Ali Budhi Kusuma
@tecnico.ulisboa.pt
iBB – Institute for Bioengineering and Biosciences
Instituto Superior Tecnico
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
Scopus Publications
Scopus Publications
Tina Keller-Costa, Selene Madureira, Ana S. Fernandes, Lydia Kozma, Jorge Gonçalves, Cristina Barroso, Ali Budhi Kusuma, Conceição Egas, and Rodrigo Costa
American Society for Microbiology
ABSTRACT 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.
Alfin Hidayat, Mamat Sugianto, Ali Budhi Kusuma, Lili Suharli, and Adhityo Wicaksono
Editorial Pontificia Universidad Javeriana
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.
Yosmina Tapilatu, Ihsan Fauzan, Ariel Pradipta, and Ali Budhi Kusuma
Springer Science and Business Media LLC
AbstractIndonesia'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.
Ali Budhi Kusuma, Gita Fenylestari, Fadhil Ammar, Imen Nououi, and Michael Goodfellow
Microbiology Society
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 .
Izzul Islam, Cut Nanda Sari, Ali Budhi Kusuma, Ika Kurniasari, Lisnawati Lisnawati, Rini Surya Ningsih, and Elisa Rosani
LEMIGAS RD Center for Oil and Gas Technology
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
Jeanmaire Molina, Roche C. de Guzman, Adhityo Wicaksono, Theodore Muth, Ronniel Pedales, Denia Diaz, Ali Budhi Kusuma, Chloe Li, Hudson Margolis, Feruza Karnitskiy,et al.
Informa UK Limited
ABSTRACT 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.
Immanuel Sanka, Ali Budhi Kusuma, Faustina Martha, Andre Hendrawan, Ihsan Tria Pramanda, Adhityo Wicaksono, Afif Pranaya Jati, Maulida Mazaya, Ari Dwijayanti, Nurul Izzati,et al.
Elsevier BV
Ali B. Kusuma, Kurniawan E. Putra, Leggina R. Vanggy, Joshua Loh, Imen Nouioui, and Michael Goodfellow
Springer Science and Business Media LLC
AbstractA polyphasic study was designed to resolve the taxonomic position of isolate MGRD01-02T which was recovered from an acidic hot spring in Indonesia and assigned to the genus Actinospica. Phylogenetic analyses based on 16S rRNA gene sequences show that the isolate is most closely related to the type strains of Actinospica acidiphila (98.5%), Actinospica robiniae (97.8%) and Actinospica durhamensis (96.8%). Morphological and chemotaxonomic data underpin the assignment of the isolate to the genus Actinospica as it forms an extensively branched substrate mycelium which carries tufts of white aerial hyphae that differentiate into straight to flexuous chains of cylindrical spores with faint rugose surfaces, contains 2,6-diamino-3-hydroxydiaminopimelic acid in the peptidoglycan, mixtures of hydrogenated menaquinones with nine isoprene units, iso-C 15:O and iso-C 16:O as major fatty acids and phosphatidylethanolamine as the diagnostic phospholipid. Whole-genome sequence analyses show that the isolate, A. durhamensis CSCA 57T and Actinocrinis puniceicyclus DSM 45168T have genome sizes of 7.9, 9.6 and 6.7 Mbp, respectively. A phylogenomic tree shows that they form distinct branches in a well-supported clade, a result supported by associated phenotypic data. Average nucleotide identity and digital DNA:DNA hybridization similarities are below the recommended thresholds for assigning strains to the same species; they also indicate that isolate MGRD01-02T is most closely related to the A. durhamensis and A. robiniae strains. Corresponding amino acid identity and conserved protein data not only support these relationships but also confirm the taxonomic integrity of the genus Actinocrinis. Based on these results, it is proposed that isolate MGRD01-02T (= CCMM B1308T = ICEBB-09T = NCIMB 15218T) be classified in the genus Actinospica as Actinospica acidithermotolerans sp. nov. The draft genome of the isolate and its closest phylogenomic neighbours contain biosynthetic gene clusters with the potential to produce new natural products, notably antibiotics.
