Luis Pedro Coelho
@luispedrocoelho.bsky.social
Content creator for Elsevier, NPG, and others
Microbiome researcher
Based in Brisbane
Microbiome researcher
Based in Brisbane
Happy to be again named as a Highly Cited Researcher for 2025 by Clarivate!
Credit to my team and collaborators who have made all of this possible and happy to also see that the Centre for Microbiome Research has 3 highly cited researchers (myself, Ben Woodcroft and Gene Tyson)!
#HighlyCited2025
Credit to my team and collaborators who have made all of this possible and happy to also see that the Centre for Microbiome Research has 3 highly cited researchers (myself, Ben Woodcroft and Gene Tyson)!
#HighlyCited2025
November 21, 2025 at 12:46 AM
Happy to be again named as a Highly Cited Researcher for 2025 by Clarivate!
Credit to my team and collaborators who have made all of this possible and happy to also see that the Centre for Microbiome Research has 3 highly cited researchers (myself, Ben Woodcroft and Gene Tyson)!
#HighlyCited2025
Credit to my team and collaborators who have made all of this possible and happy to also see that the Centre for Microbiome Research has 3 highly cited researchers (myself, Ben Woodcroft and Gene Tyson)!
#HighlyCited2025
Full thread will come later, but @annacusco.bsky.social's preprint on the dog pet gut microbiome is out!
Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases
doi.org/10.1101/2025...
Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases
doi.org/10.1101/2025...
September 18, 2025 at 12:01 PM
Full thread will come later, but @annacusco.bsky.social's preprint on the dog pet gut microbiome is out!
Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases
doi.org/10.1101/2025...
Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases
doi.org/10.1101/2025...
New feature this year, share a talk link
July 22, 2025 at 9:52 AM
New feature this year, share a talk link
Fig 4a nicely shows how the higher-than-natural SR of each species (resulting from the pooled FMT procedure) converges to a more typical value in ~8 weeks
"By 5 years after the final transplant, SRⱼ in the recipients converged near the population-wide SRⱼ measured in people not receiving FMT"
"By 5 years after the final transplant, SRⱼ in the recipients converged near the population-wide SRⱼ measured in people not receiving FMT"
January 29, 2025 at 5:22 AM
Fig 4a nicely shows how the higher-than-natural SR of each species (resulting from the pooled FMT procedure) converges to a more typical value in ~8 weeks
"By 5 years after the final transplant, SRⱼ in the recipients converged near the population-wide SRⱼ measured in people not receiving FMT"
"By 5 years after the final transplant, SRⱼ in the recipients converged near the population-wide SRⱼ measured in people not receiving FMT"
"Across 92 species in 91 people, we observed that SRⱼ in the human gut microbiome varies significantly by species (P = 2.2 × 10⁻¹⁶, Kruskal–Wallis; Dunn’s Test; Extended Data Table 2), is less than 2.0 strains per species on average (1.23 ± 0.33; mean ±s.d.), and below 3.0 for all species (Fig. 1a)"
January 29, 2025 at 3:57 AM
"Across 92 species in 91 people, we observed that SRⱼ in the human gut microbiome varies significantly by species (P = 2.2 × 10⁻¹⁶, Kruskal–Wallis; Dunn’s Test; Extended Data Table 2), is less than 2.0 strains per species on average (1.23 ± 0.33; mean ±s.d.), and below 3.0 for all species (Fig. 1a)"
"We compared the SR of the human gut microbiome with that of soil and lake microbiomes. Species in the human gut demonstrated much lower SRj (1.23 ± 0.33) than species sampled from soil (6.83 ± 5.07; 112 sequenced isolates) or lake (4.93 ± 2.08; 94 sequenced isolates; Fig. 1c) "
January 29, 2025 at 3:56 AM
"We compared the SR of the human gut microbiome with that of soil and lake microbiomes. Species in the human gut demonstrated much lower SRj (1.23 ± 0.33) than species sampled from soil (6.83 ± 5.07; 112 sequenced isolates) or lake (4.93 ± 2.08; 94 sequenced isolates; Fig. 1c) "
"Across 92 species in 91 people, we observed that SRⱼ in the human gut microbiome varies significantly by species (P = 2.2 × 10⁻¹⁶, Kruskal–Wallis; Dunn’s Test; Extended Data Table 2), is less than 2.0 strains per species on average (1.23 ± 0.33; mean ±s.d.), and below 3.0 for all species (Fig. 1a)"
January 29, 2025 at 3:56 AM
"Across 92 species in 91 people, we observed that SRⱼ in the human gut microbiome varies significantly by species (P = 2.2 × 10⁻¹⁶, Kruskal–Wallis; Dunn’s Test; Extended Data Table 2), is less than 2.0 strains per species on average (1.23 ± 0.33; mean ±s.d.), and below 3.0 for all species (Fig. 1a)"
