跟著城市嚮導「老臺北胃」，用味道認識臺北

很多朋友來臺北，
都會問我同一個問題：
「臺北小吃那麼多，到底該從哪裡開始吃？」
夜市裡攤位一字排開、老店藏在巷弄轉角，
看起來都很有名，卻又怕吃錯、踩雷，
結果行程走完，反而沒真正記住臺北的味道。
我常被朋友笑說是「老臺北胃」。
不是因為特別會吃，而是因為在這座城市待久了，
知道哪些味道是陪著臺北人成長的日常。
這篇文章，就是我整理的一份清單。
如果你第一次來臺北，
我會帶你從這 10 樣最具代表性的臺北小吃開始，
不追一時爆紅、不走浮誇路線，
而是讓你吃完後能真正理解
原來，這就是臺灣的小吃文化。
跟著老臺北胃走，
用最簡單的方式，
把臺北的味道，一樣一樣記在心裡。

我怎麼選出這 10 大臺北小吃？

在臺北，
你隨便走進一條夜市或老街，
都可以輕易列出 30 種以上的小吃。
所以這份清單，
不是「臺北最好吃」的排名，
 而是我站在「第一次來臺北的旅客」角度，
做的推薦。
身為一個被朋友稱作「老臺北胃」的人，
我選這 10 樣小吃時，心裡一直放著幾個原則。

一吃就知道：這就是臺灣味

燒烤、火鍋很好吃，
但換個城市、換個國家，也吃得到。
我挑的，是那種
只要一入口，就會讓人聯想到的臺灣味。
 不需要解釋太多，舌頭就能懂。

不只是好吃，而是有「臺北日常感」

臺北的小吃迷人，
不只在味道，
而在它融入生活的方式。
我在意的是：

1. 會不會出現在早餐、宵夜、下班後
2. 有沒有陪伴這座城市很久的記憶

吃完之後，你會記得臺北

最後一個標準很簡單。
如果你回到家，
還會突然想起某個味道、某碗熱湯、某個攤位的香氣
那它就值得被放進這份清單裡。

接下來的 10 樣臺北小吃，
就是我會親自帶朋友去吃的在地美食。
不趕行程、不拚數量，
而是一口一口，
慢慢認識臺北。

第 1 家：饌堂－黑金滷肉飯（雙連店）｜一碗就懂臺灣人的日常

如果只能用一道料理，
 來解釋臺灣人的日常飲食，
 那我一定會先帶你吃滷肉飯。
在臺北，滷肉飯不是什麼特別的節慶料理，
 而是從早餐、午餐到宵夜，
 默默陪著很多人長大的味道。
而在眾多滷肉飯之中，
饌堂－黑金滷肉飯（雙連店），
 我很常帶第一次來臺北的朋友造訪的一家。

為什麼第一站，我會選饌堂？
饌堂的滷肉飯，走的是**「黑金系」路線**。
滷汁顏色深、香氣厚，
卻不死鹹、不油膩。
滷肉切得細緻，
肥肉入口即化，搭配熱騰騰的白飯，
每一口都是很完整、很臺灣的味道。
對第一次吃滷肉飯的旅客來說，
這種風味夠經典、也夠穩定，
不需要太多心理準備，就能理解為什麼臺灣人這麼愛它。

不只是好吃，而是「現在的臺北感」
饌堂並不是那種躲在深巷裡的老攤，
空間乾淨、節奏俐落，
卻沒有失去滷肉飯該有的靈魂。
這也是我會推薦給旅客的原因之一：
它保留了臺灣小吃的核心味道，
同時也讓第一次來臺北的人，
吃得安心、坐得舒服。

老臺北胃的帶路小提醒
如果是第一次來：

1. 一定要點招牌黑金滷肉飯
   
2. 可以加一顆滷蛋，風味會更完整
3. 搭配簡單的小菜，就很有臺灣家常感

這不是那種吃完會驚呼「哇！」的料理，
而是會讓你在幾口之後，
慢慢理解
原來，臺灣人的日常，就是這樣被一碗飯照顧著。

地址：103臺北市大同區雙連街55號1樓

電話：0225501379

菜單：https://bio.site/ZhuanTang

第 2 家：富宏牛肉麵｜臺北深夜也醒著的一碗熱湯

如果說滷肉飯代表的是臺灣人的日常，
 那牛肉麵，
 就是很多臺北人心中最有份量的一餐。
而在臺北提到牛肉麵，
 富宏牛肉麵，
 幾乎是夜貓族、加班族、外地旅客一定會被帶去的一站。

為什麼老臺北胃會帶你來吃富宏？
富宏最讓人印象深刻的，
不是華麗裝潢，
而是那鍋永遠冒著熱氣的紅燒湯頭。
湯色濃而不混，
帶著牛骨與醬香慢慢熬出的厚度，
喝起來溫潤、不刺激，
卻會在嘴裡留下很深的記憶點。
牛肉給得大方，
燉到軟嫩卻不鬆散，
搭配彈性十足的麵條，
每一口都很直接、很臺北。

不分時間，任何時候都適合的一碗麵
富宏牛肉麵最迷人的地方，
在於它陪伴了無數個臺北的夜晚。
不管是深夜下班、看完演唱會、
或是剛抵達臺北、還沒適應時差，
這裡總有一碗熱湯在等你。
對旅客來說，
這種不用算時間、不用擔心打烊的安心感，
本身就是一種臺北特色。

