Ali Budhi Kusuma is a dedicated microbiologist specializing in microbial diversity, ecology, and bioprospecting. With a PhD from Newcastle University (2020) and an MSc from the University of Birmingham (2014), his research focuses on exploring extremophilic actinobacterial diversity for novel antimicrobials and industrial enzymes. He founded the Indonesian Centre for Extremophile Bioresources and Biotechnology (ICEBB) to preserve microbial bioresources in Indonesia. Ali has secured numerous grants, supervised over 20 students, and contributed to scientific publications and conferences. His work bridges basic research and biotech applications, driven by a passion for biodiversity conservation and sustainable bioinnovation.
EDUCATION
2016-2020
Doctor of Philosophy (PhD) in Extremophile Microbiology
(Passed without correction)
School of Natural and Environmental Sciences
Newcastle University
Newcastle Upon Tyne, UK
2013-2014
Master of Science (MSc) in Microbiology & Infection
(Passed with Merit)
School of Biosciences |
The University of Birmingham,
Birmingham, UK
2007-2012
Bachelor of Science (B.Sc) in
Microbiology (GPA: 3.46/4.0)
School of Life Sciences and Technology
Bandung Institute of Technology (ITB),
Bandung, Indonesia
RESEARCH, TEACHING, or OTHER INTERESTS
General Agricultural and Biological Sciences, Ecology, Evolution, Behavior and Systematics
Genome sequence of the marine bacterium Roseobacter sp. EG26, isolated from the octocoral Eunicella gazella, suggests aptitude for a host-associated lifestyle Tina Keller-Costa, Selene Madureira, Ana S. Fernandes, Lydia Kozma, Jorge Gonçalves, et al. Microbiology Resource Announcements, 2025 We present the genome sequence of the octocoral-associated Roseobacter sp. EG26. We highlight features related to type II, III, IV, and VI secretion systems, ankyrin-repeat proteins, and taurine degradation, suggesting a preference for a host-associated lifestyle. Strain EG26 also possesses genes for the degradation of phenolic compounds with bioremediation potential.
In silico antimalarial bioprospecting of neem (Azadirachta indica) quinine-derivative alkaloids Alfin Hidayat, Mamat Sugianto, Ali Budhi Kusuma, Lili Suharli, Adhityo Wicaksono Universitas Scientiarum, 2025 Malaria, driven by the protozoan Plasmodium spp. and transmitted by Anopheles mosquitoes, remains a significant global health threat. With the emergence of chloroquine-resistant malaria, alternative treatments derived from natural compounds are pressing. This study explores neem (Azadirachta indica), a Southeast Asian plant, as a source of antimalarial agents. A Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) analysis of a neem leaf extract identified 184 compounds, of which five quinone-derivative compounds were subject to in silico screening against three Plasmodium falciparum virulence proteins: Purine nucleoside phosphorylases (PNP), dihydroorotate dehydrogenase (DHODH), and erythrocyte membrane protein 1 (EMP1). Among these five compounds (A-E), compound C emerged as the top candidate, ranking highly in molecular stability (FMO energy gaps), drug-likeness (Lipinski’s Rule of 5), bioavailability, and synthetic accessibility. Compound C also exhibited strong binding affinity to PNP and DHODH in molecular docking and dynamics simulations and ranked among the top three for binding free energy in MM/PBSA calculations. However, it lacked predicted antiprotozoal activity in PASS screening, though it shared key enzyme targets with established antimalarial drugs. These findings nominate compound C as a promising candidate for further research as a potential antimalarial agent.
