukely, M.J.C., Swart, W.J., Tan, Y.P., Bank, M. van der, Wood, A.R., Zhang, Y., Groenewald, J.Z., Crous, P.W. (Pedro Willem), Wingfield, M.J., Schumacher, R.K., Summerell, B.A., Giraldo, A., Gené, J., Guarro, J., Wanasinghe, D.N., Hyde, K.D., Camporesi, E., Gareth Jones, E.B., Thambugala, K.M., Malysheva, E.F., Malysheva, V.F., Acharya, K., Álvarez, J., Alvarado, P., Assefa, A., Barnes, C.W., Bartlett, J.S., Blanchette, R.A., Burgess, T.I., Carlavilla, J.R., Coetzee, M.P.A., Damm, U., Decock, C.A., Breeÿen, A. den, Vries, B. de, Dutta, A.K., Holdom, D.G., Rooney-Latham, S., Manjón, J.L., Marincowitz, S., Mirabolfathy, M., Moreno, G., Nakashima, C., Papizadeh, M., Shahzadeh Fazeli, S.A., Amoozegar, M.A., Romberg, M.K., Shivas, R.G., Stalpers, J.A., Stielow, B., Stukely, M.J.C., Swart, W.J., Tan, Y.P., Bank, M. van der, Wood, A.R., Zhang, Y., and Groenewald, J.Z.

Abstract

Novel species of fungi described in the present study include the following from South Africa: Alanphillipsia aloeicola from Aloe sp., Arxiella dolichandrae from Dolichandra unguiscati, Ganoderma austroafricanum from Jacaranda mimosifolia, Phacidiella podocarpi and Phaeosphaeria podocarpi from Podocarpus latifolius, Phyllosticta mimusopisicola from Mimusops zeyheri and Sphaerulina pelargonii from Pelargonium sp. Furthermore, Barssia maroccana is described from Cedrus atlantica (Morocco), Codinaea pini from Pinus patula (Uganda), Crucellisporiopsis marquesiae from Marquesia acuminata (Zambia), Dinemasporium ipomoeae from Ipomoea pes-caprae (Vietnam), Diaporthe phragmitis from Phragmites australis (China), Marasmius vladimirii from leaf litter (India), Melanconium hedericola from Hedera helix (Spain), Pluteus albotomentosus and Pluteus extremiorientalis from a mixed forest (Russia), Rachicladosporium eucalypti from Eucalyptus globulus (Ethiopia), Sistotrema epiphyllum from dead leaves of Fagus sylvatica in a forest (The Netherlands), Stagonospora chrysopyla from Scirpus microcarpus (USA) and Trichomerium dioscoreae from Dioscorea sp. (Japan). Novel species from Australia include: Corynespora endiandrae from Endiandra introrsa, Gonatophragmium triuniae from Triunia youngiana, Penicillium coccotrypicola from Archontophoenix cunninghamiana and Phytophthora moyootj from soil. Novelties from Iran include Neocamarosporium chichastianum from soil and Seimatosporium pistaciae from Pistacia vera. Xenosonderhenia eucalypti and Zasmidium eucalyptigenum are newly described from Eucalyptus urophylla in Indonesia. Diaporthe acaciarum and Roussoella acacia are newly described from Acacia tortilis in Tanzania. New species from Italy include Comoclathris spartii from Spartium junceum and Phoma tamaricicola from Tamarix gallica. Novel genera include (Ascomycetes): Acremoniopsis from forest soil and Collarina from water sediments (Spain), Phellinocrescentia from a Phellinus sp. (French

Published
2014

6. Fungal Planet description sheets: 281–319

Author

Crous, P.W., primary, Wingfield, M.J., additional, Schumacher, R.K., additional, Summerell, B.A., additional, Giraldo, A., additional, Gené, J., additional, Guarro, J., additional, Wanasinghe, D.N., additional, Hyde, K.D., additional, Camporesi, E., additional, Garethjones, E.B., additional, Thambugala, K.M., additional, Malysheva, E.F., additional, Malysheva, V.F., additional, Acharya, K., additional, Álvarez, J., additional, Alvarado, P., additional, Assefa, A., additional, Barnes, C.W., additional, Bartlett, J.S., additional, Blanchette, R.A., additional, Burgess, T.I., additional, Carlavilla, J.R., additional, Coetzee, M.P.A., additional, Damm, U., additional, Decock, C.A., additional, Denbreeÿen, A., additional, Devries, B., additional, Dutta, A.K., additional, Holdom, D.G., additional, Rooney-Latham, S., additional, Manjón, J.L., additional, Marincowitz, S., additional, Mirabolfathy, M., additional, Moreno, G., additional, Nakashima, C., additional, Papizadeh, M., additional, Shahzadehfazeli, S.A., additional, Amoozegar, M.A., additional, Romberg, M.K., additional, Shivas, R.G., additional, Stalpers, J.A., additional, Stielow, B., additional, Stukely, M.J.C., additional, Swart, W.J., additional, Tan, Y.P., additional, Vanderbank, M., additional, Wood, A.R., additional, Zhang, Y., additional, and Groenewald, J.Z., additional