老臺北胃的帶路小提醒
第一次來富宏，我會這樣點：

1. 紅燒牛肉麵是首選
   
2. 如果想吃得更過癮，可以加點牛筋或牛肚
3. 湯先喝一口原味，再視情況調整辣度

這不是精緻料理，
卻是一碗能在任何時刻撐住你的牛肉麵。
在臺北，
很多夜晚，
就是靠這樣一碗熱湯走過來的。

地址：108臺北市萬華區洛陽街67號

電話：0223713028

菜單：https://www.facebook.com/pages/富宏牛肉麵-原建宏牛肉麵/

第 3 家：士林夜市・吉彖皮蛋涼麵｜臺北夏天最有記憶點的一口清爽

如果你在夏天來到臺北，
 一定會很快發現一件事
 這座城市，真的很熱。
也正因為這樣，
 臺北的小吃世界裡，
 才會出現像「涼麵」這樣的存在。
而在士林夜市，
 吉彖皮蛋涼麵，
 就是我很常帶旅客來吃的一家。

為什麼在夜市，我會帶你吃涼麵？
很多人對夜市的印象，
都是炸物、熱湯、重口味。
但真正的臺北夜市，
其實也很懂得照顧人的胃。
吉彖的涼麵，
冰涼的麵條拌上濃郁芝麻醬，
再加上切得細緻的皮蛋，
入口的第一瞬間，
就是一種「被降溫」的感覺。
那種清爽，
不是沒味道，
而是在濃香與清涼之間取得剛剛好的平衡。

皮蛋，是靈魂，也是臺灣味的關鍵
對很多外國旅客來說，
皮蛋是既好奇、又有點猶豫的存在。
但我常說，
如果要嘗試皮蛋，
涼麵是一個非常溫柔的起點。
芝麻醬的香氣會先接住味蕾，
皮蛋的風味則在後段慢慢出現，
不衝、不嗆，
反而多了一層深度。
很多人吃完後，
都會露出那種「原來是這樣啊」的表情。

老臺北胃的帶路小提醒
第一次點吉彖皮蛋涼麵，我會建議：

1. 一定要選皮蛋款，才吃得到特色
2. 醬料先拌勻，再吃，風味會更完整
3. 如果天氣真的很熱，這一碗會救你一整晚

這不是華麗的小吃，
卻非常臺北。
在悶熱的夜晚，
站在夜市人潮裡，
吃著一碗涼麵，
你會突然明白——

原來臺北的小吃，連氣候都一起考慮進去了。

地址：111臺北市士林區基河路114號

電話：0981014155

菜單：https://www.facebook.com/profile.php?id=100064238763064

第 4 家：胖老闆誠意肉粥｜臺北人深夜最踏實的一碗粥

如果你問我，
 臺北人在深夜、下班後，
 最容易感到被安慰的食物是什麼——
 我會毫不猶豫地說：肉粥。
而提到肉粥，
 胖老闆誠意肉粥，
 就是很多老臺北人口中的那一味。

為什麼這一碗粥，會被叫做「誠意」？
胖老闆的肉粥，看起來很簡單。
白粥、肉燥、配菜，
沒有華麗擺盤，也沒有複雜作法。
但真正坐下來吃，你會發現：
這碗粥，不敷衍任何一個細節。
粥體滑順、不稀薄，
肉燥香而不膩，
搭配各式家常小菜，
一口一口吃下去，
很自然就會放慢速度。
這種味道，
不是要你驚艷，
而是要你安心。

這不是觀光小吃，而是臺北人的生活片段
胖老闆誠意肉粥，
最迷人的地方，
就是它的客人。
你會看到：

1. 剛下班的上班族
2. 熬夜後來吃一碗熱粥的人
3. 熟門熟路、點菜不用看菜單的老客人

這些畫面，
比任何裝潢都更能說明這家店在臺北的位置。
對旅客來說，
這是一個走進臺北人日常的入口。

老臺北胃的帶路小提醒
第一次來吃，我會這樣建議：

1. 肉粥一定要點，這是主角
2. 配幾樣小菜一起吃，才有完整體驗
3. 不用急，慢慢吃，這碗粥就是要你放鬆

這不是為了拍照而存在的小吃，
而是那種
**會讓人記得「那天晚上，我在臺北吃了一碗很溫暖的粥」**的味道。

地址：10491臺北市中山區長春路89-3號

電話：0913806139

菜單：https://lin.ee/xxbYZyS

第 5 家：圓環邊蚵仔煎｜夜市裡最不能缺席的臺灣經典

如果要選一道
 最常出現在旅客記憶裡的臺灣小吃，
 蚵仔煎一定排得上前幾名。
而在臺北，
 圓環邊蚵仔煎，
 就是那種很多臺北人從小吃到大的存在。

為什麼蚵仔煎，這麼能代表臺灣？
蚵仔煎的魅力，
不在於精緻，
而在於它把幾種看似簡單的食材，
煎成了一種獨特的口感。
新鮮蚵仔的海味、
雞蛋的香氣、
地瓜粉形成的滑嫩外皮，
最後再淋上甜中帶鹹的醬汁，
一口下去，
就是夜市的完整畫面。
這種味道，
很難在其他國家找到替代品。

圓環邊，吃的是記憶感
圓環邊蚵仔煎，
沒有多餘的包裝，
也不刻意迎合潮流。
它留下來的原因很簡單
味道夠穩、節奏夠快、
讓人一吃就知道「對，就是這個」。
對旅客來說，
這是一家
不需要研究、不需要比較，就能安心點蚵仔煎的地方。