A first report on prokaryotic diversity in northwestern Arafura deep-sea sediments, Indonesia Yosmina Tapilatu, Ihsan Fauzan, Ariel Pradipta, Ali Budhi Kusuma Scientific Reports, 2024 Indonesia's deep-sea microbial communities remain poorly understood, prompting the need for comprehensive investigations. This study aimed to assess the bacterial and archaeal diversities in northwestern Arafura deep-sea sediments, spanning depths of 100 to 1,457 m using a 16S rRNA based-metagenomic sequencing approach, without technical and biological replicates. Principal component analyses based on the Bray–Curtis dissimilarity index indicated that most of the bacterial and archaeal communities were habitat-specific and influenced by depth. The most prevalent known bacterial phylotypes were detected from all samples belonging to the phylum of Desulfobacteriota, Pseudomonadota, and Firmicutes. In addition, the samples also harbored diverse members of the Archaea domain, including Crenarchaeota, Nanoarchaeota and Haloarchaeota. Notably, the sequencing data revealed the significant presence of rare prokaryotic taxa, including uncultured counterparts with less than 1% abundance. The findings suggest that novel and rare prokaryotic taxa are abundant in northwestern Arafura deep-sea ecosystem, offering unique opportunities for further bioprospecting and functional ecology studies.
Rhodococcus indonesiensis sp. nov. a new member of the Rhodococcus ruber lineage isolated from sediment of a neutral hot spring and reclassification of Rhodococcus electrodiphilus (Ramaprasad et al. 2018) as a later heterotypic synonym of Rhodococcus ruber (Kruse 1896) Goodfellow and Alderson 1977 (Approved Lists 1980) Ali Budhi Kusuma, Gita Fenylestari, Fadhil Ammar, Imen Nououi, Michael Goodfellow International Journal of Systematic and Evolutionary Microbiology, 2024 A polyphasic study was designed to determine the taxonomic status of isolate CSLK01-03T, which was recovered from an Indonesian neutral hot spring and provisionally assigned to the genus Rhodococcus . The isolate was found to have chemotaxonomic, cultural and morphological properties typical of rhodococci. It has a rod–coccus lifecycle and grows from 10 to 39 °C, from pH 6.5 to 8.0 and in the presence of 0–10 % (w/v) sodium chloride. Whole-organism hydrolysates contain meso-diaminopimelic acid, arabinose and galactose, the predominant menaquinone is MK-8 (H2), the polar lipid pattern consists of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylmethylethanolamine and two unidentified components, it produces mycolic acids, and C16:0 is the major fatty acid. Whole-genome analyses show that the isolate and Rhodococcus electrodiphilus LMG 29881T (GenBank accession: JAULCK000000000) have genome sizes of 5.5 and 5.1 Mbp, respectively. These strains and Rhodococcus aetherivorans DSM 44752T and Rhodococcus ruber DSM 43338T form well-supported lineages in 16S rRNA and whole-genome trees that are close to sister lineages composed of the type strains of Rhodococcus rhodochrous and related Rhodococcus species. The isolate can be distinguished from its closest evolutionary neighbours using combinations of cultural and phenotypic features, and by low DNA–DNA hybridization values. Based on these data it is proposed that isolate CSLK01-03T (=CCMM B1310T=ICEBB-06T=NCIMB 15214T) be classified in the genus Rhodococcus as Rhodococcus indonesiensis sp. nov. The genomes of the isolate and its closest phylogenomic relatives are rich in biosynthetic gene clusters with the potential to synthesize new natural products, notably antibiotics. In addition, whole-genome-based taxonomy revealed that Rhodococcus electrodiphilus LMG 29881T and Rhodococcus ruber DSM 43338T belong to a single species. It is, therefore, proposed that R. electrodiphilus be recognized as a heterotypic synonym of R. ruber .