Published
2014
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7. Development of Inactivated FAKHRAVAC ® Vaccine against SARS-CoV-2 Virus: Preclinical Study in Animal Models.

Author

Ghasemi S, Naderi Saffar K, Ebrahimi F, Khatami P, Monazah A, Alizadeh GA, Ettehadi HA, Rad I, Nojehdehi S, Kehtari M, Kouhkan F, Barjasteh H, Moradi S, Ghorbani MH, Khodaie A, Papizadeh M, Najafi R, Naghneh E, Sadeghi D, and Karimi Rahjerdi A

Abstract

The recent viral infection disease pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in a global public health crisis. Iran, as one of the countries that reported over five million infected cases by September 2021, has been concerned with the urgent development of effective vaccines against SARS-CoV-2. In this paper, we report the results of a study on potency and safety of an inactivated SARS-CoV-2 vaccine candidate (FAKHRAVAC) in a preclinical study so as to confirm its potential for further clinical evaluation. Here, we developed a pilot-scale production of FAKHRAVAC, a purified inactivated SARS-CoV-2 virus vaccine candidate that induces neutralizing antibodies in Balb/c mice, guinea pigs, rabbits, and non-human primates (Rhesus macaques-RM). After obtaining ethical code of IR.IUMS.REC.1399.566, immunizations of animals were conducted by using either of three different vaccine dilutions; High (H): 10 μg/dose, Medium (M): 5 μg/dose, and Low (L): 1 μg/dose, respectively. In the process of screening for viral seeds, viral strains that resulted in the most severe clinical manifestation in patients have been isolated for vaccine development. The viral seed produced the optimal immunity against SARS-CoV-2 virus, which suggests a possible broader neutralizing ability against SARS-CoV-2 strains. The seroconversion rate at the H-, M-, and L-dose groups of all tested animals reached 100% by 28 days after immunization. These data support the eligibility of FAKHRAVAC vaccine candidate for further evaluation in a clinical trial.

Published
2021
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8. Screening for probiotic characters in lactobacilli isolated from chickens revealed the intra-species diversity of Lactobacillus brevis .

Author

Noohi N, Papizadeh M, Rohani M, Talebi M, and Pourshafie MR

Abstract

Considering the importance of the poultry industry and the increasing interest in alternative growth promoters, probiotics are considered as a potential candidate for use in the poultry industry. In this study, Lactobacillus species were isolated from 21 rectal swabs of 11 healthy 6-day-old and 10 healthy 21-day-old chickens and their fecal and feed samples. The isolates were characterized and their probiotic characteristics, including resistance to gastric acid and bile salts, biofilm formation and adherence to epithelium or mucus, amylase and protease activity and production of inhibitory compounds, were assessed. From 31 acid and bile resistant lactobacilli, only 2 Lactobacillus brevis and 1 Lactobacillus reuteri strains showed significant probiotic properties. These isolates indicated detectable attachment to Caco-2 cells and significant antibacterial activities against Gram-positive and Gram-negative pathogens . Additionally, phenotypic and genotypic diversity of lactobacilli isolates were studied by Phene Plate (PhP) system (PhP-LB) and random amplified polymorphic DNA (RAPD)-PCR, respectively. PhP-LB results of 24 L. brevis isolates showed a high phenotypic variation among the isolates. In comparison, results of RAPD-PCR highlighted a low diversity. Therefore, it seems that combination of the 2 techniques (PhP and RAPD-PCR) could result in a significant discriminatory power than each of them used alone., Competing Interests: We declare that we have no financial or personal relationships with other people or organizations that might inappropriately influence our work, and there is no professional or other personal interest of any nature or kind in any product, service and/or company that could be construed as influencing the content of this paper., (© 2021 Chinese Association of Animal Science and Veterinary Medicine. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co. Ltd.)