老臺北胃的帶路小提醒
第一次吃蚵仔煎，我會這樣建議：

1. 趁熱吃，口感最好
   
2. 不用急著加辣，先吃原味
3. 醬汁是靈魂，別急著把它拌掉

蚵仔煎不是細嚼慢嚥的料理，
它屬於人聲鼎沸、鍋鏟作響的夜市時刻。
站在人群裡，
吃著一盤熱騰騰的蚵仔煎，
你會很清楚地感受到
這，就是臺北的夜晚。

地址：103臺北市大同區寧夏路46號

電話：0225580198

菜單：https://oystera.com.tw/menu

第 6 家：阿淑清蒸肉圓｜第一次吃肉圓，就該從這裡開始

說到臺灣小吃，
 很多人腦中一定會出現「肉圓」兩個字。
但真正吃過之後才會發現，
 肉圓，從來不只有一種樣子。
在臺北，
 阿淑清蒸肉圓，
 就是我很常拿來介紹「清蒸派肉圓」的一家。

清蒸肉圓，和你想像的不一樣
不少旅客對肉圓的第一印象，
來自油炸版本，
外皮厚、口感重。
而阿淑的清蒸肉圓，
完全是另一個方向。
外皮晶瑩、滑嫩，
帶著自然的彈性，
不油、不膩，
一入口反而顯得清爽。
內餡扎實，
豬肉香氣清楚，
搭配特製醬汁，
味道層次簡單卻很乾淨。

為什麼我會推薦給第一次來臺北的旅客？
因為這顆肉圓，
不需要適應期。
它不刺激、不厚重，
即使是第一次嘗試臺灣小吃的人，
也能輕鬆接受。
對旅客來說，
這是一顆
「吃得懂、也記得住」的肉圓。

老臺北胃的帶路小提醒
第一次來阿淑，我會這樣吃：

1. 直接點一顆清蒸肉圓，吃原味
2. 醬汁先別全部拌開，邊吃邊調整
3. 放慢速度，感受外皮的口感變化

這不是夜市裡熱鬧喧囂的料理，
而是那種
安靜地展現臺灣小吃功夫的味道。
當你吃完這顆肉圓，
會更明白一件事
臺灣小吃的魅力，
往往藏在這些細節裡。

地址：242新北市新莊區復興路一段141號

電話：0229975505

第 7 家：胡記米粉湯｜一碗最貼近臺北早晨的味道

如果說前面幾樣小吃，
 是臺北的熱鬧與記憶，
 那麼米粉湯，
 就是這座城市最真實的日常。
而在臺北，
 胡記米粉湯，
 是很多人從小吃到大的存在。

為什麼米粉湯，這麼「臺北」？
米粉湯不是重口味料理，
它靠的不是刺激，
而是一碗清澈卻有深度的湯。
胡記的湯頭，
用豬骨慢慢熬出香氣，
喝起來清爽、不油，
卻能在喉嚨留下溫度。
米粉細軟，
吸附湯汁後入口順滑，
簡單到不能再簡單，
卻正是臺北人習以為常的早晨風景。

配菜，才是這一碗的靈魂延伸
在胡記吃米粉湯，
主角雖然是湯，
但真正讓人滿足的，
往往是那些小菜。
紅燒肉、豬內臟、燙青菜，
隨意點上幾樣，
湯一口、菜一口，
就是很多臺北人記憶中的早餐組合。
對旅客來說，
這是一種
不需要解釋，就能融入的臺北生活感。

老臺北胃的帶路小提醒
第一次來胡記，我會這樣建議：

1. 一定要點米粉湯，湯先喝
2. 再配 1～2 樣小菜，體驗會完整很多
3. 這一餐適合慢慢吃，不用趕

這不是為了觀光而存在的小吃，
而是一碗
每天準時出現在臺北人生活裡的湯。
當你坐在店裡，
聽著湯勺碰撞的聲音，
你會突然感覺到——
原來，臺北的早晨，
就是從這樣一碗米粉湯開始的。

地址：106臺北市大安區大安路一段9號1樓

電話：0227212120

第 8 家：藍家割包｜一口咬下的臺灣街頭記憶

如果要選一道
 外國旅客一看到就會好奇、吃完又會記住的小吃，
 割包，一定在名單裡。
而在臺北，
 藍家割包，
 就是我很放心帶旅客來認識這道經典的一站。

割包，為什麼被叫做「臺灣漢堡」？
割包的結構其實很簡單：
鬆軟的白饅頭、
燉得入味的滷五花肉、
酸菜、花生粉、香菜。
但真正迷人的，
是這些元素組合在一起時，
形成的層次感。
肉香、甜味、鹹味、清爽度，
在一口之間同時出現，
沒有誰搶戲，
卻彼此剛好。
這種平衡感，
正是臺灣小吃很迷人的地方。

藍家割包不是走浮誇路線，
它給人的感覺很直接
就是你期待中的割包樣子。
饅頭柔軟不乾，
五花肉肥瘦比例恰到好處，
入口即化卻不膩口，
花生粉的甜香收尾，
讓整體味道非常完整。
對第一次吃割包的旅客來說，
這是一個
不會出錯、也很容易愛上的版本。