Bioprospecting of Halophilic Bacteria Staphylococcus haemolyticus Strain Stp-Griv-024 as Biosurfactant Producer and Its Potential Application for Microbial Enhanced Oil Recovery Izzul Islam, Cut Nanda Sari, Ali Budhi Kusuma, Ika Kurniasari, Lisnawati Lisnawati, et al. Scientific Contributions Oil and Gas, 2024 The use of halophilic bacteria to produce effective and stable biosurfactants in the Microbial Enhanced Oil Recovery (MEOR) process is getting much attention from researchers. A diversity of halophilic bacteria that produce biosurfactants can be found in areas with intense oil exposure, such as the waters of Bima Bay, which is closed and are one of the main sea transportation routes in eastern Indonesia. This research aims to isolate potential local halophilic bacteria in producing biosurfactants to degrade hydrocarbons. The research methodology included bacterial isolation, gram staining, hemolysis test, total petroleum hydrocarbon (TPH) analysis, emulsification, and phylogenetic analysis of the 16S rRNA marker gene. STP-GRIV-024 was successfully isolated using Kish, Halophilic, Soil extract, and Oatmeal agar media, with the highest enumeration results found on Kish media supplemented with 3% (w/v) NaCl. Microscopic morphological characterization using Gram staining showed results as a Gram-positive group with round colony shapes, smooth circular edges, sloping and white. This isolate grew in the 7-15% (w/v) NaCl range and was classified as moderately halophilic. TPH analysis showed that concentration and incubation time influenced hydrocarbon degradation activity. On day 10, the concentrations of T1 (1%), T2 (3%), T3 (5%), and T4 (7%) showed a decrease in TPH of 1.96%, 0.51%, 0.25 %, and 0.15% respectively. 16S rRNA sequencing identified the isolate as closely related to Staphylococcus haemolyticus strain MTCC3383T, with a DNA sequence similarity of 99.9%. These findings provide an important foundation for further development in applying halophilic bacteria in MEOR practices to increase the efficiency of sustainable and environmentally friendly oil production
The endophyte’s endophytes: the microbial partners of the endangered plant parasite Rafflesia speciosa (Rafflesiaceae) reveal clues about its cryptic biology and cues for cultivation Jeanmaire Molina, Roche C. de Guzman, Adhityo Wicaksono, Theodore Muth, Ronniel Pedales, et al. Journal of Plant Interactions, 2024 Rafflesia is an endangered endophytic holoparasitic plant that lives the majority of its life inside the tissues of its sole plant host, Tetrastigma. Rafflesia floral buds emerge to produce the world’s largest single flower. Like other plants, holoparasites harbor a diverse microbiome, the role(s) of which has remained largely unstudied. We characterized the bacterial microbiome of seeds of Rafflesia speciosa and cuttings of its host. We found evidence that R. speciosa seed has similar bacterial profiles to its infected host, which suggests that seeds sequester certain host bacteria, as well as acquire unique bacterial taxa from biotic associates of the fruit. We did not find evidence of mycorrhizal taxa in the microbiome. This is the first study of the microbial endophytes associated with any Rafflesia species and its host, a tripartite holobiont, and provides insights on its cryptic microbial partners. We discuss how this may aid horticultural propagation of Rafflesia.