Published
2021
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9. Using Various Approaches of Design of Experiments for High Cell Density Production of the Functionally Probiotic Lactobacillus plantarum Strain RPR42 in a Cane Molasses-based Medium.

Author

Papizadeh M, Rohani M, Nahrevanian H, Hosseini SN, Shojaosadati SA, and Pourshafie MR

Subjects
Biomass, Fermentation, Culture Media chemistry, Industrial Microbiology methods, Lactobacillus plantarum growth & development, Molasses, Probiotics
Abstract

Considering the economic importance of the probiotics, industrial production of their biomass became important. Cane molasses, as an industrial byproduct, was used in this study to design a medium for biomass overproduction of a functionally probiotic strain, designated as Lactobacillus plantarum strain RPR42. The results showed that strain RPR42 can be best grown anaerobically in 22.5% cane molasses solution. Also, the findings of the single variable at a time experiments and either factorial design indicated that the optimal growth of strain RPR42 can be observed when beef extract, casein hydrolysate, and yeast extract were added into the medium. The central composite design experiments suggested a medium which was designated as cane molasses medium (CMM). Eventually, this medium contained 21.9% cane molasses, 30.72 g/L of a combined mixture of nitrogenous compounds: 0.0754% of a 1:1:1 mixture of polysorbates 20, 60, and 80, and 18.53 gr/L of the combined minerals. Such an optimized cane molasses-based medium supported a significant biomass production since a considerably high cell density, 13.8 g/L/24 h of dry biomass, of the strain was produced. Hence, cane molasses can be regarded as a promising substrate for industrial production purposes.

Published
2020
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10. Screening for efficient nitrogen sources for overproduction of the biomass of the functionally probiotic L. plantarum strain RPR42 in a cane molasses-based medium.

Author

Papizadeh M, Rohani M, Hosseini SN, Shojaosadati SA, Nahrevanian H, Talebi M, and Pourshafie MR

Abstract

Nitrogen source has a vital role for the efficient growth of lactobacilli. The effects of cheese whey, corn steep liquor, and wheat germ extract on the growth of L. plantarum strain RPR42 in cane molasses-based media was evaluated using various approaches of design of experiments. Our results showed that such protein-rich agricultural by-products significantly increase the biomass production of the strain RPR42 in cane molasses-based media. The most affecting nitrogenous material was cheese whey followed by CSL and the minor effect was reported for wheat germ extract as revealed in factorial and Box-Behnken design experiments. The replacement of costly beef extract and yeast extract with a defined mixtures of the above nitrogenous agricultural by-products in cane molasses-based medium led to production of up to 12.64 g/L/24 h of dry biomass of strain RPR42. A detectable cell density of strain RPR42 (~ 9.81 × 10 9  CFU/mL 24 h) which was observed in such an economic medium showed that the large-scale production of the strain RPR42 tend to be feasible at significantly low costs.

Published
2020
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11. Fusarium ershadii sp. nov., a Pathogen on Asparagus officinalis and Musa acuminata .

Author

Papizadeh M, van Diepeningen AD, Zamanizadeh HR, Saba F, and Ramezani H

Abstract

Two Fusarium strains, isolated from Asparagus in Italy and Musa in Vietnam respectively, proved to be members of an undescribed clade within the Fusarium solani species complex based on phylogenetic species recognition on ITS, partial RPB2 and EF-1α gene fragments. Macro- and micro-morphological investigations followed with physiological studies done on this new species: Fusarium ershadii sp. nov can be distinguished by its conidial morphology. Both isolates of Fusarium ershadii were shown to be pathogenic to the monocot Asparagus officinalis when inoculated on roots and induced hollow root symptoms within two weeks in Asparagus officinalis seedlings. In comparison mild disease symptoms were observed by the same strains on Musa acuminata seedlings.

Published
2018
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12. Probiotic characters of Bifidobacterium and Lactobacillus are a result of the ongoing gene acquisition and genome minimization evolutionary trends.