老臺北胃的帶路小提醒
第一次吃藍家割包，我會這樣建議：

1. 直接點招牌割包，不要改配料
2. 如果有香菜，建議保留，味道會更完整
3. 趁熱吃，饅頭口感最好

割包不是精緻料理，
卻非常有記憶點。
站在街頭，
拿著一顆熱騰騰的割包，
邊走邊吃，
你會很清楚地感受到
這一口，就是臺灣的街頭生活。

地址：100臺北市中正區羅斯福路三段316巷8弄3號

電話：0223682060

菜單：https://instagram.com/lan_jia_gua_bao?utm_medium=copy_link

第 9 家：御品元冰火湯圓｜臺北夜晚最溫柔的一碗甜

吃了一整天的臺北小吃，
 到了這個時候，
 胃其實已經差不多滿了。
但只要天氣一涼，
 或夜色慢慢降下來，
 你還是會想找一碗——
 不是為了吃飽，而是為了舒服的甜點。
這時候，我通常會帶你來 御品元冰火湯圓。

為什麼叫「冰火」？這碗湯圓的關鍵就在這裡
御品元最有特色的地方，
就在於它的「冰火交錯」。
熱騰騰的湯圓，
外皮軟糯、內餡濃香，
搭配冰涼清甜的桂花蜜湯，
一口下去，
溫度在嘴裡交替出現。
不是衝突，
而是一種很細膩的平衡。
這樣的吃法，
也正是臺灣甜點很擅長的地方——
不張揚，但很有記憶點。

這是一碗，會讓人慢下來的甜點
和夜市裡熱鬧的甜品不同，
御品元的冰火湯圓，
更像是一個讓人停下腳步的存在。
你會發現，
坐在這裡吃湯圓的人，
說話聲都會不自覺地變小。
對旅客來說，
這不只是吃甜點，
而是一個
把白天的熱鬧慢慢收進回憶裡的時刻。

老臺北胃的帶路小提醒
第一次吃御品元，我會這樣建議：

1. 點招牌冰火湯圓，體驗完整特色
2. 先單吃湯圓，再搭配湯一起吃
3. 放慢速度，這一碗不適合趕時間

這不是為了拍照而存在的甜點，
而是一碗
會讓你記得「那天晚上在臺北，很舒服」的湯圓。

地址：106臺北市大安區通化街39巷50弄31號

電話：0955861816

菜單：https://instagram.com/lan_jia_gua_bao

第 10 家：頃刻間綠豆沙牛奶專賣店｜把臺北的味道，留在最後一口清甜

走到這一站，
 其實已經不需要再吃什麼大份量的東西了。
這時候，
 最適合的，
 是一杯不吵鬧、不張揚，
 卻會默默留在記憶裡的飲品。
頃刻間綠豆沙牛奶，
 就是我很常用來替一天畫下句點的選擇。

綠豆沙牛奶，為什麼這麼「臺灣」？
在臺灣，
飲料不只是解渴，
而是一種生活節奏。
綠豆沙牛奶看起來簡單，
但真正好喝的版本，
靠的是火候、比例，
還有耐心。
頃刻間的綠豆沙，
口感細緻、不粗顆，
甜度自然、不膩口，
牛奶的加入，
讓整杯變得柔順而溫和。
這不是衝擊味蕾的飲料，
而是一種
喝完之後，會覺得剛剛那一刻很舒服的甜。

為什麼我會用它當作最後一站？
因為它很臺北。
你可以外帶，
邊走邊喝；
也可以站在店門口，
慢慢把杯子喝空。
沒有儀式感，
卻很真實。
對旅客來說，
這杯綠豆沙牛奶，
就像是把今天吃過的所有味道，
溫柔地整理好，
帶走。

老臺北胃的帶路小提醒
第一次喝頃刻間，我會這樣建議：

1. 直接點招牌綠豆沙牛奶
   
2. 正常甜就很剛好，不用特別調整
3. 找個角落慢慢喝，別急著趕路

這一杯，
不會讓你驚呼，
卻會在回程的路上，
突然想起來。
原來，臺北的味道，是這樣結束一天的。

地址：111臺北市士林區小北街1號

電話：0228818619

菜單：https://instagram.com/chill_out_moment?igshid=YmMyMTA2M2Y=

如果只有 3 天的自助旅行在臺北，怎麼吃這 10 家？

第一次來臺北，
時間有限、胃容量也有限，
與其每一家都趕，不如照著節奏吃。
這份 3 天小吃路線，
是老臺北胃會帶朋友實際走的版本：
不爆走、不硬塞，
讓你每天都吃得剛剛好。

臺北 3 天小吃推薦行程表（老臺北胃版本）

天數	時段	店家名稱	小吃類型
Day 1	午餐	饌堂－黑金滷肉飯（雙連店）	滷肉飯
Day 1	下午	阿淑清蒸肉圓	肉圓
Day 1	晚餐	富宏牛肉麵	牛肉麵
Day 1	宵夜	胖老闆誠意肉粥	粥品
Day 2	早餐	胡記米粉湯	米粉湯
Day 2	下午	藍家割包	割包
Day 2	晚上	士林夜市－吉彖皮蛋涼麵	涼麵
Day 2	夜市	圓環邊蚵仔煎	蚵仔煎
Day 3	下午	御品元冰火湯圓	甜點
Day 3	收尾	頃刻間綠豆沙牛奶專賣店	飲品