Bioprospecting of Limosilactobacillus fermentum strain MH 2.3 for Anti-diabetic Properties: from Biochemical to Molecular Docking Approaches Philippine Journal of Science, 2023
Identifying Extended-spectrum β-lactamase (ESBL) producing E. coli Hotspots in Integrated Livestock Farming using Whole Genome Sequencing YV Paramitadevi, AB Kusuma, J Sölkner, A Rukmana, I Rahmatika, ... Hygiene and Environmental Health Advances, 100185 , 2026 2026
The draft genome sequence of Kitasatospora sp. HPM-01-4 isolated from Mentaos Pine Forest, heart of Borneo, Indonesia D Ariyanti, M Nuhamunada, N Izzati, M Fitriana, AR Widyaningrum, ... Microbiology Resource Announcements 15 (4), e00739-25 , 2026 2026
Genome sequence of the marine bacterium Roseobacter sp. EG26, isolated from the octocoral Eunicella gazella , suggests aptitude for a host-associated lifestyle T Keller-Costa, S Madureira, AS Fernandes, L Kozma, J Gonçalves, ... Microbiology Resource Announcements 14 (8), e00430-25 , 2025 2025
In silico antimalarial bioprospecting of neem (Azadirachta indica) quinine-derivative alkaloids A Hidayat, M Sugianto, AB Kusuma, L Suharli, A Wicaksono Universitas Scientiarum, 40-64 , 2025 2025
Onuma Kaewkla1, 2, Kawintip Kiakhunthod1, 2, Sumalee Chookhampaeng1, Busayarat Klinjantasorm1, 2, Piriya Klankeo3 and Winya Dungkaew2 R Aroca, AB Kusuma, I Khangwal, O Kaewkla 2025
The endophyte’s endophytes: the microbial partners of the endangered plant parasite Rafflesia speciosa (Rafflesiaceae) reveal clues about its cryptic biology and … J Molina, RC de Guzman, A Wicaksono, T Muth, R Pedales, D Diaz, ... Journal of Plant Interactions 19 (1), 2304221 , 2024 2024 Citations: 2
Analisis Kandungan Senyawa Bioaktif dari Produk Pupuk Hayati RiceSolutionTM, PT Archipelago Biotechnology Indonesia dengan Teknik Kromatografi dalam Menghambat Cytochrome bc1 IP Lestari, G Fenylestari, AB Kusuma BIOMARAS: Journal of Life Science and Technology 2 (2), 9-14 , 2024 2024
Bioprospecting of Halophilic Bacteria Staphylococcus Haemolyticus Strain Stp-Griv-024 as Biosurfactant Producer and its Potential Application for Microbial Enhanced Oil Recovery I Islam, CN Sari, AB Kusuma, I Kurniasari, RS Ningsih, E Rosani Scientific Contributions Oil and Gas 47 (2) , 2024 2024 Citations: 1
Rhodococcus indonesiensis sp. nov. a new member of the Rhodococcus ruber lineage isolated from sediment of a neutral hot spring and reclassification of Rhodococcus … AB Kusuma, G Fenylestari, F Ammar, I Nououi, M Goodfellow International Journal of Systematic and Evolutionary Microbiology 74 (1), 006236 , 2024 2024 Citations: 6
A first report on prokaryotic diversity in northwestern Arafura deep-sea sediments, Indonesia Y Tapilatu, I Fauzan, A Pradipta, AB Kusuma Scientific Reports 14 (1), 895 , 2024 2024 Citations: 5
Bioprospecting of Limosilactobacillus fermentum strain MH 2.3 for anti-diabetic properties: frombiochemical to molecular docking approaches. UF Whatin, B Manguntungi, H Djamaludin, H Handoko, LR Vanggy, ... 2023
Isolasi dan Uji Aktivitas Plant Growth Promoting Bacteria (PGPB) dari Isolat Lokal Asal Pupuk Hayati Majemuk Ricesolution PT. Archipelago Biotechnology Indonesia RE Damayanti, G Fenylestari, AB Kusuma BIOMARAS: Journal of Life Science and Technology 1 (1), 42-48 , 2023 2023