Author

Papizadeh M, Rohani M, Nahrevanian H, Javadi A, and Pourshafie MR

Subjects
Animals, Bifidobacterium classification, Ecology, Evolution, Molecular, Gastrointestinal Tract microbiology, Humans, Lactobacillus classification, Phylogeny, Species Specificity, Bifidobacterium genetics, Genome, Bacterial, Genomics, Lactobacillus genetics, Probiotics
Abstract

Bifidobacterium and Lactobacillus are the main probiotic genera. Collectively, these two genera harbor over 200 species among which are many strains have been introduced as probiotics. These health-promoting microbes confer health benefits upon the host and so used in food productions and as supplements. Considering the economic importance of probiotics, the biochemistry, genomics, phylogeny and physiology of such genera have been exhaustively studied. According to the genomic data, the probiotic capabilities are strain specific which may be a result of the niche-specialization of the genomes of these bacteria to certain ecological niches like gastrointestinal tract of a diverse range of animals. These microbes have a wide distribution but the culture-based studies and either genomics data suggest selective affinity of some Lactobacillus and either Bifidobacterium species to certain ecological niches. An ongoing genome degradation, which is thought to be a result of passage through an evolutionary bottleneck, is the major trend in the evolution of lactobacilli. Further, evolutionary events resulted into two categories of lactobacilli: habitat generalists and habitat specialists. In place, the main trend in the evolution of bifidobacteria tend to be the gene acquisition. However, probiotic features are the results of a co-evolutionary relationship between these bacteria and their hosts and the aforementioned evolutionary tends have driven the evolution of these probiotic genera., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Published
2017
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13. C-S targeted biodegradation of dibenzothiophene by Stenotrophomonas sp. NISOC-04.

Author

Papizadeh M, Ardakani MR, Motamedi H, Rasouli I, and Zarei M

Subjects
Biodegradation, Environmental, Biphenyl Compounds metabolism, Carbon metabolism, Chromatography, Gas, Chromatography, High Pressure Liquid, Gasoline, Phylogeny, Polymerase Chain Reaction, RNA, Bacterial analysis, Sequence Analysis, DNA, Stenotrophomonas genetics, Sulfur metabolism, Petroleum metabolism, RNA, Ribosomal, 16S analysis, Soil Pollutants metabolism, Stenotrophomonas metabolism, Thiophenes metabolism
Abstract

Crude oil-contaminated soil samples were gathered across Khuzestan oilfields (National Iranian South Oil Company, NISOC) consequently experienced a screening procedure for isolating C-S targeted dibenzothiophene-biodegrading microorganisms with previously optimized techniques. Among the isolates, a bacterial strain was selected due to its capability of biodegrading dibenzothiophene in a C-S targeted manner in aqueous phases and medium mostly consisting of separately biphasic water-gasoline. The 16S rDNA of the isolate was amplified using eubacterial-specific primers and then sequenced. Based on sequence data analysis, the microorganism, designated NISOC-04, clustered most closely with the members of the genus Stenotrophomonas. Gas chromatography indicated that Stenotrophomonas sp. NISOC-04 utilizes 82% of starting 0.8 mM dibenzothiophene within a 48-h-long exponential growth phase. Growth curve analysis revealed the inability of Stenotrophomonas sp. NISOC-04 to utilize dibenzothiophene (DBT) as the exclusive carbon or carbon/sulfur source. Gibbs' assay showed no 2-hydroxy biphenyl accumulation, but HPLC confirmed the presence of 2-hydroxy biphenyl as the final product of DBT desulfurization. Under sulfur starvation, Stenotrophomonas sp. NISOC-04 produced a huge biomass with untraceable sulfur and utilized atmospheric insignificant sulfur levels.

Published
2011
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14. Utilization of dibenzothiophene as sulfur source by Microbacterium sp. NISOC-06.

Author

Papizadeh M, Ardakani MR, Ebrahimipour G, and Motamedi H

Abstract

Oil-polluted soils were sampled from National Iranian South Oil Company (NISOC) for isolation and screening of C-S and not C-C targeted Dibenzothiophene (DBT) degrading microorganisms. Microbacterium sp. NISOC-06, a C-S targeted DBT degrading bacterium, was selected and its desulfurization ability was studied in aqueous phase and water-gasoline biphasic systems. The 16srRNA gene was amplified using universal eubacteria-specific primers, PCR product was sequenced and the sequence of nearly 1,500 bp 16srDNA was studied. Based on Gas Chromatography results Microbacterium sp. NISOC-06 utilized 94.8% of 1 mM DBT during the 2 weeks of incubation. UV Spectrophotometry and biomass production measurements showed that the Microbacterium sp. NISOC-06 was not able to utilize DBT as a carbon source. There was no accumulation of phenolic compounds as Gibb's assay showed. Biomass production in a biphasic system for which DBT-enriched gasoline was used as the sulfur source indicated the capability of Microbacterium sp. NISOC-06 to desulfurize gasoline.

Published
2010
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