雖然每個小吃的地點都有一點距離，但是你也知道，好吃的小吃，是值得你花一點時間前往品嘗
老臺北胃的小提醒

1. 不需要每一家都點到最滿
2. 留一點餘裕，才會想再回來
3. 臺北小吃的魅力，不在於吃多少，而在於記住了什麼味道
   

當你照著這 3 天走完，
你會發現，
臺北不是靠一兩道名菜被記住的，
而是靠這些看似日常、卻很真實的小吃。
下次再來，老臺北胃再帶你吃更深的那一輪。

老臺北胃帶路｜這 10 口，就是我心中的臺北

寫到這裡，
 其實已經不是在推薦哪一家小吃了。
而是在回頭看，
 這座城市，是怎麼用食物陪著人生活的。
滷肉飯、牛肉麵、肉粥、米粉湯，
 不是為了成為觀光名單而存在，
 而是每天默默出現在臺北人的日子裡。
夜市裡的蚵仔煎、涼麵、割包，
 熱鬧、吵雜、節奏很快，
 卻也正是臺北最真實的樣子。
而最後那碗湯圓、那杯綠豆沙牛奶，
 則是在一天結束時，
 替味蕾留下一個溫柔的句點。

如果你問我，
「這 10 家是不是臺北最好吃的小吃？」
我會說，
它們不一定是排行榜第一名，
卻是我真的會帶朋友去吃的版本。
因為它們吃得到：

1. 臺北人的日常
2. 巷弄裡的熟悉感
3. 不需要解釋，就能被理解的味道

如果你是第一次來臺北，
跟著這份清單走，
你不一定會吃得最飽，
但你一定會記得——
臺北，是什麼味道。
而如果有一天，
你又再回到這座城市，
走進熟悉的街口、
看到冒著熱氣的小攤，
你也會開始懂得，
為什麼老臺北胃，
總是記得這些看似平凡的滋味。
因為，真正留在心裡的，
從來不是吃過多少，
而是哪一口，讓你想起臺北。

胡記米粉湯怎麼點比較好？

走完這 10 家，

你可能會發現一件事圓環邊蚵仔煎在地人怎麼說？

臺北的小吃，其實不急著被你記住。

它們就安靜地存在在街角、夜市、轉彎處，藍家割包值得專程去吃嗎？

等你有一天，再回到這座城市。阿淑清蒸肉圓冬天適合吃嗎？

如果你是第一次來臺北，御品元冰火湯圓觀光客推薦嗎？

希望這份「老臺北胃帶路」的清單，

能幫你少一點猶豫、多一點安心。

不用擔心踩雷，士林夜市－吉彖皮蛋涼麵夏天適合吃嗎？

也不用為了排行而奔波，饌堂－黑金滷肉飯（雙連店）真的好吃嗎？

只要照著節奏走，

你就會吃到屬於自己的臺北味道。

而如果你已經來過臺北，

那更希望這篇文章，圓環邊蚵仔煎適合第一次吃嗎？

能帶你走進那些

你可能錯過、卻一直都在的日常小吃。

因為真正迷人的旅行，

從來不是把清單全部打勾，

而是某一天，

你突然想起那碗飯、那口湯、那杯甜，圓環邊蚵仔煎排隊值得嗎？

然後在心裡對自己說一句：胡記米粉湯會不會太甜？

「下次再去臺北，還想再吃一次。」

把這篇文章存起來、分享給一起旅行的人，

或是在規劃行程時，再回來看看。

讓味道，成為你認識臺北的方式。

下一次來臺北，

別急著走遠。

老臺北胃，士林夜市－吉彖皮蛋涼麵第一次適合嗎？

會一直在這些地方，

等你再回來。

Human-driven extinctions have erased significant bird species and functional diversity, erasing 3 billion years of evolution and severely impacting ecosystem health, emphasizing the need for urgent conservation action. Human-driven bird extinctions over the last 130,000 years have cut avian functional diversity and erased 3 billion years of evolution, impacting pollination, pest control, and ecosystems. Understanding these losses is key for future conservation. A new study published in Science reveals that human-driven extinctions of hundreds of bird species over the past 130,000 years have significantly reduced avian functional diversity — the variety of roles birds play in ecosystems — and led to the loss of around 3 billion years of unique evolutionary history. Whilst humans have been driving a global erosion of species richness for millennia, the consequences of past extinctions for other dimensions of biodiversity are poorly known. New research led by the University of Birmingham highlights the severe consequences of the ongoing biodiversity crisis and the urgent need to identify the ecological functions being lost through extinction. Well-Known Bird Extinctions and Their Broader Impact From the well-documented Dodo to the recent Kauaʻi ʻōʻō songbird declared extinct in 2023, scientists currently have evidence of at least 600 bird species having become extinct as a result of humans since the Late Pleistocene when modern humans started to spread throughout the world. Using the most comprehensive dataset to date of all known bird extinctions during the Late Pleistocene and Holocene, the paper ‘The global loss of avian functional and phylogenetic diversity from anthropogenic extinctions’ looks beyond the number of extinctions to the wider implications on the planet. The Kaua’i stilt owl painting shows the island of Kaua’i in Hawaii. All three depicted species have been driven extinct by humans (the Kaua’i stilt owl, wahi grosbeak, Kauaʻi ʻōʻō). Credit: Palaeontological Artist & Avian Palaeontologist Julian P. Hume Lead author Dr Tom Matthews from the University of Birmingham explained: “The sheer number of bird species that have become extinct is of course a big part of the extinction crisis but what we also need to focus on is that every species has a job or function within the environment and therefore plays a really important role in its ecosystem. Some birds control pests by eating insects, scavenger birds recycle dead matter, others eat fruit and disperse the seeds enabling more plants and trees to grow, and some, like hummingbirds, are very important pollinators. When those species die out, the important role that they play (the functional diversity) dies with them. “In addition to functional diversity each species also carries a certain amount of evolutionary history, therefore when that species becomes extinct, it’s basically like chopping off a branch of the tree of life, and all of that associated phylogenetic diversity is also lost.” The Consequences of Extinction for Ecosystems The research found that the scale of anthropologenic bird extinctions to date has resulted in a loss of approximately 3 billion years of unique evolutionary history, and 7% of global avian functional diversity – a significantly larger amount than expected based on the number of extinctions. Given the wide range of important ecological roles performed by birds, the loss of avian functional diversity in particular will likely have had far-reaching implications. These post-extinction aftershocks include reduced flower pollination, reduced seed dispersal, the breakdown of top-down control of insect populations – including many pests and disease vectors – as well as increased disease outbreaks due to reduced consumption of carrion. In addition, the downsizing of the global avifauna documented in the research will likely affect the ability of many plant species to track present and future climate change. Dr Matthews concludes: “These results are a timely reminder that the current extinction crisis is not just about species numbers. By identifying declines in avian functional and phylogenetic diversity driven by human actions, our findings highlight the urgent need to understand and predict the impacts of past anthropogenic extinctions on ecosystem function in order to prepare for the magnitude of expected future loss from the projected 1,000 bird species that are expected to die out completely over the next two centuries. This information is vital for setting effective targets for global conservation strategies, as well as ecosystem restoration and rewilding efforts.” Reference: “The global loss of avian functional and phylogenetic diversity from anthropogenic extinctions” by Thomas J. Matthews, Kostas A. Triantis, Joseph P. Wayman, Thomas E. Martin, Julian P. Hume, Pedro Cardoso, Søren Faurby, Chase D. Mendenhall, Paul Dufour, François Rigal, Rob Cooke, Robert J. Whittaker, Alex L. Pigot, Christophe Thébaud, Maria Wagner Jørgensen, Eva Benavides, Filipa C. Soares, Werner Ulrich, Yasuhiro Kubota, Jon P. Sadler, Joseph A. Tobias and Ferran Sayol, 3 October 2024, Science. DOI: 10.1126/science.adk7898