Bioprospecting of Limosilactobacillus fermentum strain MH 2.3 for Anti-diabetic Properties: from Biochemical to Molecular Docking Approaches. UF Whatin, B Manguntungi, H Djamaludin, LR Vanggy, G Fenylestari, ... Philippine Journal of Science 152 (3) , 2023 2023 Citations: 3
Analisis Strategis Kelayakan Kontrak Berbasis Kinerja (Performance Base Contract) Pada Proyek Jalan Di Kabupaten Sumbawa Barat A Rahman, AB Kusuma, S Anshori Prosiding Seminar Nasional Manajemen Inovasi 5 (001, January), 208-219 , 2023 2023 Citations: 1
Synthetic biology in Indonesia: Potential and projection in a country with mega biodiversity I Sanka, AB Kusuma, F Martha, A Hendrawan, IT Pramanda, A Wicaksono, ... Biotechnology Notes 4, 41-48 , 2023 2023 Citations: 32
Genome based classification of Streptomyces sp. SUK 48 from fruit of Brasilia sp. MIH Sulaimi, SJ Ahmad, NM Zin, AB Kusuma Asian Journal of Medicine and Biomedicine 6 (S1), 89-90 , 2022 2022
Actinospica acidithermotolerans sp. nov., a novel actinomycete isolated from sediment from an Indonesian hot spring AB Kusuma, KE Putra, LR Vanggy, J Loh, I Nouioui, M Goodfellow Archives of Microbiology 204, 518 , 2022 2022 Citations: 11
Kajian penerapan model agrosilvopastura dalam peningkatan kesejahteraan dan pendapatan kelompok tani hutan Sorowua D Fardiansyah, AB Kusuma, MT Pathiassana Jurnal Tambora 6 (2), 66-77 , 2022 2022 Citations: 18
PERAN FORUM KOMUNIKASI USAHA MIKRO KECIL DAN MENENGAH (FKUMKM) UNTUK MENINGKATKAN TINGKAT PENDAPATAN, KONSUMEN DAN PERSAINGAN BAGI PELAKU UMKM DI KABUPATEN SUMBAWA BARAT NA Saputra, AB Kusuma, I Darmawan Prosiding Seminar Nasional Manajemen Inovasi 4 (001, August), 376-384 , 2022 2022
SEAFEEDTM: INOVASI PAKAN FUNGSIONAL UNTUK TERNAK RUMINANSIA BERBASIS SELADA LAUT LOKAL SUMBAWA Ulva lactuca (Linnaeus) YANG DIFORTIFIKASI DENGAN PROBIOTIK, PREBIOTIK DAN POSTBIOTIK AB Kusuma, I Munandar, LR Vanggy Jurnal Tambora 6 (1), 39-42 , 2022 2022
MOST CITED SCHOLAR PUBLICATIONS
Synthetic biology in Indonesia: Potential and projection in a country with mega biodiversity I Sanka, AB Kusuma, F Martha, A Hendrawan, IT Pramanda, A Wicaksono, ... Biotechnology Notes 4, 41-48 , 2023 2023.0 Citations: 32
Streptomyces harenosi sp. nov., a home for a gifted strain isolated from Indonesian sand dune soil AB Kusuma, I Nouioui, HP Klenk, M Goodfellow International journal of systematic and evolutionary microbiology 70 (9 … , 2020 2020.0 Citations: 23
Biotechnological and Ecological Potential of Micromonospora provocatoris sp. nov., a Gifted Strain Isolated from the Challenger Deep of the Mariana Trench WM Abdel-Mageed, LH Al-Wahaibi, B Lehri, MSM Al-Saleem, ... Marine Drugs 19 (5), 243 , 2021 2021.0 Citations: 21
Kajian penerapan model agrosilvopastura dalam peningkatan kesejahteraan dan pendapatan kelompok tani hutan Sorowua D Fardiansyah, AB Kusuma, MT Pathiassana Jurnal Tambora 6 (2), 66-77 , 2022 2022.0 Citations: 18
Genome-based classification of the Streptomyces violaceusniger clade and description of Streptomyces sabulosicollis sp. nov. from an Indonesian sand dune AB Kusuma, I Nouioui, M Goodfellow Antonie Van Leeuwenhoek 114 (6), 859-873 , 2021 2021.0 Citations: 18
Diversity of culturable bacterial in various parts of luwak's (Paradoxurus hermaprodithus javanica) gastrointestinal Tract S SUHANDONO, H SETIADI, T KRISTIANTI, ALIB KUSUMA, ... Microbiology Indonesia 10 (2), 4-4 , 2016 2016.0 Citations: 17