Preparing a talk to the group ("State of the Lab 2025") with a slide about how we now entering a phase of "exploration over exploitation"
This is what copilot then suggested as the next slide
This is what copilot then suggested as the next slide
January 21, 2025 at 3:55 AM
Preparing a talk to the group ("State of the Lab 2025") with a slide about how we now entering a phase of "exploration over exploitation"
This is what copilot then suggested as the next slide
This is what copilot then suggested as the next slide
Fig 2: "Each rectangular marker represents a gene, colored differently for highly conserved, core, and accessory, and represents the nucleotide sequence identity of genes (y-axis) shared between seven query genomes (each row) and the same reference genome (x-axis, gene position in reference genome)"
December 18, 2024 at 8:06 AM
Fig 2: "Each rectangular marker represents a gene, colored differently for highly conserved, core, and accessory, and represents the nucleotide sequence identity of genes (y-axis) shared between seven query genomes (each row) and the same reference genome (x-axis, gene position in reference genome)"
Here, they ask whether it is recombination that is driving these observations
The authors add a disclaimer that recombination is a different mechanism than sexual reproduction, but "the lady doth protest too much, methinks" and the parallel to biological species is nice
The authors add a disclaimer that recombination is a different mechanism than sexual reproduction, but "the lady doth protest too much, methinks" and the parallel to biological species is nice
December 18, 2024 at 8:06 AM
Here, they ask whether it is recombination that is driving these observations
The authors add a disclaimer that recombination is a different mechanism than sexual reproduction, but "the lady doth protest too much, methinks" and the parallel to biological species is nice
The authors add a disclaimer that recombination is a different mechanism than sexual reproduction, but "the lady doth protest too much, methinks" and the parallel to biological species is nice
In Melbourne
December 5, 2024 at 4:24 AM
In Melbourne
"Focusing on H₂S, we found that the microbiome of healthy individuals contained more species with the potential to produce H₂S, as well as more species with the potential to consume H₂S, than the microbiomes associated with CD"
December 4, 2024 at 6:41 AM
"Focusing on H₂S, we found that the microbiome of healthy individuals contained more species with the potential to produce H₂S, as well as more species with the potential to consume H₂S, than the microbiomes associated with CD"
"MES is the harmonic mean between the number of potential producers (P) and consumers (C) inferred from metagenome-informed metabolic models"
I always have to rethink through the definitions; but the harmonic mean makes sense in reciprocal space, so we think of 1/P and 1/C (instead of C and P)...
I always have to rethink through the definitions; but the harmonic mean makes sense in reciprocal space, so we think of 1/P and 1/C (instead of C and P)...
December 4, 2024 at 6:41 AM
"MES is the harmonic mean between the number of potential producers (P) and consumers (C) inferred from metagenome-informed metabolic models"
I always have to rethink through the definitions; but the harmonic mean makes sense in reciprocal space, so we think of 1/P and 1/C (instead of C and P)...
I always have to rethink through the definitions; but the harmonic mean makes sense in reciprocal space, so we think of 1/P and 1/C (instead of C and P)...
In completely unrelated news, Clarivate named me as a #HighlyCitedResearcher again, which I'm very happy about
November 20, 2024 at 3:55 AM
In completely unrelated news, Clarivate named me as a #HighlyCitedResearcher again, which I'm very happy about
"The sequence similarity of ARGs involved in IPTs varied significantly between different phyla across environments. Most similar ARGs were found in the human and animal microbiome (median similarity of 99.22% and 98.98%, respectively), suggesting that these transfers are more recent"
November 20, 2024 at 2:56 AM
"The sequence similarity of ARGs involved in IPTs varied significantly between different phyla across environments. Most similar ARGs were found in the human and animal microbiome (median similarity of 99.22% and 98.98%, respectively), suggesting that these transfers are more recent"
Fig 2 summarizes the transfer network, with Proteobacteria at the centre
November 20, 2024 at 2:56 AM
Fig 2 summarizes the transfer network, with Proteobacteria at the centre
Multiple experts can be wrong, but you think the reviewers didn't read it?