Ali B. Kusuma, Imen Nouioui, and Michael Goodfellow
Springer Science and Business Media LLC
AbstractA polyphasic study was designed to determine the taxonomic provenance of a strain, isolate PRKS01-29T, recovered from an Indonesian sand dune and provisionally assigned to the Streptomyces violaceusniger clade. Genomic, genotypic and phenotypic data confirmed this classification. The isolate formed an extensively branched substrate mycelium which carried aerial hyphae that differentiated into spiral chains of rugose ornamented spores, contained LL-as the wall diaminopimelic acid, MK-9 (H6, H8) as predominant isoprenologues, phosphatidylethanolamine as the diagnostic phospholipid and major proportions of saturated, iso- and anteiso- fatty acids. Whole-genome sequences generated for the isolate and Streptomyces albiflaviniger DSM 41598T and Streptomyces javensis DSM 41764T were compared with phylogenetically closely related strains, the isolate formed a branch within the S. violaceusniger clade in the resultant phylogenomic tree. Whole-genome sequences data showed that isolate PRKS01-29T was most closely related to the S. albiflaviniger strain but was distinguished from the latter and from other members of the clade using combinations of phenotypic properties and average nucleotide identity and digital DNA:DNA hybridization scores. Consequently, it is proposed that isolate PRKS01-29T (= CCMM B1303T = ICEBB-02T = NCIMB 15210T) should be classified in the genus Streptomyces as Streptomyces sabulosicollis sp. nov. It is also clear that streptomycetes which produce spiral chains of rugose ornamented spores form a well-defined monophyletic clade in the Streptomyces phylogenomic tree., the taxonomic status of which requires further study. The genome of the type strain of S. sabulosicollis contains biosynthetic gene clusters predicted to produce new natural products.
Wael M. Abdel-Mageed, Lamya H. Al-Wahaibi, Burhan Lehri, Muneera S. M. Al-Saleem, Michael Goodfellow, Ali B. Kusuma, Imen Nouioui, Hariadi Soleh, Wasu Pathom-Aree, Marcel Jaspars,et al.
MDPI AG
A Micromonospora strain, isolate MT25T, was recovered from a sediment collected from the Challenger Deep of the Mariana Trench using a selective isolation procedure. The isolate produced two major metabolites, n-acetylglutaminyl glutamine amide and desferrioxamine B, the chemical structures of which were determined using 1D and 2D-NMR, including 1H-15N HSQC and 1H-15N HMBC 2D-NMR, as well as high resolution MS. A whole genome sequence of the strain showed the presence of ten natural product-biosynthetic gene clusters, including one responsible for the biosynthesis of desferrioxamine B. Whilst 16S rRNA gene sequence analyses showed that the isolate was most closely related to the type strain of Micromonospora chalcea, a whole genome sequence analysis revealed it to be most closely related to Micromonospora tulbaghiae 45142T. The two strains were distinguished using a combination of genomic and phenotypic features. Based on these data, it is proposed that strain MT25T (NCIMB 15245T, TISTR 2834T) be classified as Micromonospora provocatoris sp. nov. Analysis of the genome sequence of strain MT25T (genome size 6.1 Mbp) revealed genes predicted to responsible for its adaptation to extreme environmental conditions that prevail in deep-sea sediments.
Ali Budhi Kusuma, Imen Nouioui, Hans-Peter Klenk, and Michael Goodfellow
Microbiology Society
A polyphasic study was undertaken to establish the position of a Streptomyces strain, isolate PRKS01-65T, recovered from sand dune soil collected at Parangkusumo, Yogyakarta Province, Java, Indonesia. A combination of chemotaxonomic, cultural and morphological properties confirmed its position in the genus of Streptomyces . Comparative 16S rRNA gene sequence analyses showed that the isolate was most closely related to Streptomyces leeuwenhoekii C34T (99.9 % similarity) and loosely associated with the type strains of Streptomyces chiangmaiensis (98.7 % similarity) and Streptomyces glomeratus (98.9 % similarity). Multilocus sequence analyses based on five conserved housekeeping gene alleles confirmed the close relationship between the isolate and S. leeuwenhoekii C34T, although both strains belonged to a well-supported clade that encompassed the type strains of S. glomeratus , Streptomyces griseomycini , Streptomyces griseostramineus , Streptomyces labedae , Streptomyces lomondensis and Streptomyces spinoverrucosus . A comparison of the draft genome sequence generated for the isolate with corresponding whole genome sequences of its closest phylogenomic neighbours showed that it formed a well-separated lineage with S. leeuwenhoekii C34T. These strains can also be distinguished using a combination of phenotypic properties and by average nucleotide identity and digital DNA–DNA hybridization similarities of 94.3 and 56 %, values consistent with their classification in different species. Based on this wealth of data it is proposed that isolate PRKS01-65T (=NCIMB 15211T=CCMM B1302T=ICEBB-03T) be classified as Streptomyces harenosi sp. nov. The genome of the isolate contains several biosynthetic gene clusters with the potential to produce new natural products.