Researchers at MIT, the Broad Institute, and the National Institutes of Health have developed a new search algorithm that has identified 188 kinds of new rare CRISPR systems in bacterial genomes. Credit: Broad Institute By analyzing bacterial data, researchers have discovered thousands of rare new CRISPR systems that have a range of functions and could enable gene editing, diagnostics, and more. Microbial sequence databases contain a wealth of information about enzymes and other molecules that could be adapted for biotechnology. But these databases have grown so large in recent years that they’ve become difficult to search efficiently for enzymes of interest. New Search Algorithm for CRISPR Systems Now, scientists at the McGovern Institute for Brain Research at MIT, the Broad Institute of MIT and Harvard, and the National Center for Biotechnology Information (NCBI) at the National Institutes of Health have developed a new search algorithm that has identified 188 kinds of new rare CRISPR systems in bacterial genomes, encompassing thousands of individual systems. The work was published on November 23 in the journal Science. The algorithm, which comes from the lab of pioneering CRISPR researcher Professor Feng Zhang, uses big-data clustering approaches to rapidly search massive amounts of genomic data. The team used their algorithm, called Fast Locality-Sensitive Hashing-based clustering (FLSHclust) to mine three major public databases that contain data from a wide range of unusual bacteria, including ones found in coal mines, breweries, Antarctic lakes, and dog saliva. The scientists found a surprising number and diversity of CRISPR systems, including ones that could make edits to DNA in human cells, others that can target RNA, and many with a variety of other functions. The new systems could potentially be harnessed to edit mammalian cells with fewer off-target effects than current Cas9 systems. They could also one day be used as diagnostics or serve as molecular records of activity inside cells. Exploring CRISPR’s Diversity The researchers say their search highlights an unprecedented level of diversity and flexibility of CRISPR and that there are likely many more rare systems yet to be discovered as databases continue to grow. “Biodiversity is such a treasure trove, and as we continue to sequence more genomes and metagenomic samples, there is a growing need for better tools, like FLSHclust, to search that sequence space to find the molecular gems,” says Zhang, a co-senior author on the study and the James and Patricia Poitras Professor of Neuroscience at MIT with joint appointments in the departments of Brain and Cognitive Sciences and Biological Engineering. Zhang is also an investigator at the McGovern Institute for Brain Research at MIT, a core institute member at the Broad, and an investigator at the Howard Hughes Medical Institute. Eugene Koonin, a distinguished investigator at the NCBI, is co-senior author on the study as well. Searching for CRISPR CRISPR, which stands for clustered regularly interspaced short palindromic repeats, is a bacterial defense system that has been engineered into many tools for genome editing and diagnostics. To mine databases of protein and nucleic acid sequences for novel CRISPR systems, the researchers developed an algorithm based on an approach borrowed from the big data community. This technique, called locality-sensitive hashing, clusters together objects that are similar but not exactly identical. Using this approach allowed the team to probe billions of protein and DNA sequences — from the NCBI, its Whole Genome Shotgun database, and the Joint Genome Institute — in weeks, whereas previous methods that look for identical objects would have taken months. They designed their algorithm to look for genes associated with CRISPR. “This new algorithm allows us to parse through data in a time frame that’s short enough that we can actually recover results and make biological hypotheses,” says Soumya Kannan PhD ’23, who is a co-first author on the study. Kannan was a graduate student in Zhang’s lab when the study began and is currently a postdoc and Junior Fellow at Harvard University. Han Altae-Tran PhD ’23, a graduate student in Zhang’s lab during the study and currently a postdoc at the University of Washington, was the study’s other co-first author. “This is a testament to what you can do when you improve on the methods for exploration and use as much data as possible,” says Altae-Tran. “It’s really exciting to be able to improve the scale at which we search.” Discovering New CRISPR Variants In their analysis, Altae-Tran, Kannan, and their colleagues noticed that the thousands of CRISPR systems they found fell into a few existing and many new categories. They studied several of the new systems in greater detail in the lab. They found several new variants of known Type I CRISPR systems, which use a guide RNA that is 32 base pairs long rather than the 20-nucleotide guide of Cas9. Because of their longer guide RNAs, these Type I systems could potentially be used to develop more precise gene-editing technology that is less prone to off-target editing. Zhang’s team showed that two of these systems could make short edits in the DNA of human cells. And because these Type I systems are similar in size to CRISPR-Cas9, they could likely be delivered to cells in animals or humans using the same gene-delivery technologies being used today for CRISPR. One of the Type I systems also showed “collateral activity” — broad degradation of nucleic acids after the CRISPR protein binds its target. Scientists have used similar systems to make infectious disease diagnostics such as SHERLOCK, a tool capable of rapidly sensing a single molecule of DNA or RNA. Zhang’s team thinks the new systems could be adapted for diagnostic technologies as well. The researchers also uncovered new mechanisms of action for some Type IV CRISPR systems, and a Type VII system that precisely targets RNA, which could potentially be used in RNA editing. Other systems could potentially be used as recording tools — a molecular document of when a gene was expressed — or as sensors of specific activity in a living cell. Mining Biochemical Data The scientists say their algorithm could aid in the search for other biochemical systems. “This search algorithm could be used by anyone who wants to work with these large databases for studying how proteins evolve or discovering new genes,” Altae-Tran says. The researchers add that their findings illustrate not only how diverse CRISPR systems are, but also that most are rare and only found in unusual bacteria. “Some of these microbial systems were exclusively found in water from coal mines,” Kannan says. “If someone hadn’t been interested in that, we may never have seen those systems. Broadening our sampling diversity is really important to continue expanding the diversity of what we can discover.” Reference: “Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering” by Han Altae-Tran, Soumya Kannan, Anthony J. Suberski, Kepler S. Mears, F. Esra Demircioglu, Lukas Moeller, Selin Kocalar, Rachel Oshiro, Kira S. Makarova, Rhiannon K. Macrae, Eugene V. Koonin and Feng Zhang, 23 November 2023, Science. DOI: 10.1126/science.adi1910 This work was supported by the Howard Hughes Medical Institute; the K. Lisa Yang and Hock E. Tan Molecular Therapeutics Center at MIT; Broad Institute Programmable Therapeutics Gift Donors; The Pershing Square Foundation, William Ackman and Neri Oxman; James and Patricia Poitras; BT Charitable Foundation; Asness Family Foundation; Kenneth C. Griffin; the Phillips family; David Cheng; and Robert Metcalfe.