In any case, citations for that paper are through the roof! Hardly a validation for citations being a better proxy if you think the paper had flaws
scholar.google.com/citations?vi...
In any case, citations for that paper are through the roof! Hardly a validation for citations being a better proxy if you think the paper had flaws
scholar.google.com/citations?vi...
November 18, 2024 at 9:08 AM
Multiple experts can be wrong, but you think the reviewers didn't read it?
In any case, citations for that paper are through the roof! Hardly a validation for citations being a better proxy if you think the paper had flaws
scholar.google.com/citations?vi...
In any case, citations for that paper are through the roof! Hardly a validation for citations being a better proxy if you think the paper had flaws
scholar.google.com/citations?vi...
If I take the data from that preprint, it does show JIF is a decent proxy
Here is JIF diff between journals (estimated from the data) vs. the probability that a paper from journal A is more highly cited than a paper from journal B
I'm actually surprised at how good it is!
Here is JIF diff between journals (estimated from the data) vs. the probability that a paper from journal A is more highly cited than a paper from journal B
I'm actually surprised at how good it is!
November 17, 2024 at 10:15 PM
If I take the data from that preprint, it does show JIF is a decent proxy
Here is JIF diff between journals (estimated from the data) vs. the probability that a paper from journal A is more highly cited than a paper from journal B
I'm actually surprised at how good it is!
Here is JIF diff between journals (estimated from the data) vs. the probability that a paper from journal A is more highly cited than a paper from journal B
I'm actually surprised at how good it is!
Blueksy is acing the metagenomics test now!
November 11, 2024 at 10:56 PM
Blueksy is acing the metagenomics test now!
September 24, 2024 at 6:25 AM
You know what this looks like?
Wales!
No, not North Wales. South Wales!
Wales!
No, not North Wales. South Wales!
September 19, 2024 at 7:21 AM
You know what this looks like?
Wales!
No, not North Wales. South Wales!
Wales!
No, not North Wales. South Wales!
Every once in a while, I log in here and search for "metagenomics"
Today was the first day that I see multiple results that are not weeks old
Still fewer hits than on Twitter, but it's definitely a progression
Today was the first day that I see multiple results that are not weeks old
Still fewer hits than on Twitter, but it's definitely a progression
September 12, 2024 at 11:50 PM
Every once in a while, I log in here and search for "metagenomics"
Today was the first day that I see multiple results that are not weeks old
Still fewer hits than on Twitter, but it's definitely a progression
Today was the first day that I see multiple results that are not weeks old
Still fewer hits than on Twitter, but it's definitely a progression
Often we see a pattern where a mutated, truncated smORF is present next to its homolog in the genome
June 6, 2024 at 4:20 AM
Often we see a pattern where a mutated, truncated smORF is present next to its homolog in the genome
We looked at AMPs that are encoded by their own genes (smORFs)
In real life, many peptides are encoded as a large protein that gets broken up However, we observed that some of the peptides seem to have emerged from mutations of larger proteins!
In real life, many peptides are encoded as a large protein that gets broken up However, we observed that some of the peptides seem to have emerged from mutations of larger proteins!
June 6, 2024 at 4:19 AM
We looked at AMPs that are encoded by their own genes (smORFs)
In real life, many peptides are encoded as a large protein that gets broken up However, we observed that some of the peptides seem to have emerged from mutations of larger proteins!
In real life, many peptides are encoded as a large protein that gets broken up However, we observed that some of the peptides seem to have emerged from mutations of larger proteins!
Peptides from the ocean can have clinical applications!
Most peptides are habitat-specific: peptides we find in the ocean microbiome are not the same that we find soils
This is true to an even greater extent than for longer proteins, which we had studied earlier: www.nature.com/articles/s41...
Most peptides are habitat-specific: peptides we find in the ocean microbiome are not the same that we find soils
This is true to an even greater extent than for longer proteins, which we had studied earlier: www.nature.com/articles/s41...
June 6, 2024 at 4:19 AM
Peptides from the ocean can have clinical applications!
Most peptides are habitat-specific: peptides we find in the ocean microbiome are not the same that we find soils
This is true to an even greater extent than for longer proteins, which we had studied earlier: www.nature.com/articles/s41...
Most peptides are habitat-specific: peptides we find in the ocean microbiome are not the same that we find soils
This is true to an even greater extent than for longer proteins, which we had studied earlier: www.nature.com/articles/s41...