Actinospica acidithermotolerans sp. nov., a novel actinomycete isolated from sediment from an Indonesian hot spring AB Kusuma, KE Putra, LR Vanggy, J Loh, I Nouioui, M Goodfellow Archives of Microbiology 204, 518 , 2022 2022.0 Citations: 11
Pemanfaatan limbah kelapa sawit melalui pengolahan biologis dalam rangka integrasi industri kelapa sawit dan ternak ruminansia L Liman, A Kusuma, Y Widodo Jurnal Penelitian Pertanian Terapan 10 (2) , 2010 2010.0 Citations: 11
Rhodococcus indonesiensis sp. nov. a new member of the Rhodococcus ruber lineage isolated from sediment of a neutral hot spring and reclassification of Rhodococcus … AB Kusuma, G Fenylestari, F Ammar, I Nououi, M Goodfellow International Journal of Systematic and Evolutionary Microbiology 74 (1), 006236 , 2024 2024.0 Citations: 6
A first report on prokaryotic diversity in northwestern Arafura deep-sea sediments, Indonesia Y Tapilatu, I Fauzan, A Pradipta, AB Kusuma Scientific Reports 14 (1), 895 , 2024 2024.0 Citations: 5
Microbiology of Indonesian extremobiospheres: from unexplored actinobacteria diversity to novel antimicrobial discovery AB Kusuma Newcastle University , 2021 2021.0 Citations: 5
Penambahan Enkapsulan Dalam Proses Pembuatan Yoghurt Powder Probiotik Dengan Metode Spray Drying J Sahib, N Miskiyah, A Kusuma Jurnal Penelitian Pascapanen Pertanian 16 (2), 56 , 2020 2020.0 Citations: 4
Bioprospecting of Limosilactobacillus fermentum strain MH 2.3 for Anti-diabetic Properties: from Biochemical to Molecular Docking Approaches. UF Whatin, B Manguntungi, H Djamaludin, LR Vanggy, G Fenylestari, ... Philippine Journal of Science 152 (3) , 2023 2023.0 Citations: 3
Yulianti., Asmawati., Dan Yunianti., 2016, Pengaruh Kombinasi Ekstrak Kirinyuh (Chromolaena odorata) dan Sirih (Piper betle L.) dalam Pengendalian Penyakit Vibriosis pada Udang B Manguntungi, AB Kusuma Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati 1 (3), 138-144 , 0 Citations: 3
The endophyte’s endophytes: the microbial partners of the endangered plant parasite Rafflesia speciosa (Rafflesiaceae) reveal clues about its cryptic biology and … J Molina, RC de Guzman, A Wicaksono, T Muth, R Pedales, D Diaz, ... Journal of Plant Interactions 19 (1), 2304221 , 2024 2024.0 Citations: 2
Pengaruh Kombinasi Ekstrak Kirinyuh (Chromolaena odorata) dan Sirih (Piper betle L) dalam Pengendalian Penyakit Vibriosis pada Udang BMABK Yulianti, A Yunianti Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati, 138-144 , 2016 2016.0 Citations: 2
Bioprospecting of Halophilic Bacteria Staphylococcus Haemolyticus Strain Stp-Griv-024 as Biosurfactant Producer and its Potential Application for Microbial Enhanced Oil Recovery I Islam, CN Sari, AB Kusuma, I Kurniasari, RS Ningsih, E Rosani Scientific Contributions Oil and Gas 47 (2) , 2024 2024.0 Citations: 1
Analisis Strategis Kelayakan Kontrak Berbasis Kinerja (Performance Base Contract) Pada Proyek Jalan Di Kabupaten Sumbawa Barat A Rahman, AB Kusuma, S Anshori Prosiding Seminar Nasional Manajemen Inovasi 5 (001, January), 208-219 , 2023 2023.0 Citations: 1
PELATIHAN MODEL PEMBELAJARAN DARING DENGAN MENGGUNAKAN APLIKASI WHATSAPP PADA MUSIM WABAH COVID-19 DI SD PAHLAWAN YY Kusuma Jurnal Pengabdian Masyarakat (ABDIRA) 1 (1), 1-7 , 2021 2021.0 Citations: 1
Green Electricity from Wetland Plants–Derived Microbial Fuel Cell as an Electricity Source for Indonesia’s Coastal Region I Nurulita, A Elviantari, F Dwilaksono, B Manguntungi, AB Kusuma Biologica Samudra 2 (2), 87-94 , 2020 2020.0 Citations: 1