Experiments to measure a fruit fly’s top speed involved releasing tens of thousands of fruit flies and luring them away with fragrant cocktails of fermenting apple juice. The flies took about 16 minutes to travel one kilometer. Fully fed, these fruit flies can fly for three continuous hours, implying that the insects could cover a distance of 12 to 15 kilometers in a single flight. Credit: Floris van Breugel In search of food, a fly can travel six million times its body length. In 2005, an ultramarathon runner ran continuously 560 kilometers (350 miles) in 80 hours, without sleeping or stopping. This distance was roughly 324,000 times the runner’s body length. Yet this extreme feat pales in comparison to the relative distances that fruit flies can travel in a single flight, according to new research from Caltech. Caltech scientists have now discovered that fruit flies can fly up to 15 kilometers (about 9 miles) in a single journey—6 million times their body length, or the equivalent of over 10,000 kilometers (6,200 miles) for the average human. In comparison to body length, this is further than many migratory species of birds can fly in a day. To discover this, the team conducted experiments in a dry lake bed in California’s Mojave Desert, releasing flies and luring them into traps containing fermenting juice in order to determine their top speeds. The research was conducted in the laboratory of Michael Dickinson, Esther M., and Abe M. Zarem Professor of Bioengineering and Aeronautics and executive officer for biology and biological engineering. A paper describing the study was published in the journal Proceedings of the National Academy of Sciences on April 20. The work was motivated by a longstanding paradox that was identified in the 1940s by Theodosius Dobzhansky and other pioneers of population genetics who studied Drosophila species across the Southwest United States. Dobzhansky and others found that fly populations separated by thousands of kilometers appeared much more genetically similar than could be easily explained by their estimates of how far the tiny flies could actually travel. Indeed, when biologists would release flies outdoors, the insects would often simply buzz around in circles over short distances, as they do in our kitchens. Did flies behave differently when out in the wild, in search of food? In the 1970s and ’80s, a group of population geneticists attempted to address this paradox by coating hundreds of thousands of flies in fluorescent powder and releasing them one evening in Death Valley. Remarkably, the group detected a few fluorescent flies in buckets of rotting bananas up to 15 kilometers away the next day. “These simple experiments raised so many questions,” says Dickinson. “How long did it take them to fly there? Were they just blown by the wind? Was it an accident? I have read that paper many times and found it very inspiring. No one had tried to repeat the experiment in a way that would make it possible to measure whether the flies were carried by the wind, how fast they were flying, and how far they can really go.” To measure how flies disperse and interact with the wind, the team designed “release and recapture” experiments. Led by former postdoctoral scholar Kate Leitch, the team made several trips to Coyote Lake, a dry lakebed 140 miles from Caltech in the Mojave Desert, with hundreds of thousands of the common lab fruit fly, Drosophila melanogaster, in tow. The aim was to release the flies, lure them into traps at set locations, and measure how long it took the insects to fly there. To do this, the team set up 10 “odor traps” in a circular ring, each located along a one-kilometer radius around the release site. Each trap contained a tantalizing cocktail of fermenting apple juice and champagne yeast, a combination that produces carbon dioxide and ethanol, which are irresistible to a fruit fly. The traps also each had a camera, and were constructed with one-way valves so that the flies could crawl into the trap toward the cocktail but not back out. In addition, the researchers set up a weather station to measure the wind speed and direction at the release site throughout each experiment; this would indicate how the flies’ flight was affected by the wind. So as not to interfere with their flight performance, the team did not coat the flies with identifiers like fluorescent powder. So how did they know they were catching their own fruit flies? Before the release, the team first placed the traps and checked them over time, and found that although D. melanogaster are found at date farms within the Mojave, they are extremely rare at Coyote Lake. The flies released by the team had been originally collected at a fruit stand and then were raised in the lab, but they were not genetically modified in any way. The team performed the experiments after receiving permits from the Bureau of Land Management. At experiment time, the team drove the buckets of flies to the center of the circle of traps. The buckets contained plenty of sugar, so that the insects would be fully energized for their flight; however, they contained no protein, giving the flies a strong drive to search for protein-rich food. The team estimated that the flies would not be able to smell the traps from the center of the ring, forcing them to disperse and search. At a precise time, a team member at the center of the circle opened up the buckets simultaneously and quickly released the flies. “The person who stayed at the center of the ring to open the lids off of all the buckets witnessed quite a spectacle,” says Leitch. “It was beautiful. There were so many flies—so many that you were overwhelmed by the whirring drone. A few of them would land on you, often crawling in your mouth, ears, and nose.” The team repeated these experiments under various wind conditions. It took about 16 minutes for the first fruit flies to cover one kilometer to reach the traps, corresponding to a speed of approximately 1 meter per second. The team interpreted this speed as a lower limit (perhaps these first flies had buzzed around in circles a bit after release or did not fly in a perfectly straight line). Previous studies from the lab showed that a fully fed fruit fly has the energy to fly continuously for up to three hours; extrapolating, the team concluded that D. melanogaster can fly roughly 12 to 15 kilometers in a single flight, even into a gentle breeze, and will go further if aided by a tailwind. This distance is approximately 6 million times the average body length of a fruit fly (2.5 millimeters, or one-tenth of an inch). As an analogy, this would be like the average human covering just over 10,000 kilometers in a single journey—roughly the distance from the North Pole to the equator. “The dispersal capability of these little fruit flies has been vastly underestimated. They can travel as far or farther than most migratory birds in a single flight. These flies are the standard laboratory model organism, but they are almost never studied outside of the laboratory and so we had little idea what their flight capabilities were,” Dickinson says. In 2018, the Dickinson laboratory discovered that fruit flies use the sun as a landmark in order to fly in a straight line in search of food; flying aimlessly in circles could be deadly, so there is an evolutionary benefit to being able to navigate efficiently. After completing the release experiments described in this study, the team proposed a model that suggests that each fly chooses a direction at random, uses the sun to fly straight in that direction, and carefully regulates its forward speed while allowing itself to be blown sideways by the wind. This enables it to cover as much distance as possible and increases the probability that it will encounter a plume of odor from a food source. The team compared their model with traditional models of random insect dispersal and found that their model could explain the results of the desert releases more accurately because of the flies’ propensity to maintain a constant heading once released. Even though D. melanogaster has been co-evolving with humans, this work shows that the fly brain still contains ancient behavioral modules. Dickinson explains: “For any animal, if you find yourself in the middle of nowhere and there’s no food, what do you do? Do you just hop around and hope you find some fruit? Or do you say—’Okay, I’m going to pick a direction and go as far as I can in that direction and hope for the best.’ These experiments suggest that that’s what the flies do.” The research has broader implications for the field of movement ecology, which studies how populations move around the world, essentially shifting biomass for other animals to eat. In fact, during their early pre-release experiments to check for local populations of Drosophila, the team several times caught an invasive species of fly, the spotted-wing Drosophila (Drosophila suzukii), which causes significant agricultural damage across the West Coast. “We set up these traps in the middle of nowhere, not the Central Valley where there would be fields of food, and still we find these agricultural pests cruising through,” says Dickinson. “It’s kind of scary to see how far these introduced species can travel using simple navigational strategies.” Reference: “The long-distance flight behavior of Drosophila supports an agent-based model for wind-assisted dispersal in insects” by Katherine J. Leitch, Francesca V. Ponce, William B. Dickson, Floris van Breugel and Michael H. Dickinson, 20 April 2021, Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.2013342118 The paper is titled “The long-distance flight behavior of Drosophila supports an agent-based model for wind-assisted dispersal in insects.” In addition to Leitch and Dickinson, additional co-authors are Francesca Ponce, William Dickson, and former Dickinson laboratory postdoctoral scholar Floris van Breugel (PhD ’14, now of the University of Nevada, Reno). Funding was provided by the Simons Foundation and the National Science Foundation. Dickinson is an affiliated faculty member of the Tianqiao and Chrissy Chen Institute for Neuroscience at Caltech.

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